Changeset 4964


Ignore:
Timestamp:
Jun 20, 2021 9:33:41 AM (4 months ago)
Author:
toby
Message:

divide up help into a few files

Location:
trunk
Files:
82 added
52 deleted
3 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIctrlGUI.py

    r4955 r4964  
    53445344    '''Create a help button that displays help information.
    53455345    The text can be displayed in a modal message window or it can be
    5346     a reference to a location in the gsasII.html help web page, in which
     5346    a reference to a location in the gsasII.html (etc.) help web page, in which
    53475347    case that page is opened in a web browser.
    53485348
     
    64216421    global htmlFirstUse,htmlPanel,htmlFrame
    64226422    # no defined link to use, create a default based on key
    6423     helplink = 'gsasII.html'
    6424     if helpType:
    6425         helplink += '#'+helpType.replace(')','').replace('(','_').replace(' ','_')
     6423    if helpType.lower().startswith('pwdr'):
     6424        helplink = 'gsasII-pwdr.html#'+helpType.replace(')','').replace('(','_').replace(' ','_')
     6425    elif helpType.lower().startswith('phase'):
     6426        helplink = 'gsasII-phase.html#'+helpType.replace(')','').replace('(','_').replace(' ','_')
     6427    elif helpType:
     6428        helplink = 'gsasII.html#'+helpType.replace(')','').replace('(','_').replace(' ','_')
     6429    else:
     6430        helplink = 'gsasII.html'
    64266431    # determine if a web browser or the internal viewer should be used for help info
    64276432    if GSASIIpath.GetConfigValue('Help_mode'):
  • trunk/GSASIIphsGUI.py

    r4954 r4964  
    1276612766        text = G2frame.phaseDisplay.GetPageText(page)
    1276712767        G2frame.lastSelectedPhaseTab = text
    12768         G2frame.dataWindow.helpKey = text # use name of Phase tab for help lookup
     12768        G2frame.dataWindow.helpKey = 'Phase-'+text # use name of Phase tab for help lookup
    1276912769        if text == 'General':
    1277012770            G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.DataGeneral)
  • trunk/help/gsasII.html

    r4963 r4964  
    2424 <o:DocumentProperties>
    2525  <o:Author>Von Dreele</o:Author>
    26   <o:LastAuthor>Von Dreele, Robert B.</o:LastAuthor>
    27   <o:Revision>158</o:Revision>
    28   <o:TotalTime>4529</o:TotalTime>
     26  <o:LastAuthor>Toby, Brian H.</o:LastAuthor>
     27  <o:Revision>160</o:Revision>
     28  <o:TotalTime>4536</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2021-06-19T21:45:00Z</o:LastSaved>
    31   <o:Pages>1</o:Pages>
    32   <o:Words>21290</o:Words>
    33   <o:Characters>121354</o:Characters>
     30  <o:LastSaved>2021-06-20T13:59:00Z</o:LastSaved>
     31  <o:Pages>24</o:Pages>
     32  <o:Words>8410</o:Words>
     33  <o:Characters>47938</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    35   <o:Lines>1011</o:Lines>
    36   <o:Paragraphs>284</o:Paragraphs>
    37   <o:CharactersWithSpaces>142360</o:CharactersWithSpaces>
     35  <o:Lines>399</o:Lines>
     36  <o:Paragraphs>112</o:Paragraphs>
     37  <o:CharactersWithSpaces>56236</o:CharactersWithSpaces>
    3838  <o:Version>16.00</o:Version>
    3939 </o:DocumentProperties>
     
    4242 </o:OfficeDocumentSettings>
    4343</xml><![endif]-->
    44 <link rel=dataStoreItem href="gsasII_files/item0056.xml"
    45 target="gsasII_files/props057.xml">
     44<link rel=dataStoreItem href="gsasII_files/item0006.xml"
     45target="gsasII_files/props007.xml">
    4646<link rel=themeData href="gsasII_files/themedata.thmx">
    4747<link rel=colorSchemeMapping href="gsasII_files/colorschememapping.xml">
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    4949 <w:WordDocument>
     50  <w:View>Print</w:View>
     51  <w:Zoom>197</w:Zoom>
     52  <w:SpellingState>Clean</w:SpellingState>
     53  <w:GrammarState>Clean</w:GrammarState>
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    5155  <w:TrackFormatting/>
     
    292296   Name="HTML Variable"/>
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    294300   Name="annotation subject"/>
    295301  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     
    376382   Name="Table Professional"/>
    377383  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     384   Name="Table Subtle 1"/>
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    378386   Name="Table Subtle 2"/>
    379387  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
    380388   Name="Table Web 1"/>
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     390   Name="Table Web 2"/>
     391  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     392   Name="Table Web 3"/>
    381393  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
    382394   Name="Balloon Text"/>
     
    677689        {font-family:Wingdings;
    678690        panose-1:5 0 0 0 0 0 0 0 0 0;
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    769781        font-weight:bold;}
    770782h4
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    795808        font-style:italic;}
    796809h5
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    798812        mso-style-qformat:yes;
    799813        mso-style-link:"Heading 5 Char";
     
    940954        mso-font-kerning:14.0pt;}
    941955a:link, span.MsoHyperlink
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     957        mso-style-priority:99;
    943958        color:blue;
    944959        text-decoration:underline;
     
    11151130        mso-themeshade:191;
    11161131        font-weight:bold;}
     1132span.Heading2Char
     1133        {mso-style-name:"Heading 2 Char";
     1134        mso-style-noshow:yes;
     1135        mso-style-priority:9;
     1136        mso-style-unhide:no;
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     1142        mso-ascii-font-family:"Calibri Light";
     1143        mso-ascii-theme-font:major-latin;
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     1145        mso-fareast-theme-font:major-fareast;
     1146        mso-hansi-font-family:"Calibri Light";
     1147        mso-hansi-theme-font:major-latin;
     1148        mso-bidi-font-family:"Times New Roman";
     1149        mso-bidi-theme-font:major-bidi;
     1150        color:#5B9BD5;
     1151        mso-themecolor:accent1;
     1152        font-weight:bold;}
    11171153span.Heading3Char
    11181154        {mso-style-name:"Heading 3 Char";
     
    11381174span.Heading4Char
    11391175        {mso-style-name:"Heading 4 Char";
     1176        mso-style-noshow:yes;
    11401177        mso-style-priority:9;
    11411178        mso-style-unhide:no;
     
    11591196span.Heading5Char
    11601197        {mso-style-name:"Heading 5 Char";
     1198        mso-style-noshow:yes;
    11611199        mso-style-priority:9;
    11621200        mso-style-unhide:no;
     
    12541292        mso-hansi-font-family:Tahoma;
    12551293        mso-bidi-font-family:Tahoma;}
    1256 span.Heading2Char
    1257         {mso-style-name:"Heading 2 Char";
    1258         mso-style-noshow:yes;
    1259         mso-style-priority:9;
    1260         mso-style-unhide:no;
    1261         mso-style-locked:yes;
    1262         mso-style-link:"Heading 2";
    1263         mso-ansi-font-size:13.0pt;
    1264         mso-bidi-font-size:13.0pt;
    1265         font-family:"Calibri Light",sans-serif;
    1266         mso-ascii-font-family:"Calibri Light";
    1267         mso-ascii-theme-font:major-latin;
    1268         mso-fareast-font-family:"Times New Roman";
    1269         mso-fareast-theme-font:major-fareast;
    1270         mso-hansi-font-family:"Calibri Light";
    1271         mso-hansi-theme-font:major-latin;
    1272         mso-bidi-font-family:"Times New Roman";
    1273         mso-bidi-theme-font:major-bidi;
    1274         color:#5B9BD5;
    1275         mso-themecolor:accent1;
    1276         font-weight:bold;}
    12771294p.gsastext, li.gsastext, div.gsastext
    12781295        {mso-style-name:"gsas text";
     
    12921309        font-family:"Times New Roman",serif;
    12931310        mso-fareast-font-family:"Times New Roman";}
     1311span.SpellE
     1312        {mso-style-name:"";
     1313        mso-spl-e:yes;}
     1314span.GramE
     1315        {mso-style-name:"";
     1316        mso-gram-e:yes;}
    12941317.MsoChpDefault
    12951318        {mso-style-type:export-only;
     
    28332856<link href=gsasIIfav.png rel="SHORTCUT ICON">
    28342857<!--[if gte mso 9]><xml>
    2835  <o:shapedefaults v:ext="edit" spidmax="1029"/>
     2858 <o:shapedefaults v:ext="edit" spidmax="1027"/>
    28362859</xml><![endif]--><!--[if gte mso 9]><xml>
    28372860 <o:shapelayout v:ext="edit">
     
    28652888 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    28662889 <o:lock v:ext="edit" aspectratio="t"/>
    2867 </v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1028" type="#_x0000_t75"
     2890</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1026" type="#_x0000_t75"
    28682891 alt="Description: GSAS-II logo" style='position:absolute;margin-left:44.8pt;
    28692892 margin-top:0;width:96pt;height:96pt;z-index:251657728;visibility:visible;
     
    28762899 <v:imagedata src="gsas2logo.png"/>
    28772900 <w:wrap type="square" anchory="line"/>
    2878 </v:shape><![endif]--><![if !vml]><img width=128 height=128 src=gsas2logo.png
     2901</v:shape><![endif]--><![if !vml]><img width=96 height=96 src=gsas2logo.png
    28792902align=right alt="Description: GSAS-II logo" v:shapes="Picture_x0020_2"><![endif]><span
    28802903style='mso-fareast-font-family:"Times New Roman"'>Help for GSAS-II<o:p></o:p></span></h1>
     
    28922915
    28932916<h2><a name=Index><span style='mso-fareast-font-family:"Times New Roman"'>Help
    2894 Index</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
    2895 
    2896 <ol start=1 type=1>
    2897  <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    2898      mso-list:l15 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family:
    2899      "Times New Roman"'><a href="#Tutorials">Learning GSAS-II: tutorials</a><o:p></o:p></span></li>
    2900  <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    2901      mso-list:l15 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family:
    2902      "Times New Roman"'><a href="#Data_tree">Application windows</a><o:p></o:p></span></li>
    2903  <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    2904      mso-list:l15 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family:
    2905      "Times New Roman"'><a href="#main_menu">Main menu commands</a><o:p></o:p></span></li>
    2906  <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    2907      mso-list:l15 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family:
    2908      "Times New Roman"'>Data Tree headings, graphics windows and menu commands<o:p></o:p></span></li>
    2909  <ol start=1 type=A>
    2910   <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2911       auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span
    2912       style='mso-fareast-font-family:"Times New Roman"'><a
    2913       href="#Data_tree_items">Top-level </a>Data Tree headings<o:p></o:p></span></li>
    2914   <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2915       auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span
    2916       style='mso-fareast-font-family:"Times New Roman"'><a href="#Phase">Phase </a>Data
    2917       Tree headings<o:p></o:p></span></li>
    2918   <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2919       auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span
    2920       style='mso-fareast-font-family:"Times New Roman"'><a href="#IMG">Image
    2921       (IMG) </a>Data Tree headings<o:p></o:p></span></li>
    2922   <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2923       auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span
    2924       style='mso-fareast-font-family:"Times New Roman"'><a href="#PWDR">Powder
    2925       histogram (PWDR) </a>Data Tree headings<o:p></o:p></span></li>
    2926   <ul type=square>
    2927    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2928        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2929        style='mso-fareast-font-family:"Times New Roman"'><a
    2930        href="#PWDR_Comments">Comments</a><o:p></o:p></span></li>
    2931    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2932        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2933        style='mso-fareast-font-family:"Times New Roman"'><a href="#PWDR_Limits">Limits</a><o:p></o:p></span></li>
    2934    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2935        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2936        style='mso-fareast-font-family:"Times New Roman"'><a
    2937        href="#PWDR_Background">Background</a><o:p></o:p></span></li>
    2938    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2939        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2940        style='mso-fareast-font-family:"Times New Roman"'><a
    2941        href="#PWDR_Instrument_Parameters">Instrument Parameters</a><o:p></o:p></span></li>
    2942    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2943        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2944        style='mso-fareast-font-family:"Times New Roman"'><a
    2945        href="#PWDR_Sample_Parameters">Sample Parameters</a><o:p></o:p></span></li>
    2946    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2947        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2948        style='mso-fareast-font-family:"Times New Roman"'><a
    2949        href="#PWDR_Peak_List">Peak List</a><o:p></o:p></span></li>
    2950    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2951        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2952        style='mso-fareast-font-family:"Times New Roman"'><a
    2953        href="#PWDR_Index_Peak_List">Index Peak List</a><o:p></o:p></span></li>
    2954    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2955        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2956        style='mso-fareast-font-family:"Times New Roman"'><a
    2957        href="#PWDR_Unit_Cells_List">Unit Cells List</a><o:p></o:p></span></li>
    2958    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2959        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2960        style='mso-fareast-font-family:"Times New Roman"'><a
    2961        href="#PWDR_Reflection_Lists">Reflection Lists</a><o:p></o:p></span></li>
    2962   </ul>
    2963   <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2964       auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span
    2965       style='mso-fareast-font-family:"Times New Roman"'><a href="#HKLF">Single
    2966       Crystal histogram (HKLF)</a> Data Tree headings<o:p></o:p></span></li>
    2967   <ul type=square>
    2968    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2969        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2970        style='mso-fareast-font-family:"Times New Roman"'><a
    2971        href="#HKLF_Instrument_Parameters">Instrument Parameters</a><o:p></o:p></span></li>
    2972    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2973        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2974        style='mso-fareast-font-family:"Times New Roman"'><a
    2975        href="#HKLF_HKL_Plot_Controls">HKL Plot Controls</a><o:p></o:p></span></li>
    2976    <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2977        auto;mso-list:l15 level3 lfo1;tab-stops:list 1.5in'><span
    2978        style='mso-fareast-font-family:"Times New Roman"'><a
    2979        href="#HKLF_Reflection_List">Reflection List</a><o:p></o:p></span></li>
    2980   </ul>
    2981   <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2982       auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span
    2983       style='mso-fareast-font-family:"Times New Roman"'><a href="#PDF">Pair
    2984       Distribution Functions (PDF) </a>Data Tree headings<o:p></o:p></span></li>
    2985   <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2986       auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span
    2987       style='mso-fareast-font-family:"Times New Roman"'><a href="#PKS">Powder
    2988       Peaks (PKS) </a>Data Tree headings<o:p></o:p></span></li>
    2989   <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
    2990       auto;mso-list:l15 level2 lfo1;tab-stops:list 1.0in'><span
    2991       style='mso-fareast-font-family:"Times New Roman"'><a href="#SASD">Small
    2992       Angle Scattering (SASD) </a>Data Tree headings<o:p></o:p></span></li>
    2993  </ol>
    2994  <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    2995      mso-list:l15 level1 lfo1;tab-stops:list .5in'><span style='mso-fareast-font-family:
    2996      "Times New Roman"'>Other: <a href="#Mac">Macintosh notes</a>, <a
    2997      href="#Preferences">Configuration options</a> and <a href="#Programmers">Programmers
    2998      documentation</a> <o:p></o:p></span></li>
    2999 </ol>
    3000 
    3001 <h2><a name=Tutorials><strong><span style='mso-fareast-font-family:"Times New Roman"'>Learning
    3002 GSAS-II: Tutorials</span></strong></a><span style='mso-bookmark:Tutorials'></span><span
    3003 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
    3004 
    3005 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3006 "Times New Roman"'>The best way to learn about how different sections of
    3007 GSAS-II is used is to work through tutorials. A list of available tutorial
    3008 topics appears on a <a href="Tutorials.html">separate web page</a>. <o:p></o:p></span></p>
     2917Index</span></a><span style='mso-fareast-font-family:"Times New Roman"'> <o:p></o:p></span></h2>
     2918
     2919<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     2920"Times New Roman"'>[<a href="gsasII-index.html">see separate page</a>]<o:p></o:p></span></p>
    30092921
    30102922<div class=MsoNormal align=center style='text-align:center'><span
    3011 style='mso-fareast-font-family:"Times New Roman"'>
    3012 
    3013 <hr size=2 width="100%" align=center>
     2923style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     2924
     2925<hr size=3 width="100%" align=center>
    30142926
    30152927</span></div>
    30162928
    30172929<div class=MsoNormal align=center style='text-align:center'><span
    3018 style='mso-fareast-font-family:"Times New Roman"'>
    3019 
    3020 <hr size=2 width="100%" align=center>
     2930style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     2931
     2932<hr size=3 width="100%" align=center>
    30212933
    30222934</span></div>
    30232935
    3024 <h2><a name="Data_tree"><span style='mso-fareast-font-family:"Times New Roman"'>1.
    3025 GSAS-II Data Tree</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
     2936<h2><a name="Data_tree"></a><a name=Tutorials><span style='mso-bookmark:Data_tree'><strong><span
     2937style='mso-fareast-font-family:"Times New Roman"'>Learning GSAS-II: Tutorials</span></strong></span></a><span
     2938style='mso-bookmark:Tutorials'></span><span style='mso-bookmark:Data_tree'><span
     2939style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h2>
     2940
     2941<p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Data_tree'><span
     2942style='mso-fareast-font-family:"Times New Roman"'>The best way to learn about
     2943how different sections of GSAS-II is used is to work through tutorials. A list
     2944of available tutorial topics appears on a </span></span><a href="Tutorials.html"><span
     2945style='mso-bookmark:Data_tree'><span style='mso-fareast-font-family:"Times New Roman"'>separate
     2946web page</span></span><span style='mso-bookmark:Data_tree'></span></a><span
     2947style='mso-bookmark:Data_tree'><span style='mso-fareast-font-family:"Times New Roman"'>.
     2948<o:p></o:p></span></span></p>
     2949
     2950<h2><span style='mso-bookmark:Data_tree'><span style='mso-fareast-font-family:
     2951"Times New Roman"'>1. GSAS-II Data Tree</span></span><span style='mso-fareast-font-family:
     2952"Times New Roman"'><o:p></o:p></span></h2>
    30262953
    30272954<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    30282955"Times New Roman"'>The data tree shows contents of a GSAS-II project (which can
    3029 be read or saved as a .gpx file) in a hierarchical view. Clicking on any item
    3030 in the tree opens that information on the right side of the window in the
    3031 &quot;Data Editing&quot; section, where information in that item can be viewed
    3032 or edited. For example, the <a href="#PWDR_Sample_Parameters">&quot;Sample
    3033 Parameters&quot;</a> item under a ‘PWDR’ entry contains information about how
    3034 data were collected, such as the sample temperature <a
    3035 href="#PWDR_Sample_Parameters">(see below)</a>. The arrow keys (up &amp; down)
    3036 move the selection to successive entries in the data tree; both the data window
    3037 and the associated plot (if any) will change.<o:p></o:p></span></p>
     2956be read or saved as a .<span class=SpellE>gpx</span> file) in a hierarchical
     2957view. Clicking on any item in the tree opens that information on the right side
     2958of the window in the &quot;Data Editing&quot; section, where information in
     2959that item can be viewed or edited. For example, the <a
     2960href="gsasII-pwdr.html#PWDR_Sample_Parameters">&quot;Sample Parameters&quot;</a> item under a
     2961‘PWDR’ entry contains information about how data were collected, such as the
     2962sample temperature <a href="gsasII-pwdr.html#PWDR_Sample_Parameters">(see below)</a>. The arrow
     2963keys (up &amp; down) move the selection to successive entries in the data tree;
     2964both the data window and the associated plot (if any) will change.<o:p></o:p></span></p>
    30382965
    30392966<h4 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
     
    30472974
    30482975<div class=MsoNormal align=center style='text-align:center'><span
    3049 style='mso-fareast-font-family:"Times New Roman"'>
    3050 
    3051 <hr size=2 width="100%" align=center>
     2976style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     2977
     2978<hr size=3 width="100%" align=center>
    30522979
    30532980</span></div>
    30542981
    30552982<div class=MsoNormal align=center style='text-align:center'><span
    3056 style='mso-fareast-font-family:"Times New Roman"'>
    3057 
    3058 <hr size=2 width="100%" align=center>
     2983style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     2984
     2985<hr size=3 width="100%" align=center>
    30592986
    30602987</span></div>
     
    30722999
    30733000<div class=MsoNormal align=center style='text-align:center'><span
    3074 style='mso-fareast-font-family:"Times New Roman"'>
    3075 
    3076 <hr size=2 width="100%" align=center>
     3001style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     3002
     3003<hr size=3 width="100%" align=center>
    30773004
    30783005</span></div>
    30793006
    30803007<div class=MsoNormal align=center style='text-align:center'><span
    3081 style='mso-fareast-font-family:"Times New Roman"'>
    3082 
    3083 <hr size=2 width="100%" align=center>
     3008style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     3009
     3010<hr size=3 width="100%" align=center>
    30843011
    30853012</span></div>
     
    30893016
    30903017<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3091 "Times New Roman"'>This window presents all the graphical material as a
    3092 multipage tabbed set of plots utilizing the matplotlib python package. Each
    3093 page has a tool with the controls</span><span class=MsoHyperlink><span
    3094 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></p>
     3018"Times New Roman"'>This window presents all the graphical material as a multipage
     3019tabbed set of plots utilizing the matplotlib python package. Each page has a
     3020tool with the controls</span><span class=MsoHyperlink><span style='color:windowtext;
     3021text-decoration:none;text-underline:none'><o:p></o:p></span></span></p>
    30953022
    30963023<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><img
    3097 border=0 width=727 height=55 id="_x0000_i1044" src=graphbar.jpg
     3024border=0 width=727 height=55 id="_x0000_i1037" src=graphbar.jpg
    30983025alt="toolbar on plots"></span></p>
    30993026
     
    31033030normal'>Back</b>, <b style='mso-bidi-font-weight:normal'>Forward</b>, <b
    31043031style='mso-bidi-font-weight:normal'>Pan</b>, <b style='mso-bidi-font-weight:
    3105 normal'>Zoom</b>, <b>Resize plot</b>, <b style='mso-bidi-font-weight:normal'>Save</b>,
    3106 <b>Key Press</b> and <b style='mso-bidi-font-weight:normal'>Help</b>,
    3107 respectively and are described below. The remainder (yellow arrows) move or
    3108 rescale the plot. Note that <b>Resize plot</b> is removed from the toolbar
    3109 where matplotlib allows this and should not be used. <span class=MsoHyperlink><span
    3110 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
     3032normal'>Zoom</b>, <span class=GramE><b>Resize</b></span><b> plot</b>, <b
     3033style='mso-bidi-font-weight:normal'>Save</b>, <b>Key Press</b> and <b
     3034style='mso-bidi-font-weight:normal'>Help</b>, respectively and are described
     3035below. The remainder (yellow arrows) move or rescale the plot. Note that <b>Resize
     3036plot</b> is removed from the toolbar where matplotlib allows this and should
     3037not be used. <span class=MsoHyperlink><span style='color:windowtext;text-decoration:
     3038none;text-underline:none'><o:p></o:p></span></span></span></p>
    31113039
    31123040<p class=MsoNormal style='margin-left:.5in'><b><span style='mso-fareast-font-family:
     
    31913119
    31923120<p class=MsoNormal style='margin-left:.5in'><b><span style='mso-fareast-font-family:
    3193 "Times New Roman"'>{less than}+{greater than}</span></b><span style='mso-fareast-font-family:
    3194 "Times New Roman"'><o:p></o:p></span></p>
     3121"Times New Roman"'>{less <span class=GramE>than}+</span>{greater than}</span></b><span
     3122style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    31953123
    31963124<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     
    31993127
    32003128<p class=MsoNormal style='margin-left:.5in'><b><span style='mso-fareast-font-family:
    3201 "Times New Roman"'>{greater than}+{less than}</span></b><span style='mso-fareast-font-family:
    3202 "Times New Roman"'><o:p></o:p></span></p>
     3129"Times New Roman"'>{greater <span class=GramE>than}+</span>{less than}</span></b><span
     3130style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    32033131
    32043132<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     
    32073135
    32083136<p class=MsoNormal style='margin-left:.5in'><b><span style='mso-fareast-font-family:
    3209 "Times New Roman"'>{up arrow}/{down arrow}</span></b><span style='mso-fareast-font-family:
    3210 "Times New Roman"'><o:p></o:p></span></p>
     3137"Times New Roman"'>{up arrow}<span class=GramE>/{</span>down arrow}</span></b><span
     3138style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    32113139
    32123140<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     
    32153143
    32163144<p class=MsoNormal style='margin-left:.5in'><b><span style='mso-fareast-font-family:
    3217 "Times New Roman"'>{down arrow}/{up arrow}</span></b><span style='mso-fareast-font-family:
    3218 "Times New Roman"'><o:p></o:p></span></p>
     3145"Times New Roman"'>{down arrow}<span class=GramE>/{</span>up arrow}</span></b><span
     3146style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    32193147
    32203148<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     
    32233151
    32243152<p class=MsoNormal style='margin-left:.5in'>Below the toolbar may be a status
    3225 bar that on the left may show either an instruction for a keyed input or a pull
    3226 down selection of keyed input; on the right may be displayed position dependent
    3227 information that is updated as the mouse is moved over the plot region.</p>
     3153bar that on the left may show either an instruction for a keyed input or a <span
     3154class=GramE>pull down</span> selection of keyed input; on the right may be
     3155displayed position dependent information that is updated as the mouse is moved
     3156over the plot region.</p>
    32283157
    32293158<div class=MsoNormal align=center style='text-align:center'><span
    3230 style='mso-fareast-font-family:"Times New Roman"'>
    3231 
    3232 <hr size=2 width="100%" align=center>
     3159style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     3160
     3161<hr size=3 width="100%" align=center>
    32333162
    32343163</span></div>
    32353164
    32363165<div class=MsoNormal align=center style='text-align:center'><span
    3237 style='mso-fareast-font-family:"Times New Roman"'>
    3238 
    3239 <hr size=2 width="100%" align=center>
     3166style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     3167
     3168<hr size=3 width="100%" align=center>
    32403169
    32413170</span></div>
     
    32473176margin-left:.7in;text-indent:-.25in;mso-list:l9 level1 lfo2;tab-stops:list .5in'><![if !supportLists]><span
    32483177style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    3249 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3250 style='mso-fareast-font-family:"Times New Roman"'>Menu <b>File</b> <o:p></o:p></span></p>
     3178style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     3179dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Menu <b>File</b>
     3180<o:p></o:p></span></p>
    32513181
    32523182<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    32553185
    32563186<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3257 "Times New Roman"'>Open a previously saved GSAS-II project file ({project}.gpx).
    3258 If you currently have a project file open, you are asked if it is OK to
    3259 overwrite it; Cancel will cancel the read process. <o:p></o:p></span></p>
     3187"Times New Roman"'>Open a previously saved GSAS-II project file ({project}.<span
     3188class=SpellE>gpx</span>). If you currently have a project file open, you are
     3189asked if it is OK to overwrite it; Cancel will cancel the read process. <o:p></o:p></span></p>
    32603190
    32613191<p style='margin-left:.5in'>Note that as files are saved, copies of the
    3262 previous version are saved as backup files, named as {project}.bak{<i>i</i>}.gpx,
    3263 where <i>i</i> starts as 0 and is increased after each save operation. NB: you
    3264 may open a backup .gpx file (e.g. name.bak3.gpx) to return to a previous
     3192previous version are saved as backup files, named as {project}.<span
     3193class=SpellE>bak</span>{<span class=SpellE><i>i</i></span>}.<span class=SpellE>gpx</span>,
     3194where <span class=SpellE><i>i</i></span> starts as 0 and is increased after
     3195each save operation. NB: you may open a backup .<span class=SpellE>gpx</span>
     3196file (<span class=GramE>e.g.</span> name.bak3.gpx) to return to a previous
    32653197version of your project, but if you do so, it is best to immediately use the <b'>Save
    3266 As... menu command (you may wish to use name.gpx to overwrite the current
    3267 version or select a new name.) If you forget specify a project name, then
    3268 name.bak3 will be considered the project name and backups will then be named
    3269 name.bak3.bak0.gpx, etc.</p>
     3198As... menu command (you may wish to use <span class=SpellE>name.gpx</span> to
     3199overwrite the current version or select a new name.) If you forget <span
     3200class=GramE>specify</span> a project name, then name.bak3 will be considered
     3201the project name and backups will then be named name.bak3.bak0.gpx, etc.</p>
    32703202
    32713203<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    33193251margin-left:.7in;text-indent:-.25in;mso-list:l9 level1 lfo2;tab-stops:list .5in'><![if !supportLists]><span
    33203252style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    3321 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3322 style='mso-fareast-font-family:"Times New Roman"'>Menu <b>Data</b> <o:p></o:p></span></p>
     3253style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     3254dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Menu <b>Data</b>
     3255<o:p></o:p></span></p>
    33233256
    33243257<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    33633296the space group symbol and then the lattice parameters. <br>
    33643297Note that nonstandard space group symbols are permitted; space group names must
    3365 have spaces between the axial fields (e.g. use ‘P n a 21’ not ‘Pna21’). <o:p></o:p></span></p>
     3298have spaces between the axial fields (<span class=GramE>e.g.</span> use ‘P n a
     329921’ not ‘Pna21’). <o:p></o:p></span></p>
    33663300
    33673301<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    33793313<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    33803314"Times New Roman"'>Rename a histogram entry. This should only be done before
    3381 the histogram is used in any phases: e.g. only rename data immediately after
    3382 reading. <o:p></o:p></span></p>
     3315the histogram is used in any phases: <span class=GramE>e.g.</span> only rename
     3316data immediately after reading. <o:p></o:p></span></p>
    33833317
    33843318<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    33883322<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    33893323"Times New Roman"'>This will remove an item from the data tree. A dialog box
    3390 with a list of choices for histograms is presented. Be sure to remove a
    3391 histograms from all phases before deleting it from the tree. <o:p></o:p></span></p>
     3324with a list of choices for histograms is presented. Be sure to remove a <span
     3325class=GramE>histograms</span> from all phases before deleting it from the tree.
     3326<o:p></o:p></span></p>
    33923327
    33933328<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    34103345margin-left:.7in;text-indent:-.25in;mso-list:l9 level1 lfo2;tab-stops:list .5in'><![if !supportLists]><span
    34113346style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    3412 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3413 style='mso-fareast-font-family:"Times New Roman"'>Menu <a name="Calculate_menu"><b>Calculate</b></a>
    3414 <o:p></o:p></span></p>
     3347style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     3348dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Menu <a
     3349name="Calculate_menu"><b>Calculate</b></a> <o:p></o:p></span></p>
    34153350
    34163351<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    34253360
    34263361<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    3427 "Times New Roman"'>View LS parms</span></b><span style='mso-fareast-font-family:
    3428 "Times New Roman"'> <o:p></o:p></span></p>
     3362"Times New Roman"'>View LS <span class=SpellE>parms</span></span></b><span
     3363style='mso-fareast-font-family:"Times New Roman"'> <o:p></o:p></span></p>
    34293364
    34303365<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    34313366"Times New Roman"'>This shows a dialog box with all the parameters for your
    34323367project; those to be refined are flagged ‘True’, otherwise ‘False’. Blanks
    3433 indicate parameters that are not refinable. The total number of refined parameters
    3434 is also shown at the top of the list. The value of each parameter is also
    3435 given. The parameter names are of the form ‘p:h:name:id’ where ‘p’ is the phase
    3436 index, ‘h’ is the histogram index and ‘id’ is the item index (if needed).
    3437 Indexes all begin with ‘0’ (zero). <o:p></o:p></span></p>
     3368indicate parameters that are not refinable. The total number of refined
     3369parameters is also shown at the top of the list. The value of each parameter is
     3370also given. The parameter names are of the form ‘<span class=SpellE>p:h:name:id</span>’
     3371where ‘p’ is the phase index, ‘h’ is the histogram index and ‘id’ is the item
     3372index (if needed). Indexes all begin with ‘0’ (zero). <o:p></o:p></span></p>
    34383373
    34393374<p style='margin-left:.5in'>Note that for atom positions, the coordinate values
    3440 (named as ‘p::A<i>w</i>:n’, where p is the phase number, n is the atom number
    3441 and <i>w</i> is x, y or z) is not a refinable parameter, but the shift in the
    3442 value is. The refined parameters are ‘p::A<i>w</i>:n’. The reason this is done
    3443 is that by treating an atom position as x+dx,y+dy,z+dz where the “d” values
    3444 indicate shifts from the starting position and the shifts are refined rather
    3445 than the x,y, or z values is that this simplifies symmetry constraints. As an example,
    3446 suppose we have an atom on a symmetry constrained site, x,1/2-x,z. The process
    3447 needed to define this constraint, so that if x moves positively y has to move
    3448 negatively by the same amount would be messy. With refinement of shifts, all we
    3449 need to do is constrain dy (‘0::dAy:n’) to be equal to -dx (-1*‘0::dAx:n’). </p>
     3375(named as ‘<span class=GramE>p::</span><span class=SpellE>A<i>w</i>:n</span>’,
     3376where p is the phase number, n is the atom number and <i>w</i> is x, y or z) is
     3377not a refinable parameter, but the shift in the value is. The refined
     3378parameters are ‘<span class=GramE>p::</span><span class=SpellE>A<i>w</i>:n</span>’.
     3379The reason this is done is that by treating an atom position as <span
     3380class=SpellE>x+<span class=GramE>dx,y</span>+dy,z+dz</span> where the “d”
     3381values indicate shifts from the starting position and the shifts are refined
     3382rather than the <span class=SpellE>x,y</span>, or z values is that this
     3383simplifies symmetry constraints. As an example, suppose we have an atom on a
     3384symmetry constrained site, x,1/2-<span class=GramE>x,z.</span> The process
     3385needed to define this constraint, so that if x moves positively y <span
     3386class=GramE>has to</span> move negatively by the same amount would be messy.
     3387With refinement of shifts, all we need to do is constrain <span class=SpellE>dy</span>
     3388(‘<span class=GramE>0::</span><span class=SpellE>dAy:n</span>’) to be equal to
     3389-dx (-1*‘0::<span class=SpellE>dAx:n</span>’). </p>
    34503390
    34513391<p style='margin-left:.5in'>Press the window exit button to exit this dialog
     
    34773417<p style='margin-left:.5in'>GSAS-II uses separate routines to read in
    34783418information from external files that can be created and customized easily. See
    3479 the GSAS-II Import Modules section of the <a href="#Programmers"><strong>Programmers
    3480 documentation</strong></a> for more information on this. Since it is easy to
    3481 support new formats, the documentation below may not list all supported
    3482 formats. </p>
     3419the GSAS-II Import Modules section of the <a href="#Programmers"><span
     3420class=GramE><strong>Programmers</strong></span><strong> documentation</strong></a>
     3421for more information on this. Since it is easy to support new formats, the
     3422documentation below may not list all supported formats. </p>
    34833423
    34843424<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    34923432are available. Any of these files can be accessed from a zip file. GSAS-II can
    34933433read many different image file formats including MAR345 files, Quantum ADSC
    3494 files, and tiff files from Perkin-Elmer, Pilatus, and GE. Although many of
    3495 these formats have data fields that should contain relevant information for the
    3496 exposure (e.g. wavelength), these are rarely filled in correctly by the data
    3497 acquisition software. Thus, you should have separately noted this information
    3498 as it will be needed <o:p></o:p></span></p>
     3434files, and tiff files from <span class=GramE>Perkin-Elmer</span>, Pilatus, and
     3435GE. Although many of these formats have data fields that should contain
     3436relevant information for the exposure (<span class=GramE>e.g.</span>
     3437wavelength), these are rarely filled in correctly by the data acquisition
     3438software. Thus, you should have separately noted this information as it will be
     3439needed <o:p></o:p></span></p>
    34993440
    35003441<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    35043445<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    35053446"Times New Roman"'>Creates a new phase by reading unit cell/symmetry/atom
    3506 coordinate information. GSAS-II can read information from a number of different
    3507 format files including: <o:p></o:p></span></p>
    3508 
    3509 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3510 "Times New Roman"'>GSAS .EXP <o:p></o:p></span></p>
    3511 
    3512 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3513 "Times New Roman"'>This reads one phase from a (old) GSAS experiment file
    3514 (name.EXP). The file name is found in a directory dialog; you can change
    3515 directories as needed. Only .EXP (or .exp) file names are shown. If the
    3516 selected file has more than one phase, a dialog is shown with the choices; only
    3517 one can be chosen. If you want more than one, redo this command. After
    3518 selecting a phase, a dialog box is shown with the proposed phase name. You can
    3519 change it if desired. <o:p></o:p></span></p>
     3447coordinate information. GSAS-II can read information from <span class=GramE>a
     3448number of</span> different format files including: <o:p></o:p></span></p>
     3449
     3450<p class=MsoNormal style='margin-left:.5in'><span class=GramE><span
     3451style='mso-fareast-font-family:"Times New Roman"'>GSAS .EXP</span></span><span
     3452style='mso-fareast-font-family:"Times New Roman"'> <o:p></o:p></span></p>
     3453
     3454<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     3455"Times New Roman"'>This reads one phase from a (old) GSAS experiment file (<span
     3456class=SpellE>name.EXP</span>). The file name is found in a directory dialog;
     3457you can change directories as needed. <span class=GramE>Only .EXP</span> (or
     3458.exp) file names are shown. If the selected file has more than one phase, a
     3459dialog is shown with the <span class=GramE>choices;</span> only one can be
     3460chosen. If you want more than one, redo this command. After selecting a phase,
     3461a dialog box is shown with the proposed phase name. You can change it if
     3462desired. <o:p></o:p></span></p>
    35203463
    35213464<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     
    35243467<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    35253468"Times New Roman"'>This reads the macromolecular phase information from a
    3526 Protein Data Base file (name.PDB or name.ENT). The file name is found in a
    3527 directory dialog; you can change directories as needed. Only .PDB (or .pdb) or
    3528 .ENT (or .ent) file names are shown. Be careful that the space group symbol on
    3529 the ‘CRYST1’ record in the PDB file follows the GSAS-II conventions (e.g. with
    3530 spaces between axial fields). A dialog box is shown with the proposed phase
    3531 name. You can change it if desired. <o:p></o:p></span></p>
     3469Protein Data Base file (name.PDB or <span class=SpellE>name.ENT</span>). The
     3470file name is found in a directory dialog; you can change directories as needed.
     3471Only .PDB (or .<span class=SpellE>pdb</span>) <span class=GramE>or .ENT</span>
     3472(or .<span class=SpellE>ent</span>) file names are shown. Be careful that the
     3473space group symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II
     3474conventions (<span class=GramE>e.g.</span> with spaces between axial fields). A
     3475dialog box is shown with the proposed phase name. You can change it if desired.
     3476<o:p></o:p></span></p>
    35323477
    35333478<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     
    35363481<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    35373482"Times New Roman"'>This reads one phase from a Crystallographic Information
    3538 File ({name}.CIF (or .cif). The file name is found in a directory dialog; you
    3539 can change directories as needed. If the selected file has more than one phase,
    3540 a dialog is shown with the choices; only one can be chosen. If you want more
     3483File ({name<span class=GramE>}.CIF</span> (or .<span class=SpellE>cif</span>).
     3484The file name is found in a directory dialog; you can change directories as
     3485needed. If the selected file has more than one phase, a dialog is shown with
     3486the <span class=GramE>choices;</span> only one can be chosen. If you want more
    35413487than one, redo this command. After selecting a phase, a dialog box is shown
    35423488with the proposed phase name. You can change it if desired. <o:p></o:p></span></p>
    35433489
    35443490<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3545 "Times New Roman"'>GSAS-II .gpx file <o:p></o:p></span></p>
    3546 
    3547 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3548 "Times New Roman"'>This reads one phase from a GSAS-II project file
    3549 ({name}.gpx). The file name is found in a directory dialog; you can change
    3550 directories as needed. If the selected file has more than one phase, a dialog
    3551 is shown with the choices; If you want more than one, redo this command. After
    3552 selecting a phase, a dialog box is shown with the proposed phase name. You can
    3553 change it if desired. <o:p></o:p></span></p>
     3491"Times New Roman"'>GSAS-II .<span class=SpellE>gpx</span> file <o:p></o:p></span></p>
     3492
     3493<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     3494"Times New Roman"'>This reads one phase from a GSAS-II project file ({name}.<span
     3495class=SpellE>gpx</span>). The file name is found in a directory dialog; you can
     3496change directories as needed. If the selected file has more than one phase, a
     3497dialog is shown with the choices; If you want more than one, redo this command.
     3498After selecting a phase, a dialog box is shown with the proposed phase name.
     3499You can change it if desired. <o:p></o:p></span></p>
    35543500
    35553501<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     
    35713517needed for processing a powder diffraction data set, such as data type,
    35723518calibration constants (such as wavelength) and default profile parameters are
    3573 read from a separate file, either a (old) GSAS instrument parameter file
    3574 (usually .prm, .ins or .inst extension) or a new GSAS-II .instparm file. <o:p></o:p></span></p>
     3519read from a separate file, either a (old) GSAS instrument parameter file (<span
     3520class=GramE>usually .<span class=SpellE>prm</span></span>, .ins or .<span
     3521class=SpellE>inst</span> extension) or a new GSAS-II .<span class=SpellE>instparm</span>
     3522file. <o:p></o:p></span></p>
    35753523
    35763524<p style='margin-left:.5in'>Note that it is possible to apply corrections to
    35773525the 2-theta, intensity or weight values by adding a Python command(s) to the
    3578 instrument (.instprm) parameter with a variable named CorrectionCode. See the <tt><span
    3579 style='font-size:10.0pt'>CorrectionCode.instprm.sample</span></tt> file
    3580 provided in the GSAS-II source directory for an example of how this is done. </p>
     3526instrument <span class=GramE>(.<span class=SpellE>instprm</span></span>)
     3527parameter with a variable named <span class=SpellE>CorrectionCode</span>. See
     3528the <span class=SpellE><tt><span style='font-size:10.0pt'>CorrectionCode.instprm.sample</span></tt></span>
     3529file provided in the GSAS-II source directory for an example of how this is
     3530done. </p>
    35813531
    35823532<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     
    35853535<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    35863536"Times New Roman"'>This reads one powder pattern (histogram) from a
    3587 Crystallographic Information File ({name}.CIF). The file name is found in a
    3588 directory dialog; you can change directories as needed. Only one .cif can be
    3589 chosen. If you want more than one, redo this command. <o:p></o:p></span></p>
    3590 
    3591 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3592 "Times New Roman"'>GSAS-II .gpx file <o:p></o:p></span></p>
     3537Crystallographic Information File ({name<span class=GramE>}.CIF</span>). The
     3538file name is found in a directory dialog; you can change directories as needed.
     3539Only <span class=GramE>one .<span class=SpellE>cif</span></span> can be chosen.
     3540If you want more than one, redo this command. <o:p></o:p></span></p>
     3541
     3542<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     3543"Times New Roman"'>GSAS-II .<span class=SpellE>gpx</span> file <o:p></o:p></span></p>
    35933544
    35943545<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    35953546"Times New Roman"'>This reads powder patterns from a previously created GSAS-II
    3596 gpx project file. If the selected file has more than one powder pattern, a
    3597 dialog is shown with the choices; one or more can be selected. It will ask for
    3598 an appropriate instrument parameter file to go with the selected powder data
    3599 sets. <o:p></o:p></span></p>
    3600 
    3601 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3602 "Times New Roman"'>GSAS .fxye files <o:p></o:p></span></p>
     3547<span class=SpellE>gpx</span> project file. If the selected file has more than
     3548one powder pattern, a dialog is shown with the choices; one or more can be
     3549selected. It will ask for an appropriate instrument parameter file to go with
     3550the selected powder data sets. <o:p></o:p></span></p>
     3551
     3552<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     3553"Times New Roman"'>GSAS .<span class=SpellE>fxye</span> files <o:p></o:p></span></p>
    36033554
    36043555<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    36053556"Times New Roman"'>This reads powder patterns (histograms) from the defined
    3606 GSAS format powder data files. GSAS file types STD, ESD, FXY and FXYE are
    3607 recognized. Neutron TOF data with a ‘TIME-MAP’ are also recognized. The file
    3608 names are found in a directory dialog; you can change directories as needed. If
    3609 the selected files have more than one powder pattern, a dialog is shown with
    3610 the choice(s). <o:p></o:p></span></p>
    3611 
    3612 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3613 "Times New Roman"'>TOPAS .xye files. <o:p></o:p></span></p>
    3614 
    3615 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3616 "Times New Roman"'>This format is a simple 3-column (2-theta, intensity &amp;
    3617 sig) text file. The file names are found in a directory dialog; you can change
     3557GSAS format powder data files. GSAS file <span class=GramE>types</span> STD,
     3558ESD, FXY and FXYE are recognized. Neutron TOF data with a ‘TIME-MAP’ are also
     3559recognized. The file names are found in a directory dialog; you can change
     3560directories as needed. If the selected files have more than one powder pattern,
     3561a dialog is shown with the choice(s). <o:p></o:p></span></p>
     3562
     3563<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     3564"Times New Roman"'>TOPAS .<span class=SpellE>xye</span> files. <o:p></o:p></span></p>
     3565
     3566<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     3567"Times New Roman"'>This format is a simple 3-column (2-theta, intensity &amp; sig)
     3568text file. The file names are found in a directory dialog; you can change
    36183569directories as needed. <o:p></o:p></span></p>
    36193570
     
    36403591<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    36413592"Times New Roman"'>This reads squared structure factors (as F**2) and sig(F**2)
    3642 from a SHELX format .hkl file. The file names are found in a directory dialog;
    3643 you can change directories as needed. You must know the file contains structure
    3644 factors (as F**2) as the file itself has no internal indication of this. <o:p></o:p></span></p>
     3593from a SHELX format .<span class=SpellE>hkl</span> file. The file names are
     3594found in a directory dialog; you can change directories as needed. You must
     3595know the file contains structure factors (as F**2) as the file itself has no
     3596internal indication of this. <o:p></o:p></span></p>
    36453597
    36463598<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     
    36493601<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    36503602"Times New Roman"'>This reads structure factors (as F) and sig(F) from a SHELX
    3651 format .hkl file. The file names are found in a directory dialog; you can
    3652 change directories as needed. You must know the file contains structure factors
    3653 (as F values) as the file itself has no internal indication of this. <o:p></o:p></span></p>
     3603format .<span class=SpellE>hkl</span> file. The file names are found in a
     3604directory dialog; you can change directories as needed. You must know the file
     3605contains structure factors (as F values) as the file itself has no internal
     3606indication of this. <o:p></o:p></span></p>
    36543607
    36553608<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     
    36573610
    36583611<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3659 "Times New Roman"'>This reads structure factors (as F**2 or F) and sig(F**2 or
    3660 F) from a .CIF (or .cif) or .FCF (or .fcf) format file. The file names are
     3612"Times New Roman"'>This reads structure factors (as F**2 or F) and <span
     3613class=GramE>sig(</span>F**2 or F) from a .CIF (or .<span class=SpellE>cif</span>)
     3614or .FCF (or .<span class=SpellE>fcf</span>) format file. The file names are
    36613615found in a directory dialog; you can change directories as needed. The internal
    36623616structure of this file indicates in which form the structure factors are used. <o:p></o:p></span></p>
     
    36673621<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    36683622"Times New Roman"'>This attempts to read one data set from a file trying the
    3669 formats as described above. However, since it cannot be determined if SHELX
    3670 format .hkl contaings F or F**2 values, do not use this command for those
    3671 files. On occasion, this command may not succeed in correctly determining a
    3672 file format. If it fails, retry by selecting the correct format from the list. <o:p></o:p></span></p>
     3623formats as described above. However, since it cannot be determined if SHELX <span
     3624class=GramE>format .<span class=SpellE>hkl</span></span> <span class=SpellE>contaings</span>
     3625F or F**2 values, do not use this command for those files. On occasion, this
     3626command may not succeed in correctly determining a file format. If it fails,
     3627retry by selecting the correct format from the list. <o:p></o:p></span></p>
    36733628
    36743629<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    36903645<p style='margin-left:.5in'>GSAS-II uses separate routines to write out files
    36913646with information inside GSAS-II. These routines can be created and customized
    3692 easily. See the GSAS-II Export Modules section of the <a href="#Programmers"><strong>Programmers
    3693 documentation</strong></a> for more information on this. Since it is easy to
    3694 support new formats, the documentation below may not list all supported
    3695 formats. </p>
     3647easily. See the GSAS-II Export Modules section of the <a href="#Programmers"><span
     3648class=GramE><strong>Programmers</strong></span><strong> documentation</strong></a>
     3649for more information on this. Since it is easy to support new formats, the
     3650documentation below may not list all supported formats. </p>
    36963651
    36973652<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    37343689"Times New Roman"'> <o:p></o:p></span></p>
    37353690
    3736 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3737 "Times New Roman"'>This exports selected images as a portable networks graphics
    3738 format (PNG) file. Alternately, the image controls and masks can be written for
    3739 selected images. If strain analysis has been performed on images, the results
    3740 can also be exported here as a spreadsheet (.csv file). <o:p></o:p></span></p>
     3691<p class=MsoNormal style='margin-left:.5in'><span class=GramE><span
     3692style='mso-fareast-font-family:"Times New Roman"'>This exports</span></span><span
     3693style='mso-fareast-font-family:"Times New Roman"'> selected images as a
     3694portable networks graphics format (PNG) file. Alternately, the image controls
     3695and masks can be written for selected images. If strain analysis has been
     3696performed on images, the results can also be exported here as a spreadsheet
     3697(.csv file). <o:p></o:p></span></p>
    37413698
    37423699<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
     
    37713728<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    37723729"Times New Roman"'>This allows computed PDFs peak lists from selected
    3773 histograms to be written as two simple text files, {name}.gr and {name}.sq,
    3774 containing g(r) and s(q), respectively as 2 columns of data; a header on each
    3775 indicated the source file name and the column headings. The file name comes
    3776 from the PDF entry in the GSAS-II data tree. <o:p></o:p></span></p>
     3730histograms to be written as two simple text files, {name}.gr and {name<span
     3731class=GramE>}.sq</span>, containing g(r) and s(q), respectively as 2 columns of
     3732data; a header on each indicated the source file name and the column headings.
     3733The file name comes from the PDF entry in the GSAS-II data tree. <o:p></o:p></span></p>
    37773734
    37783735<div class=MsoNormal align=center style='text-align:center'><span
    3779 style='mso-fareast-font-family:"Times New Roman"'>
    3780 
    3781 <hr size=2 width="100%" align=center>
     3736style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     3737
     3738<hr size=3 width="100%" align=center>
    37823739
    37833740</span></div>
    37843741
    37853742<div class=MsoNormal align=center style='text-align:center'><span
    3786 style='mso-fareast-font-family:"Times New Roman"'>
    3787 
    3788 <hr size=2 width="100%" align=center>
     3743style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     3744
     3745<hr size=3 width="100%" align=center>
    37893746
    37903747</span></div>
     
    37983755"Times New Roman"'>This window provides a place for you to enter whatever text
    37993756commentary you wish. Each time you enter this window, a date/time entry is
    3800 provided for you. A possibly useful technique is to select a portion of the
    3801 project.lst file after a refinement completes (it will contain refinement
    3802 results with residuals, new values &amp; esds) and paste it into this Notebook
    3803 window so it becomes a part of your project file.</span> </p>
     3757provided for you. A possibly useful technique is to select a portion of the <span
     3758class=SpellE>project.lst</span> file after a refinement completes (it will contain
     3759refinement results with residuals, new values &amp; <span class=SpellE>esds</span>)
     3760and paste it into this Notebook window so it becomes a part of your project
     3761file.</span> </p>
    38043762
    38053763<h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
     
    38383796style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    38393797mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    3840 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3841 </span></span></span><![endif]><u><span style='mso-fareast-font-family:"Times New Roman"'>analytic
    3842 Hessian</span></u><span style='mso-fareast-font-family:"Times New Roman"'>:
    3843 This is the default option and is usually the most useful. It uses a
    3844 custom-developed least-squares minimizer that uses singular-value decomposition
    3845 (SVD) to reduce the errors caused by correlated variables and the
     3798style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     3799</span></span></span><![endif]><span dir=LTR></span><u><span style='mso-fareast-font-family:
     3800"Times New Roman"'>analytic Hessian</span></u><span style='mso-fareast-font-family:
     3801"Times New Roman"'>: This is the default option and is usually the most useful.
     3802It uses a custom-developed least-squares minimizer that uses singular-value
     3803decomposition (SVD) to reduce the errors caused by correlated variables and the
    38463804Levenberg-Marquardt algorithm to up-weight diagonal Hessian terms when
    38473805refinements fail to lower χ<sup>2</sup>. <o:p></o:p></span></p>
     
    38513809style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    38523810mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    3853 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3854 </span></span></span><![endif]><u><span style='mso-fareast-font-family:"Times New Roman"'>analytic
    3855 Jacobian</span></u><span style='mso-fareast-font-family:"Times New Roman"'>:
    3856 This uses a numpy-provided <i>leastsq</i> minimizer, which not applicable for problem
    3857 with a large number of histograms as it requires much more memory than the
    3858 Hessian routines. This because it creates a Jacobian matrix that is shaped N x
    3859 M (N parameters x M observations) while the Hessian methods create a Jacobian
    3860 matrix only each histogram. <o:p></o:p></span></p>
     3811style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     3812</span></span></span><![endif]><span dir=LTR></span><u><span style='mso-fareast-font-family:
     3813"Times New Roman"'>analytic Jacobian</span></u><span style='mso-fareast-font-family:
     3814"Times New Roman"'>: This uses a <span class=SpellE>numpy</span>-provided <span
     3815class=SpellE><i>leastsq</i></span> minimizer, which not applicable for problem
     3816with <span class=GramE>a large number of</span> histograms as it requires much
     3817more memory than the Hessian routines. This because it creates a Jacobian
     3818matrix that is shaped N x M (N parameters x M observations) while the Hessian
     3819methods create a Jacobian matrix only each histogram. <o:p></o:p></span></p>
    38613820
    38623821<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     
    38643823style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    38653824mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    3866 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3867 </span></span></span><![endif]><u><span style='mso-fareast-font-family:"Times New Roman"'>numeric</span></u><span
    3868 style='mso-fareast-font-family:"Times New Roman"'>: This also uses the numpy <i>leastsq</i>
    3869 minimizer, and is also not applicable for larger problems. Unlike, the
    3870 &quot;analytic Jacobian&quot;, numerical derivatives are computed rather than
    3871 use the analytical derivatives that are coded directly into GSAS-II. This will
    3872 be slower than the analytical derivatives and will is often less accurate which
    3873 results in slower convergence. It is typically used for code development to
    3874 check the accuracy of the analytical derivative formulations. <o:p></o:p></span></p>
     3825style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     3826</span></span></span><![endif]><span dir=LTR></span><u><span style='mso-fareast-font-family:
     3827"Times New Roman"'>numeric</span></u><span style='mso-fareast-font-family:"Times New Roman"'>:
     3828This also uses the <span class=SpellE>numpy</span> <span class=SpellE><i>leastsq</i></span>
     3829<span class=GramE>minimizer, and</span> is also not applicable for larger
     3830problems. Unlike, the &quot;analytic Jacobian&quot;, numerical derivatives are
     3831computed rather than use the analytical derivatives that are coded directly
     3832into GSAS-II. This will be slower than the analytical derivatives and will is
     3833often less accurate which results in slower convergence. It is typically used
     3834for code development to check the accuracy of the analytical derivative
     3835formulations. <o:p></o:p></span></p>
    38753836
    38763837<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     
    38783839style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    38793840mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    3880 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3881 </span></span></span><![endif]><u><span style='mso-fareast-font-family:"Times New Roman"'>Hessian
    3882 SVD</span></u><span style='mso-fareast-font-family:"Times New Roman"'>: This is
    3883 very similar to <u>analytic Hessian</u> but does not include the
    3884 Levenberg-Marquardt algorithm. It can be faster, but is more prone to diverge
    3885 when severe correlation is present. It is possible that it might be better for
    3886 single-crystal refinements. <o:p></o:p></span></p>
     3841style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     3842</span></span></span><![endif]><span dir=LTR></span><u><span style='mso-fareast-font-family:
     3843"Times New Roman"'>Hessian SVD</span></u><span style='mso-fareast-font-family:
     3844"Times New Roman"'>: This is very similar to <u>analytic Hessian</u> but does
     3845not include the Levenberg-Marquardt algorithm. It can be <span class=GramE>faster,
     3846but</span> is more prone to diverge when severe correlation is present. It is
     3847possible that it might be better for single-crystal refinements. <o:p></o:p></span></p>
    38873848
    38883849<p style='margin-left:1.25in'>Note that the Jacobian refinement tools are the
    3889 Fortran MINPACK <i>lmdif</i> and <i>lmder</i> algorithms wrapped in python as
    3890 provided in the Scipy package. The Hessian routines are were developed for
    3891 GSAS-II based on routines in numpy and scipy and using the material in
    3892 Numerical Recipes (Press, Flannery, Teulosky &amp; Vetterling) for the
    3893 Levenberg-Marquardt. The purpose is to minimize the sum of the squares of M<span
    3894 style='mso-fareast-font-family:"Times New Roman"'> nonlinear functions in N
    3895 variables by a modification of the Levenberg-Marquardt algorithm. The lmdif and
    3896 lmder routines were written by </span>Burton S. Garbow, Kenneth E. Hillstrom,
    3897 Jorge J. More (Argonne National Laboratory, 1980). </p>
     3850Fortran MINPACK <span class=SpellE><i>lmdif</i></span> and <span class=SpellE><i>lmder</i></span>
     3851algorithms wrapped in python as provided in the <span class=SpellE>Scipy</span>
     3852package. The Hessian routines <span class=GramE>are were</span> developed for
     3853GSAS-II based on routines in <span class=SpellE>numpy</span> and <span
     3854class=SpellE>scipy</span> and using the material in Numerical Recipes (Press,
     3855Flannery, <span class=SpellE>Teulosky</span> &amp; <span class=SpellE>Vetterling</span>)
     3856for the Levenberg-Marquardt. The purpose is to minimize the sum of the squares
     3857of M<span style='mso-fareast-font-family:"Times New Roman"'> nonlinear
     3858functions in N variables by a modification of the Levenberg-Marquardt
     3859algorithm. The <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
     3860routines were written by </span>Burton S. <span class=SpellE>Garbow</span>,
     3861Kenneth E. <span class=SpellE>Hillstrom</span>, Jorge J. More (Argonne National
     3862Laboratory, 1980). </p>
    38983863
    38993864<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
    3900 "Times New Roman"'>Min delta-M/M</span></b><span style='mso-fareast-font-family:
    3901 "Times New Roman"'><o:p></o:p></span></p>
     3865"Times New Roman"'>Min <span class=GramE>delta-M</span>/M</span></b><span
     3866style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    39023867
    39033868<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    39043869"Times New Roman"'>A refinement will stop when the change in the minimization
    3905 function (M=Σ[w(Io-Ic)<sup>2</sup>]) is less than this value. The allowed range
    3906 is 10<sup>-9</sup> to 1.0, with a default of 0.001. A value of 1.0 stops the
    3907 refinement after a single cycle. Values less than 10<sup>-4</sup> cause
    3908 refinements to continue even if there is no meaningful improvement. <o:p></o:p></span></p>
     3870function (M=Σ[w(Io-<span class=SpellE>Ic</span>)<sup>2</sup>]) is less than
     3871this value. The allowed range is 10<sup>-9</sup> to 1.0, with a default of
     38720.001. A value of 1.0 stops the refinement after a single cycle. Values less
     3873than 10<sup>-4</sup> cause refinements to continue even if there is no meaningful
     3874improvement. <o:p></o:p></span></p>
    39093875
    39103876<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
     
    39253891weight of 1+λ is applied to the diagonal elements of the Hessian. When λ is
    39263892large, this down-weights the significance of the off-diagonal terms in the
    3927 Hessian. Thus, when λ is large, the refinement is effectively one of
    3928 steepest-descents, where correlation between variables is ignored. Note that
    3929 steepest-descents minimization is typically slow and may not always find the
    3930 local minimum. This is only available with the &quot;analytical Hessian&quot;
    3931 minimizer. <o:p></o:p></span></p>
     3893Hessian. Thus, when λ is large, the refinement is effectively one of <span
     3894class=GramE>steepest-descents</span>, where correlation between variables is
     3895ignored. Note that steepest-descents minimization is typically slow and may not
     3896always find the local minimum. This is only available with the &quot;analytical
     3897Hessian&quot; minimizer. <o:p></o:p></span></p>
    39323898
    39333899<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
     
    39503916See the <a
    39513917href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.leastsq.html">SciPy
    3952 leastsq docs</a> for more information. <o:p></o:p></span></p>
     3918<span class=SpellE>leastsq</span> docs</a> for more information. <o:p></o:p></span></p>
    39533919
    39543920<p style='margin-left:.75in'><a name=SingleXtlSettings></a><u>Single Crystal:</u><i>
     
    39653931
    39663932<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
    3967 "Times New Roman"'>Min obs/sig</span></b><span style='mso-fareast-font-family:
    3968 "Times New Roman"'><o:p></o:p></span></p>
    3969 
    3970 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3971 "Times New Roman"'>Conventional cutoff for single crystal refinements as to
    3972 what reflections should be considered observed, typical values are 2.0 (2σ) or
    3973 3.0 (3σ). <o:p></o:p></span></p>
     3933"Times New Roman"'>Min <span class=SpellE>obs</span>/sig</span></b><span
     3934style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     3935
     3936<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     3937"Times New Roman"'>Conventional cutoff for single crystal refinements as to what
     3938reflections should be considered observed, typical values are 2.0 (2σ) or 3.0
     3939(3σ). <o:p></o:p></span></p>
    39743940
    39753941<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
     
    39783944
    39793945<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3980 "Times New Roman"'>(needs further work) <o:p></o:p></span></p>
     3946"Times New Roman"'>(<span class=GramE>needs</span> further work) <o:p></o:p></span></p>
    39813947
    39823948<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
     
    39863952<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    39873953"Times New Roman"'>Removes reflections that are very poorly fit. Should be used
    3988 only with extreme care, since poorly-fit reflections could be an indication
    3989 that the structure is wrong. <o:p></o:p></span></p>
     3954only with extreme care, since <span class=GramE>poorly-fit</span> reflections
     3955could be an indication that the structure is wrong. <o:p></o:p></span></p>
    39903956
    39913957<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
     
    40243990or more histograms are selected, a sequential refinement is used. If none are
    40253991selected, then the refinement be set as &quot;normal&quot;. The button is
    4026 labeled &quot;Select&quot; when in normal refinement mode and
    4027 &quot;Reselect&quot; in sequential refinement mode. <o:p></o:p></span></p>
     3992labeled &quot;Select&quot; when in normal refinement mode and &quot;Reselect&quot;
     3993in sequential refinement mode. <o:p></o:p></span></p>
    40283994
    40293995<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
     
    40323998
    40333999<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4034 "Times New Roman"'>Normally, in a sequential histograms are fit in the order
    4035 they are in the data tree (which can be reordered by dragging tree items), but
    4036 when this option is selected, the sequential fit is performed with the last
    4037 tree entry first. <o:p></o:p></span></p>
     4000"Times New Roman"'>Normally, in <span class=GramE>a sequential histograms</span>
     4001are fit in the order they are in the data tree (which can be reordered by
     4002dragging tree items), but when this option is selected, the sequential fit is
     4003performed with the last tree entry first. <o:p></o:p></span></p>
    40384004
    40394005<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
     
    40444010"Times New Roman"'>When this option is selected, the fitted parameters from
    40454011each refinement are copied to the next histogram, so that the starting point
    4046 for each refinement will be the results from fitting the previous. This works
    4047 well for parametric experiments where parameters such as the lattice parameters
     4012for each refinement will be the results from fitting the previous. This works well
     4013for parametric experiments where parameters such as the lattice parameters
    40484014change gradually over the course of successive measurements. This option is
    40494015usually used only for the initial refinement after a sequential fit is started
     
    40764042
    40774043<p style='margin-left:.75in'>This offers a place to change how GSAS-II performs
    4078 refinements, but has no specific menu commands or graphics. </p>
     4044<span class=GramE>refinements, but</span> has no specific menu commands or
     4045graphics. </p>
    40794046
    40804047<h4 style='margin-left:.25in'><a name=Covariance>Covariance</a></h4>
     
    40874054<h5 style='margin-left:.5in'>What is plotted here?</h5>
    40884055
    4089 <p style='margin-left:1.0in'>The variance-covariance matrix as a color coded
    4090 array is shown on this page. The color bar to the right shows the range of
    4091 covariances (-1 to 1) and corresponding colors. The parameter names are to the
    4092 right and the parameter numbers are below the plot. </p>
     4056<p style='margin-left:1.0in'>The variance-covariance matrix as a <span
     4057class=GramE>color coded</span> array is shown on this page. The color bar to
     4058the right shows the range of covariances (-1 to 1) and corresponding colors.
     4059The parameter names are to the right and the parameter numbers are below the
     4060plot. </p>
    40934061
    40944062<h5 style='margin-left:.5in'>What can I do with the plot?</h5>
    40954063
    40964064<p style='margin-left:1.0in'>Move the mouse cursor across the plot. If on a
    4097 diagonal cell, the parameter name, value and esd is shown both as a tool tip
    4098 and in the right hand portion of the status bar. If the cursor is off the
    4099 diagonal, the two parameter names and their covariance are shown in the tool
    4100 tip and the status bar. </p>
     4065diagonal cell, the parameter name, value and <span class=SpellE>esd</span> is
     4066shown both as a tool tip and in the <span class=GramE>right hand</span> portion
     4067of the status bar. If the cursor is off the diagonal, the two parameter names
     4068and their covariance are shown in the tool tip and the status bar. </p>
    41014069
    41024070<p style='margin-left:1.0in'>Use the Zoom and Pan buttons to focus on some
     
    41054073<p style='margin-left:1.0in'>Press ‘s’ – A color scheme selection dialog is
    41064074shown. Select a color scheme and press OK, the new color scheme will be
    4107 plotted. The default is ‘RdYlGn’. </p>
     4075plotted. The default is ‘<span class=SpellE>RdYlGn</span>’. </p>
    41084076
    41094077<p style='margin-left:1.0in'>Press ‘p’ – Saves the covariance values in a text
     
    41154083<span style='mso-bookmark:Constraints'></span>
    41164084
    4117 <p class=MsoNormal style='margin-left:.5in'>This window shows the constraints
    4118 to be used in a refinement. It is organized into three tabbed pages. ‘Phase
     4085<p class=MsoNormal style='margin-left:.5in'>This window shows the constraints to
     4086be used in a refinement. It is organized into three tabbed pages. ‘Phase
    41194087constraints’ contain those involving parameters that describe aspects of the
    4120 crystalline phases to be used in the refinement (e.g. atom coordinates, thermal
    4121 motion and site fraction parameters). ‘Histogram/Phase constraints’ are those
    4122 which describe aspects of the pattern that depend on both the phase and the
    4123 data set used in the refinement (e.g. microstrain and crystallite size
    4124 parameters). ‘Histogram constraints’ are those that depend only on the data set
    4125 (e.g. profile coefficients U, V, W, X and Y). </p>
     4088crystalline phases to be used in the refinement (<span class=GramE>e.g.</span>
     4089atom coordinates, thermal motion and site fraction parameters).
     4090‘Histogram/Phase constraints’ are those which describe aspects of the pattern
     4091that depend on both the phase and the data set used in the refinement (<span
     4092class=GramE>e.g.</span> <span class=SpellE>microstrain</span> and crystallite
     4093size parameters). ‘Histogram constraints’ are those that depend only on the
     4094data set (<span class=GramE>e.g.</span> profile coefficients U, V, W, X and Y).
     4095</p>
    41264096
    41274097<h5 style='margin-left:.5in'>What can I do here?</h5>
    41284098
    41294099<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    4130 text-indent:-.25in;mso-list:l20 level1 lfo5'><![if !supportLists]><span
     4100text-indent:-.25in;mso-list:l20 level1 lfo4'><![if !supportLists]><span
    41314101style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    4132 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4133 style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the
    4134 parameter types you wish to constrain. Each will have the same possibilities in
    4135 the ‘<b style='mso-bidi-font-weight:normal'>Edit’</b> menu.<o:p></o:p></span></p>
     4102style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4103dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Select
     4104the tab for the parameter types you wish to constrain. Each will have the same
     4105possibilities in the ‘<b style='mso-bidi-font-weight:normal'>Edit’</b> menu.<o:p></o:p></span></p>
    41364106
    41374107<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4138 auto;text-indent:-.25in;mso-list:l20 level1 lfo5'><![if !supportLists]><span
     4108auto;text-indent:-.25in;mso-list:l20 level1 lfo4'><![if !supportLists]><span
    41394109style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    4140 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4141 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:
    4142 normal'>Edit</b>’ – <o:p></o:p></span></p>
     4110style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4111dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b
     4112style='mso-bidi-font-weight:normal'>Edit</b>’ – <o:p></o:p></span></p>
    41434113
    41444114<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4145 auto;text-indent:-.25in;mso-list:l20 level2 lfo5'><![if !supportLists]><span
     4115auto;text-indent:-.25in;mso-list:l20 level2 lfo4'><![if !supportLists]><span
    41464116style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    4147 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4148 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
    4149 Hold</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – select
    4150 a parameter that you wish to remain fixed although other parameters of the same
    4151 type may be selected as a group for refinement. For example, if the space group
    4152 for a phase has a polar axis (e.g. the b-axis in P2<sub>1</sub>), then one atom
     4117style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4118dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4119"Times New Roman"'>Add Hold</span></b><span style='mso-fareast-font-family:
     4120"Times New Roman"'> – select a parameter that you wish to remain fixed although
     4121other parameters of the same type may be selected as a group for refinement.
     4122For example, if the space group for a phase has a polar axis (<span
     4123class=GramE>e.g.</span> the b-axis in P2<sub>1</sub>), then one atom
    41534124y-parameter is arbitrary and should be selected for a Hold to keep the
    41544125structure from drifting up or down the y-axis during refinement. If selected, a
     
    41594130
    41604131<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4161 auto;text-indent:-.25in;mso-list:l20 level2 lfo5'><![if !supportLists]><span
     4132auto;text-indent:-.25in;mso-list:l20 level2 lfo4'><![if !supportLists]><span
    41624133style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    4163 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4164 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
    4165 equivalence</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    4166 – select a list of parameters that should have the same value (possibly with a
    4167 non-unitary multiplier for some). Examples are a list of atoms with the same
    4168 thermal motion Uiso, sets of profile coefficients U,V,W across multiple data
    4169 sets. If selected, a dialog box will appear with a list of the available
    4170 parameters. Select one and press OK; a second dialog box will appear with only
    4171 those parameters that can be made equivalent to the first one. Choose those and
    4172 press OK. Cancel in either dialog will cancel the operation. The equivalenced
     4134style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4135dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4136"Times New Roman"'>Add equivalence</span></b><span style='mso-fareast-font-family:
     4137"Times New Roman"'> – select a list of parameters that should have the same
     4138value (possibly with a non-unitary multiplier for some). Examples are a list of
     4139atoms with the same thermal motion <span class=SpellE>Uiso</span>, sets of
     4140profile coefficients <span class=GramE>U,V</span>,W across multiple data sets.
     4141If selected, a dialog box will appear with a list of the available parameters.
     4142Select one and press OK; a second dialog box will appear with only those
     4143parameters that can be made equivalent to the first one. Choose those and press
     4144OK. Cancel in either dialog will cancel the operation. The equivalenced
    41734145parameters will show as an equation of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0;
    4174 usually M1=1.0 and M2=-1.0, but can be changed via the ‘Edit’ button. The
    4175 keyword ‘EQUIV’ marks it as an equivalence. A Delete button can be used to
    4176 remove it.<o:p></o:p></span></p>
     4146usually M1=1.0 and M2=-<span class=GramE>1.0, but</span> can be changed via the
     4147‘Edit’ button. The keyword ‘EQUIV’ marks it as an equivalence. A Delete button
     4148can be used to remove it.<o:p></o:p></span></p>
    41774149
    41784150<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4179 auto;text-indent:-.25in;mso-list:l20 level2 lfo5'><![if !supportLists]><span
     4151auto;text-indent:-.25in;mso-list:l20 level2 lfo4'><![if !supportLists]><span
    41804152style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    4181 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4182 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
    4183 constraint</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    4184 select a list of parameters whose sum (with possible non-unitary multipliers)
    4185 is fixed. For example, the sum of site fractions for atoms on the same site
    4186 could be fixed to unity. If selected, a dialog box will appear with a list of
    4187 the available parameters. Select one and press OK; a second dialog box will
    4188 appear with only those parameters that can be used in a constraint with the
    4189 first one. Choose those and press OK. Cancel in either dialog will cancel the
    4190 operation. The equivalenced parameters will show as an equation of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+…=C;
     4153style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4154dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4155"Times New Roman"'>Add constraint</span></b><span style='mso-fareast-font-family:
     4156"Times New Roman"'> – select a list of parameters whose sum (with possible
     4157non-unitary multipliers) is fixed. For example, the sum of site fractions for
     4158atoms on the same site could be fixed to unity. If selected, a dialog box will
     4159appear with a list of the available parameters. Select one and press OK; a
     4160second dialog box will appear with only those parameters that can be used in a
     4161constraint with the first one. Choose those and press OK. Cancel in either
     4162dialog will cancel the operation. The equivalenced parameters will show as an
     4163equation of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+…=C;
    41914164the multipliers M1, M2, … and C can be changed via the ‘Edit’ button. The
    41924165keyword ‘CONSTR’ marks it as a constraint. A Delete button can be used to
     
    41944167
    41954168<p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto;
    4196 text-indent:-.25in;mso-list:l20 level2 lfo5'><![if !supportLists]><span
     4169text-indent:-.25in;mso-list:l20 level2 lfo4'><![if !supportLists]><span
    41974170style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    4198 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4199 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
    4200 function</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    4201 this is very similar the “Add constraint” type except that the result of the
    4202 sum can be varied in the refinement. The keyword ‘FUNCT’ marks it as a
    4203 function; the ‘Refine?’ box indicates your choice to refine the result of the
    4204 sum. A Delete button can be used to remove it.<o:p></o:p></span></p>
     4171style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4172dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4173"Times New Roman"'>Add function</span></b><span style='mso-fareast-font-family:
     4174"Times New Roman"'> – this is very similar the “Add constraint” type except
     4175that the result of the sum can be varied in the refinement. The keyword ‘FUNCT’
     4176marks it as a function; the ‘Refine?’ box indicates your choice to refine the
     4177result of the sum. A Delete button can be used to remove it.<o:p></o:p></span></p>
    42054178
    42064179<h4 style='margin-left:.25in'><a name=Restraints><span style='mso-fareast-font-family:
     
    42184191
    42194192<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    4220 text-indent:-.25in;mso-list:l12 level1 lfo7'><![if !supportLists]><span
     4193text-indent:-.25in;mso-list:l12 level1 lfo5'><![if !supportLists]><span
    42214194style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    4222 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4223 style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the
    4224 restraint type you wish to use. Each will have the same possibilities in the ‘<b
    4225 style='mso-bidi-font-weight:normal'>Edit’</b> menu.<o:p></o:p></span></p>
     4195style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4196dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Select
     4197the tab for the restraint type you wish to use. Each will have the same possibilities
     4198in the ‘<b style='mso-bidi-font-weight:normal'>Edit’</b> menu.<o:p></o:p></span></p>
    42264199
    42274200<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4228 auto;text-indent:-.25in;mso-list:l12 level1 lfo7'><![if !supportLists]><span
     4201auto;text-indent:-.25in;mso-list:l12 level1 lfo5'><![if !supportLists]><span
    42294202style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    4230 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4231 style='mso-fareast-font-family:"Times New Roman"'>You can change the <b
    4232 style='mso-bidi-font-weight:normal'>Restraint weight factor</b> – this is used
    4233 to scale the weights for the entire set of restraints of this type. Default
    4234 value for the weight factor is 1.0.<o:p></o:p></span></p>
     4203style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4204dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>You can
     4205change the <b style='mso-bidi-font-weight:normal'>Restraint weight factor</b> –
     4206this is used to scale the weights for the entire set of restraints of this
     4207type. Default value for the weight factor is 1.0.<o:p></o:p></span></p>
    42354208
    42364209<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4237 auto;text-indent:-.25in;mso-list:l12 level1 lfo7'><![if !supportLists]><span
     4210auto;text-indent:-.25in;mso-list:l12 level1 lfo5'><![if !supportLists]><span
    42384211style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    4239 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4240 style='mso-fareast-font-family:"Times New Roman"'>You can choose to use or not
    4241 use the restraints in subsequent refinements. Default is to use the restraints.<o:p></o:p></span></p>
     4212style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4213dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>You can
     4214choose to use or not use the restraints in subsequent refinements. Default is
     4215to use the restraints.<o:p></o:p></span></p>
    42424216
    42434217<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4244 auto;text-indent:-.25in;mso-list:l12 level1 lfo7'><![if !supportLists]><span
     4218auto;text-indent:-.25in;mso-list:l12 level1 lfo5'><![if !supportLists]><span
    42454219style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    4246 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4247 style='mso-fareast-font-family:"Times New Roman"'>You can change the search
    4248 range used to find the bonds/angles that meet your criteria for restraint.<o:p></o:p></span></p>
     4220style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4221dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>You can
     4222change the search range used to find the bonds/angles that meet your criteria
     4223for restraint.<o:p></o:p></span></p>
    42494224
    42504225<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4251 auto;text-indent:-.25in;mso-list:l12 level1 lfo7'><![if !supportLists]><span
     4226auto;text-indent:-.25in;mso-list:l12 level1 lfo5'><![if !supportLists]><span
    42524227style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    4253 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4254 style='mso-fareast-font-family:"Times New Roman"'>You can examine the table of
    4255 restraints and change individual values; grayed out regions cannot be changed.
    4256 The ‘calc’ values are determined from the atom positions in your structure,
    4257 ‘obs’ values are the target values for the restraint and ‘esd’ is the
     4228style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4229dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>You can
     4230examine the table of restraints and change individual values; grayed out
     4231regions cannot be changed. The ‘calc’ values are determined from the atom
     4232positions in your structure, ‘<span class=SpellE>obs</span>’ values are the
     4233target values for the restraint and ‘<span class=SpellE>esd</span>’ is the
    42584234uncertainty used to weight the restraint in the refinement (multiplied by the
    42594235weight factor).<o:p></o:p></span></p>
    42604236
    42614237<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4262 auto;text-indent:-.25in;mso-list:l12 level1 lfo7'><![if !supportLists]><span
     4238auto;text-indent:-.25in;mso-list:l12 level1 lfo5'><![if !supportLists]><span
    42634239style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span
    4264 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4265 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:
    4266 normal'>Edit</b>’ – some entries may be grayed out if not appropriate for your
    4267 phase or for the selected restraint.<o:p></o:p></span></p>
     4240style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4241dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b
     4242style='mso-bidi-font-weight:normal'>Edit</b>’ – some entries may be grayed out
     4243if not appropriate for your phase or for the selected restraint.<o:p></o:p></span></p>
    42684244
    42694245<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4270 auto;text-indent:-.25in;mso-list:l12 level2 lfo7'><![if !supportLists]><span
     4246auto;text-indent:-.25in;mso-list:l12 level2 lfo5'><![if !supportLists]><span
    42714247style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    4272 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4273 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select
    4274 phase</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    4275 active if there is more than one phase in your project. A dialog box will
    4276 appear with a list of the phases, select the one you want for restraint
    4277 development.<o:p></o:p></span></p>
     4248style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4249dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4250"Times New Roman"'>Select phase</span></b><span style='mso-fareast-font-family:
     4251"Times New Roman"'> – active if there is more than one phase in your project. A
     4252dialog box will appear with a list of the phases, select the one you want for
     4253restraint development.<o:p></o:p></span></p>
    42784254
    42794255<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4280 auto;text-indent:-.25in;mso-list:l12 level2 lfo7'><![if !supportLists]><span
     4256auto;text-indent:-.25in;mso-list:l12 level2 lfo5'><![if !supportLists]><span
    42814257style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    4282 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4283 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
    4284 restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    4285 this takes you through a sequence of dialog boxes which ask for the identities
    4286 of the atoms involved in the restraint and the value to be assigned to the
    4287 restraint. The esd is given a default value which can be changed after the
    4288 restraints are created.<o:p></o:p></span></p>
     4258style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4259dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4260"Times New Roman"'>Add restraints</span></b><span style='mso-fareast-font-family:
     4261"Times New Roman"'> – this takes you through a sequence of dialog boxes which
     4262ask for the identities of the atoms involved in the restraint and the value to
     4263be assigned to the restraint. The <span class=SpellE>esd</span> is given a
     4264default value which can be changed after the restraints are created.<o:p></o:p></span></p>
    42894265
    42904266<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4291 auto;text-indent:-.25in;mso-list:l12 level2 lfo7'><![if !supportLists]><span
     4267auto;text-indent:-.25in;mso-list:l12 level2 lfo5'><![if !supportLists]><span
    42924268style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    4293 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4294 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
    4295 residue restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    4296 – if the phase is a ‘macromolecule’ then develop the restraints from a selected
    4297 ‘macro’ file based on those used in GSAS for this purpose. A file dialog box is
    4298 shown directed to /GSASIImacros; be sure to select the correct file.<o:p></o:p></span></p>
     4269style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4270dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4271"Times New Roman"'>Add residue restraints</span></b><span style='mso-fareast-font-family:
     4272"Times New Roman"'> – if the phase is a ‘macromolecule’ then develop the
     4273restraints from a selected ‘macro’ file based on those used in GSAS for this
     4274purpose. A file dialog box is shown directed to /<span class=SpellE>GSASIImacros</span>;
     4275be sure to select the correct file.<o:p></o:p></span></p>
    42994276
    43004277<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4301 auto;text-indent:-.25in;mso-list:l12 level2 lfo7'><![if !supportLists]><span
     4278auto;text-indent:-.25in;mso-list:l12 level2 lfo5'><![if !supportLists]><span
    43024279style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    4303 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4304 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Plot
    4305 residue restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    4306 – if the phase is a ‘macromolecule’ and the restraint type is either ‘<b
    4307 style='mso-bidi-font-weight:normal'>Torsion restraints</b>’ or ‘<b
    4308 style='mso-bidi-font-weight:normal'>Ramachandran restraints</b>’, then a plot will
    4309 be made of the restraint distribution; torsions as 1-D plots of angle vs.
     4280style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4281dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4282"Times New Roman"'>Plot residue restraints</span></b><span style='mso-fareast-font-family:
     4283"Times New Roman"'> – if the phase is a ‘macromolecule’ and the restraint type
     4284is either ‘<b style='mso-bidi-font-weight:normal'>Torsion restraints</b>’ or ‘<b
     4285style='mso-bidi-font-weight:normal'>Ramachandran restraints</b>’, then a plot
     4286will be made of the restraint distribution; torsions as 1-D plots of angle vs.
    43104287pseudopotential energy and Ramachandran ones as 2-D plot of psi vs phi. In each
    43114288case a dialog box will appear asking for the residue types or specific torsion
    43124289angles to plot. Each plot will show the observed distribution (blue) obtained
    4313 from a wide variety of high resolution protein structures and those found (red
    4314 dots) for your structure. The restraints are based on a pseudopotential (red
    4315 curve or contours – favorable values at the peaks) which has been developed
    4316 from the observed distributions for each residue type.<o:p></o:p></span></p>
     4290from a wide variety of <span class=GramE>high resolution</span> protein
     4291structures and those found (red dots) for your structure. The restraints are
     4292based on a pseudopotential (red curve or contours – favorable values at the peaks)
     4293which has been developed from the observed distributions for each residue type.<o:p></o:p></span></p>
    43174294
    43184295<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4319 auto;text-indent:-.25in;mso-list:l12 level2 lfo7'><![if !supportLists]><span
     4296auto;text-indent:-.25in;mso-list:l12 level2 lfo5'><![if !supportLists]><span
    43204297style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    4321 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4322 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Change
    4323 value</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – this
    4324 changes the ‘obsd’ value for selected restraints; a dialog box will appear
    4325 asking for the new value. <o:p></o:p></span></p>
     4298style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4299dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4300"Times New Roman"'>Change value</span></b><span style='mso-fareast-font-family:
     4301"Times New Roman"'> – this changes the ‘<span class=SpellE>obsd</span>’ value
     4302for selected restraints; a dialog box will appear asking for the new value. <o:p></o:p></span></p>
    43264303
    43274304<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4328 auto;text-indent:-.25in;mso-list:l12 level2 lfo7'><![if !supportLists]><span
     4305auto;text-indent:-.25in;mso-list:l12 level2 lfo5'><![if !supportLists]><span
    43294306style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    4330 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4331 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    4332 style='mso-fareast-font-family:"Times New Roman"'>Change esd</span></b><span
    4333 style='mso-fareast-font-family:"Times New Roman"'> – this changes the ‘esd’
    4334 value for selected restraints; a dialog box will appear asking for the new
    4335 value.<o:p></o:p></span></p>
     4307style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4308dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4309"Times New Roman"'>Change <span class=SpellE>esd</span></span></b><span
     4310style='mso-fareast-font-family:"Times New Roman"'> – this changes the ‘<span
     4311class=SpellE>esd</span>’ value for selected restraints; a dialog box will
     4312appear asking for the new value.<o:p></o:p></span></p>
    43364313
    43374314<p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto;
    4338 text-indent:-.25in;mso-list:l12 level2 lfo7'><![if !supportLists]><span
     4315text-indent:-.25in;mso-list:l12 level2 lfo5'><![if !supportLists]><span
    43394316style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
    4340 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4341 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Delete
    4342 restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    4343 this deletes selected restraints from the list. A single click in the blank box
    4344 in the upper left corner of the table will select/deselect all restraints.<o:p></o:p></span></p>
     4317style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4318dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4319"Times New Roman"'>Delete restraints</span></b><span style='mso-fareast-font-family:
     4320"Times New Roman"'> – this deletes selected restraints from the list. A single
     4321click in the blank box in the upper left corner of the table will
     4322select/deselect all restraints.<o:p></o:p></span></p>
    43454323
    43464324<h4 style='margin-left:.25in'><a name="Rigid_bodies"><span style='mso-fareast-font-family:
     
    43594337
    43604338<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    4361 text-indent:-.25in;mso-list:l25 level1 lfo9'><![if !supportLists]><span
     4339text-indent:-.25in;mso-list:l25 level1 lfo6'><![if !supportLists]><span
    43624340style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    4363 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4364 style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the rigid
    4365 body type you wish to use. Each will have the different possibilities in the ‘<b
    4366 style='mso-bidi-font-weight:normal'>Edit’</b> menu depending on whether a rigid
    4367 body has been defined.<o:p></o:p></span></p>
     4341style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4342dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Select
     4343the tab for the rigid body type you wish to use. Each will have the different
     4344possibilities in the ‘<b style='mso-bidi-font-weight:normal'>Edit’</b> menu
     4345depending on whether a rigid body has been defined.<o:p></o:p></span></p>
    43684346
    43694347<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4370 auto;text-indent:-.25in;mso-list:l25 level1 lfo9'><![if !supportLists]><span
     4348auto;text-indent:-.25in;mso-list:l25 level1 lfo6'><![if !supportLists]><span
    43714349style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    4372 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4373 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:
    4374 normal'>Edit</b>’ – the entries listed below depend on which type of rigid body
    4375 is selected.<o:p></o:p></span></p>
     4350style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4351dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b
     4352style='mso-bidi-font-weight:normal'>Edit</b>’ – the entries listed below depend
     4353on which type of rigid body is selected.<o:p></o:p></span></p>
    43764354
    43774355<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4378 auto;text-indent:-.25in;mso-list:l25 level2 lfo9'><![if !supportLists]><b
     4356auto;text-indent:-.25in;mso-list:l25 level2 lfo6'><![if !supportLists]><b
    43794357style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span
    4380 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4381 </span></span></span></b><![endif]><b style='mso-bidi-font-weight:normal'><span
    4382 style='mso-fareast-font-family:"Times New Roman"'>Add rigid body</span></b><span
     4358style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     4359</span></span></span></b><![endif]><span dir=LTR></span><b style='mso-bidi-font-weight:
     4360normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add rigid body</span></b><span
    43834361style='mso-fareast-font-family:"Times New Roman"'> – (Vector rigid bodies) this
    43844362creates a vector description of a rigid body. A dialog box asks the number of
     
    43894367
    43904368<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4391 auto;text-indent:-.25in;mso-list:l25 level2 lfo9'><![if !supportLists]><span
     4369auto;text-indent:-.25in;mso-list:l25 level2 lfo6'><![if !supportLists]><span
    43924370style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    4393 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4394 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Import
    4395 XYZ</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    4396 (Residue rigid bodies) this reads a text file containing a set of Cartesian
    4397 coordinates describing a rigid body model. Each line has atom type (e.g. C, Na,
    4398 etc.) and Cartesian X, Y and Z.<o:p></o:p></span></p>
     4371style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4372dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4373"Times New Roman"'>Import XYZ</span></b><span style='mso-fareast-font-family:
     4374"Times New Roman"'> – (Residue rigid bodies) this reads a text file containing
     4375a set of Cartesian coordinates describing a rigid body model. Each line has
     4376atom type (<span class=GramE>e.g.</span> C, Na, etc.) and Cartesian X, Y and Z.<o:p></o:p></span></p>
    43994377
    44004378<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4401 auto;text-indent:-.25in;mso-list:l25 level2 lfo9'><![if !supportLists]><span
     4379auto;text-indent:-.25in;mso-list:l25 level2 lfo6'><![if !supportLists]><span
    44024380style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    4403 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4404 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Define
    4405 sequence</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    4406 (Residue rigid bodies) this defines a variable torsion angle in a sequence of
    4407 dialog boxes. The first one asks for the origin and the second asks for the
    4408 pivot atom for the torsion from the nearest neighbors to the origin atom; the
    4409 atoms that ride on the selected torsion are automatically found from their bond
    4410 lengths.<o:p></o:p></span></p>
     4381style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4382dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4383"Times New Roman"'>Define sequence</span></b><span style='mso-fareast-font-family:
     4384"Times New Roman"'> – (Residue rigid bodies) this defines a variable torsion
     4385angle in a sequence of dialog boxes. The first one asks for the origin and the
     4386second asks for the pivot atom for the torsion from the nearest neighbors to
     4387the origin atom; the atoms that ride on the selected torsion are automatically
     4388found from their bond lengths.<o:p></o:p></span></p>
    44114389
    44124390<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    4413 auto;text-indent:-.25in;mso-list:l25 level2 lfo9'><![if !supportLists]><span
     4391auto;text-indent:-.25in;mso-list:l25 level2 lfo6'><![if !supportLists]><span
    44144392style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    4415 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    4416 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Import
    4417 residues</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    4418 (Residue rigid bodies) this reads a predetermined macro file that contains
    4419 standard (Engh &amp; Huber) coordinates for the amino acids found in natural
    4420 proteins along with predetermined variable torsion angle definitions.<o:p></o:p></span></p>
     4393style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4394dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4395"Times New Roman"'>Import residues</span></b><span style='mso-fareast-font-family:
     4396"Times New Roman"'> – (Residue rigid bodies) this reads a predetermined macro
     4397file that contains standard (<span class=SpellE>Engh</span> &amp; Huber)
     4398coordinates for the amino acids found in natural proteins along with
     4399predetermined variable torsion angle definitions.<o:p></o:p></span></p>
    44214400
    44224401<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4423 auto;text-indent:-.25in;mso-list:l25 level1 lfo9'><![if !supportLists]><span
     4402auto;text-indent:-.25in;mso-list:l25 level1 lfo6'><![if !supportLists]><span
    44244403style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    4425 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4426 style='mso-fareast-font-family:"Times New Roman"'>Once a rigid body is defined
    4427 you can plot it, change its name or manipulate any torsion angle to see the
    4428 effect on the plot.<o:p></o:p></span></p>
     4404style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4405dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Once a
     4406rigid body is defined you can plot it, change its name or manipulate any
     4407torsion angle to see the effect on the plot.<o:p></o:p></span></p>
    44294408
    44304409<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    4431 text-indent:-.25in;mso-list:l25 level1 lfo9'><![if !supportLists]><span
     4410text-indent:-.25in;mso-list:l25 level1 lfo6'><![if !supportLists]><span
    44324411style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    4433 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4434 style='mso-fareast-font-family:"Times New Roman"'>The translation magnitudes in
    4435 a vector rigid body can be refined.<o:p></o:p></span></p>
     4412style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4413dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>The
     4414translation magnitudes in a vector rigid body can be refined.<o:p></o:p></span></p>
    44364415
    44374416<h4 style='margin-left:.25in'><a name=Sequential></a><u><span style='mso-fareast-font-family:
     
    44394418
    44404419<p class=MsoNormal style='margin-left:.5in'>This tree entry is available after
    4441 a sequential refinement has been run. (See the <a href="#Controls">Controls
    4442 tree item</a> to set the histograms to be used in a sequential refinement and
    4443 use the Calculate/Sequential refine menu command to run the refinement.) When
    4444 this is selected, the window tabulates the sequential refinement results. The
    4445 columns are the parameter names; the naming convention is ‘p:h:name:n’ where
    4446 ‘p’ is the phase number,’ h’ is the histogram number, ‘name’ is the parameter
    4447 name, and ‘n’ (if needed) is the item number (e.g. atom number). The rows are
    4448 the data sets used in the sequential refinement.</p>
     4420a sequential refinement has been run. (See the <a href="#Controls"><span
     4421class=GramE>Controls</span> tree item</a> to set the histograms to be used in a
     4422sequential refinement and use the Calculate/Sequential refine menu command to
     4423run the refinement.) When this is selected, the window tabulates the sequential
     4424refinement results. The columns are the parameter names; the naming convention
     4425is ‘<span class=SpellE>p:h:<span class=GramE>name:n</span></span>’ where ‘p’ is
     4426the phase number,’ h’ is the histogram number, ‘name’ is the parameter name,
     4427and ‘n’ (if needed) is the item number (e.g. atom number). The rows are the
     4428data sets used in the sequential refinement.</p>
    44494429
    44504430<h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    44514431can I do here?<o:p></o:p></span></h5>
    44524432
    4453 <h5 style='margin-left:1.25in;text-indent:-.25in;mso-list:l24 level1 lfo11'><![if !supportLists]><span
     4433<h5 style='margin-left:1.25in;text-indent:-.25in;mso-list:l24 level1 lfo7'><![if !supportLists]><span
    44544434style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    44554435normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>1.<span
    4456 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4457 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Select a row</span><span
    4458 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    4459 normal;mso-bidi-font-weight:bold'> – this will display the variance-covariance
    4460 matrix for the refinement with that data set.<o:p></o:p></span></h5>
    4461 
    4462 <h5 style='margin-left:1.25in;text-indent:-.25in;mso-list:l24 level1 lfo11'><![if !supportLists]><span
     4436style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4437dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman";
     4438color:windowtext'>Select a row</span><span style='mso-fareast-font-family:"Times New Roman";
     4439color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this will
     4440display the variance-covariance matrix for the refinement with that data set.<o:p></o:p></span></h5>
     4441
     4442<h5 style='margin-left:1.25in;text-indent:-.25in;mso-list:l24 level1 lfo7'><![if !supportLists]><span
    44634443style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    44644444normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>2.<span
    4465 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4466 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Select a
    4467 column</span><span style='mso-fareast-font-family:"Times New Roman";color:windowtext;
    4468 font-weight:normal;mso-bidi-font-weight:bold'> – this will display a plot of
    4469 that parameter across the sequence of data sets. Error bars for each value are
    4470 also shown.<o:p></o:p></span></h5>
    4471 
    4472 <h5 style='margin-left:1.25in;text-indent:-.25in;mso-list:l24 level1 lfo11'><![if !supportLists]><span
     4445style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4446dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman";
     4447color:windowtext'>Select a column</span><span style='mso-fareast-font-family:
     4448"Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight:
     4449bold'> – this will display a plot of that parameter across the sequence of data
     4450sets. Error bars for each value are also shown.<o:p></o:p></span></h5>
     4451
     4452<h5 style='margin-left:1.25in;text-indent:-.25in;mso-list:l24 level1 lfo7'><![if !supportLists]><span
    44734453style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    44744454normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>3.<span
    4475 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4476 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    4477 normal;mso-bidi-font-weight:bold'>Menu ‘</span><span style='mso-fareast-font-family:
    4478 "Times New Roman";color:windowtext'>Background’ – </span><span
    4479 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    4480 normal;mso-bidi-font-weight:bold'><o:p></o:p></span></h5>
    4481 
    4482 <h5 style='margin-left:1.75in;text-indent:-.25in;mso-list:l24 level2 lfo11'><![if !supportLists]><span
     4455style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4456dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman";
     4457color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'>Menu ‘</span><span
     4458style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Background’
     4459– </span><span style='mso-fareast-font-family:"Times New Roman";color:windowtext;
     4460font-weight:normal;mso-bidi-font-weight:bold'><o:p></o:p></span></h5>
     4461
     4462<h5 style='margin-left:1.75in;text-indent:-.25in;mso-list:l24 level2 lfo7'><![if !supportLists]><span
    44834463style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    44844464normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>a.<span
    4485 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4486 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Save</span><span
    4487 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    4488 normal;mso-bidi-font-weight:bold'> – this will create a text file of selected
    4489 columns with values and corresponding esds. A file dialog box will appear; give
    4490 a suitable file name; you may change directory if desired.<o:p></o:p></span></h5>
     4465style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4466dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman";
     4467color:windowtext'>Save</span><span style='mso-fareast-font-family:"Times New Roman";
     4468color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this will
     4469create a text file of selected columns with values and corresponding <span
     4470class=SpellE>esds</span>. A file dialog box will appear; give a suitable file name;
     4471you may change directory if desired.<o:p></o:p></span></h5>
    44914472
    44924473<div class=MsoNormal align=center style='text-align:center'><span
    4493 style='mso-fareast-font-family:"Times New Roman"'>
    4494 
    4495 <hr size=2 width="100%" align=center>
     4474style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     4475
     4476<hr size=3 width="100%" align=center>
    44964477
    44974478</span></div>
    44984479
    44994480<div class=MsoNormal align=center style='text-align:center'><span
    4500 style='mso-fareast-font-family:"Times New Roman"'>
    4501 
    4502 <hr size=2 width="100%" align=center>
     4481style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     4482
     4483<hr size=3 width="100%" align=center>
    45034484
    45044485</span></div>
     
    45074488tree items<o:p></o:p></span></h2>
    45084489
    4509 <p class=MsoNormal style='margin-left:.25in'>These are shown in the data tree
    4510 with a prefix of ‘PWDR’, ’HKLF’, ‘IMG’, or ‘PDF’ and usually a file name. These
     4490<p class=MsoNormal style='margin-left:.25in'>These are shown in the data tree with
     4491a prefix of ‘PWDR’, ’HKLF’, ‘IMG’, or ‘PDF’ and usually a file name. These
    45114492constitute the data sets (‘Histograms’) to be used by GSAS-II for analysis.
    45124493Selection of these items does not produce any information in the data window
     
    45174498style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
    45184499
    4519 <p class=MsoNormal style='margin-left:.5in'>When a powder diffraction dataset
    4520 (prefix ‘PWDR’) is selected from the <a href="#Data_tree"><span
    4521 style='mso-fareast-font-family:"Times New Roman"'>data tree</span></a> the
    4522 dataset is plotted. The observed data points are shown as blue crosses and
    4523 where fit, the calculated pattern is shown as a green line; the background is
    4524 shown as red line. The difference curve is shown as a cyan line. Reflection
    4525 positions are shown with small vertical lines. </p>
    4526 
    4527 <p class=MsoNormal style='margin-left:.5in'>Each powder diffraction dataset has
    4528 a number of children in the tree as are shown below. Clicking on any of them
    4529 produces changes in the plot and allows access to different parameters
    4530 associated with the dataset. </p>
    4531 
    4532 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4533 margin-left:.75in;text-indent:-.25in;mso-list:l7 level1 lfo12;tab-stops:list .5in'><![if !supportLists]><span
    4534 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4535 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4536 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4537 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'><a
    4538 href="#PWDR_Comments">Comments</a><o:p></o:p></span></p>
    4539 
    4540 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4541 margin-left:.75in;text-indent:-.25in;mso-list:l7 level1 lfo12;tab-stops:list .5in'><![if !supportLists]><span
    4542 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4543 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4544 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4545 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'><a
    4546 href="#PWDR_Limits">Limits</a><o:p></o:p></span></p>
    4547 
    4548 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4549 margin-left:.75in;text-indent:-.25in;mso-list:l7 level1 lfo12;tab-stops:list .5in'><![if !supportLists]><span
    4550 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4551 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4552 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4553 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'><a
    4554 href="#PWDR_Background">Background</a><o:p></o:p></span></p>
    4555 
    4556 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4557 margin-left:.75in;text-indent:-.25in;mso-list:l7 level1 lfo12;tab-stops:list .5in'><![if !supportLists]><span
    4558 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4559 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4560 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4561 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'><a
    4562 href="#PWDR_Instrument_Parameters">Instrument Parameters</a><o:p></o:p></span></p>
    4563 
    4564 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4565 margin-left:.75in;text-indent:-.25in;mso-list:l7 level1 lfo12;tab-stops:list .5in'><![if !supportLists]><span
    4566 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4567 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4568 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4569 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'><a
    4570 href="#PWDR_Sample_Parameters">Sample Parameters</a><o:p></o:p></span></p>
    4571 
    4572 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4573 margin-left:.75in;text-indent:-.25in;mso-list:l7 level1 lfo12;tab-stops:list .5in'><![if !supportLists]><span
    4574 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4575 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4576 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4577 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'><a
    4578 href="#PWDR_Peak_List">Peak List</a><o:p></o:p></span></p>
    4579 
    4580 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4581 margin-left:.75in;text-indent:-.25in;mso-list:l7 level1 lfo12;tab-stops:list .5in'><![if !supportLists]><span
    4582 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4583 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4584 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4585 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'><a
    4586 href="#PWDR_Index_Peak_List">Index Peak List</a><o:p></o:p></span></p>
    4587 
    4588 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4589 margin-left:.75in;text-indent:-.25in;mso-list:l7 level1 lfo12;tab-stops:list .5in'><![if !supportLists]><span
    4590 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4591 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4592 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4593 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'><a
    4594 href="#PWDR_Unit_Cells_List">Unit Cells List</a><o:p></o:p></span></p>
    4595 
    4596 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4597 margin-left:.75in;text-indent:-.25in;mso-list:l7 level1 lfo12;tab-stops:list .5in'><![if !supportLists]><span
    4598 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4599 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4600 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4601 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'><a
    4602 href="#PWDR_Reflection_Lists">Reflection Lists</a><o:p></o:p></span></p>
    4603 
    4604 <h5 style='margin-left:.5in'>What can I do here?</h5>
    4605 
    4606 <p style='margin-left:1.0in'>Menu <b>Commands</b> </p>
    4607 
    4608 <p class=MsoListParagraph style='margin-left:1.5in;mso-add-space:auto;
    4609 text-indent:-.25in;mso-list:l21 level1 lfo14'><![if !supportLists]><span
    4610 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    4611 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>a.&nbsp;<b>Error
    4612 Analysis</b> – this produces a ‘normal probability’ plot for the refinement
    4613 result as bounded by the limits. The slope and intercept of the curve in the
    4614 central region (-1 &lt; / &lt; 1) are shown on the plot status line. The slope
    4615 is the square root of GOF for the best fit set of data points (~68% of the
    4616 data).</p>
    4617 
    4618 <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    4619 is plotted here?</span></h5>
    4620 
    4621 <p style='margin-left:1.0in'>The powder patterns that are part of your project
    4622 are shown on this page. They can be displayed as a stack of powder patterns,
    4623 just a single pattern or as a contour image of the peak intensities. What can
    4624 be done here will depend on home many patterns are shown as well as what mode
    4625 is selected. Note that the tick marks and difference curve positions can be
    4626 customized, as <a href="#PWDR_dragticks">discussed below</a>. </p>
    4627 
    4628 <p class=MsoNormal style='margin-left:1.0in'>Similar plots to the one here are
    4629 displayed when different subtree items are selected and on those plots it is
    4630 possible to view and in some cases edit information associated with the
    4631 histogram. As examples: </p>
    4632 
    4633 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4634 margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><a
    4635 name=otherPWDR></a><![if !supportLists]><span style='font-size:10.0pt;
    4636 mso-bidi-font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
    4637 mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
    4638 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4639 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>By
    4640 selecting the <a href="#PWDR_Limits">Limits</a> entry, range of data used, as
    4641 well as possible excluded regions, can be set. <o:p></o:p></span></p>
    4642 
    4643 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4644 margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><![if !supportLists]><span
    4645 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4646 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4647 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4648 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Selecting
    4649 <a href="#PWDR_Reflection_Lists">Reflection Lists</a> allows display of
    4650 reflection indicies (hkl values) for a selected phase. Letting the mouse rest
    4651 unmoved at the position of a reflection in 2-theta, Q, etc. (the vertical
    4652 position does not matter) will cause these to be displayed. After a short delay
    4653 a &quot;tool tip&quot; will appear with indicies for any reflections close to
    4654 the lateral mouse position. <o:p></o:p></span></p>
    4655 
    4656 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4657 margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><![if !supportLists]><span
    4658 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4659 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4660 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4661 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Selecting
    4662 <a href="#PWDR_Background">Background</a> allows a mouse to be used to define
    4663 fixed points where a background curve can be fitted to those points. <o:p></o:p></span></p>
    4664 
    4665 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4666 margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><![if !supportLists]><span
    4667 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4668 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4669 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4670 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Selecting
    4671 <a href="#PWDR_Instrument_Parameters">Instrument Parameters</a>displays plot of
    4672 peak widths as a function of 2theta or Q. <o:p></o:p></span></p>
    4673 
    4674 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4675 margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><![if !supportLists]><span
    4676 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4677 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4678 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4679 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Selecting
    4680 <a href="#PWDR_Peak_List">Peak List</a> allows postions of peaks to be defined
    4681 for use in direct peak fitting. <o:p></o:p></span></p>
    4682 
    4683 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    4684 margin-left:1.0in;text-indent:-.25in;mso-list:l8 level1 lfo15;tab-stops:list .5in'><![if !supportLists]><span
    4685 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    4686 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    4687 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    4688 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Selecting
    4689 <a href="#PWDR_Unit_Cells_List">Unit Cells List</a> can show the positions of
    4690 reflections for an arbitrary set of unit cell parameters, optionally with space
    4691 group extinctions applied. <o:p></o:p></span></p>
    4692 
    4693 <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    4694 can I do with the plot?</span></h5>
    4695 
    4696 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4697 "Times New Roman"'>Move mouse <o:p></o:p></span></p>
    4698 
    4699 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4700 "Times New Roman"'>As the mouse cursor is moved across the plot, the plot
    4701 status line will show the cursor position as 2Theta, d-spacing and the
    4702 intensity. For a Q-plot, Q is shown instead of 2Theta. <o:p></o:p></span></p>
    4703 
    4704 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4705 "Times New Roman"'>Press keyboard keys <o:p></o:p></span></p>
    4706 
    4707 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4708 "Times New Roman"'><a href="#PWDR_keylist">See below</a>. The &quot;s&quot; and
    4709 &quot;w&quot; modes are commonly used. <a name="PWDR_dragticks"></a><o:p></o:p></span></p>
    4710 
    4711 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4712 "Times New Roman"'>Drag tickmarks <o:p></o:p></span></p>
    4713 
    4714 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4715 "Times New Roman"'>Click on any tick mark and while holding the left mouse
    4716 button down move them to where you want them to be displayed (press the s key
    4717 for Sqrt(I) mode to reset to the defaults). With multiple phases, clicking on
    4718 the 2nd phase, etc. changes the vertical spacing between phases. Tick marks can
    4719 be dragged only when the main PWDR or Reflection Lists tree items are selected.
    4720 <o:p></o:p></span></p>
    4721 
    4722 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4723 "Times New Roman"'>Drag the difference curve <o:p></o:p></span></p>
    4724 
    4725 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4726 "Times New Roman"'>When the &quot;normal&quot; obs-calc plot is shown (as
    4727 opposed to the preferred &quot;w&quot; mode plot where (obs-calc)/sigma is
    4728 displayed, click on any point in the difference curve and while holding the
    4729 left mouse button down move the curve to where you want it to be displayed
    4730 (press the s key for Sqrt(I) mode to reset it to the default). The difference
    4731 curve can be dragged only when the main PWDR or Reflection Lists tree items are
    4732 selected. <o:p></o:p></span></p>
    4733 
    4734 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4735 "Times New Roman"'>Display/edit histogram information <o:p></o:p></span></p>
    4736 
    4737 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4738 "Times New Roman"'>By selecting different tree items within the current
    4739 histogram, it is possible to display and in some cases edit information
    4740 associated with the histogram. <a href="#otherPWDR">See above.</a> <o:p></o:p></span></p>
    4741 
    4742 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4743 "Times New Roman"'>Create a Publication-ready plot <o:p></o:p></span></p>
    4744 
    4745 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4746 "Times New Roman"'>Press the green &quot;P&quot; button to generate a
    4747 customizable version of the displayed plot that can be exported at high
    4748 resolution. <o:p></o:p></span></p>
    4749 
    4750 <p style='margin-left:.5in'><a name="PWDR_keylist"></a>The following key press
    4751 characters are defined (not for all plot modes). These actions can also be
    4752 initiated from the <b>Key Press</b> button on the plot toolbar. </p>
    4753 
    4754 <h4 style='margin-left:.5in'>For line plots:</h4>
    4755 
    4756 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4757 "Times New Roman"'>s: Sqrt(I) on/off</span></b><span style='mso-fareast-font-family:
    4758 "Times New Roman"'><o:p></o:p></span></p>
    4759 
    4760 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4761 "Times New Roman"'>changes the y-axis to be the square-root of the intensity.
    4762 The tick mark and the difference curve location is reset. <o:p></o:p></span></p>
    4763 
    4764 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4765 "Times New Roman"'>w: toggle diff plot mode</span></b><span style='mso-fareast-font-family:
    4766 "Times New Roman"'><o:p></o:p></span></p>
    4767 
    4768 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4769 "Times New Roman"'>for the pattern selected from the data tree, this will
    4770 replace the difference (obs-calc) curve with the differences divided by their
    4771 standard uncertainty (esd) values [(obs-calc)/sigma], which shows the
    4772 significance of the deviations in the fit of the pattern. <i>(Recommended)</i>.
    4773 <o:p></o:p></span></p>
    4774 
    4775 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4776 "Times New Roman"'>b: subtract background</span></b><span style='mso-fareast-font-family:
    4777 "Times New Roman"'><o:p></o:p></span></p>
    4778 
    4779 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4780 "Times New Roman"'>Subtracts the fitted background from the powder pattern.
    4781 Pressing this again turns the mode off. <o:p></o:p></span></p>
    4782 
    4783 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4784 "Times New Roman"'>n: log(I) on/off</span></b><span style='mso-fareast-font-family:
    4785 "Times New Roman"'><o:p></o:p></span></p>
    4786 
    4787 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4788 "Times New Roman"'>changes the y-axis to be the log10 of the intensity;
    4789 difference curve is not shown for log(I) on. <o:p></o:p></span></p>
    4790 
    4791 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4792 "Times New Roman"'>q: toggle Q plot</span></b><span style='mso-fareast-font-family:
    4793 "Times New Roman"'><o:p></o:p></span></p>
    4794 
    4795 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4796 "Times New Roman"'>changes the x-axis from 2Theta to Q. This will put multiple
    4797 powder patterns taken at different wavelengths/types on the same x-axis scale. <o:p></o:p></span></p>
    4798 
    4799 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4800 "Times New Roman"'>t: toggle D-space plot</span></b><span style='mso-fareast-font-family:
    4801 "Times New Roman"'><o:p></o:p></span></p>
    4802 
    4803 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4804 "Times New Roman"'>changes the x-axis from 2Theta to d-space. This will put
    4805 multiple powder patterns taken at different wavelengths/types on the same
    4806 x-axis scale. May not be very useful with data over a wide range. <o:p></o:p></span></p>
    4807 
    4808 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4809 "Times New Roman"'>e: set excluded region</span></b><span style='mso-fareast-font-family:
    4810 "Times New Roman"'> <o:p></o:p></span></p>
    4811 
    4812 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4813 "Times New Roman"'>Defines a new excluded region: press the &quot;e&quot; key
    4814 with the mouse on one side of the region. Move the mouse to the other side and
    4815 and press &quot;e&quot; again. The region markers (magenta dashed lines) can be
    4816 dragged to new positions. Available only when the <a href="#PWDR_Limits">Limits</a>
    4817 tree entry is selected. <o:p></o:p></span></p>
    4818 
    4819 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4820 "Times New Roman"'>x: show excluded region</span></b><span style='mso-fareast-font-family:
    4821 "Times New Roman"'> <o:p></o:p></span></p>
    4822 
    4823 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4824 "Times New Roman"'>Normally all observed data is plotted. When the
    4825 &quot;x&quot; key is pressed, data inside excluded regions are not shown. <o:p></o:p></span></p>
    4826 
    4827 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4828 "Times New Roman"'>.: scaling diagnostic</span></b><span style='mso-fareast-font-family:
    4829 "Times New Roman"'> <o:p></o:p></span></p>
    4830 
    4831 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4832 "Times New Roman"'>When the '.' key is pressed, data are plotted where the
    4833 intensity scale shows the equivalent number of counts so that uncertainty on
    4834 each point is the sqrt(I). <o:p></o:p></span></p>
    4835 
    4836 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4837 "Times New Roman"'>g: grid lines</span></b><span style='mso-fareast-font-family:
    4838 "Times New Roman"'> <o:p></o:p></span></p>
    4839 
    4840 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4841 "Times New Roman"'>Draws vertical and horizontal grid lines at all axis label
    4842 positions. <o:p></o:p></span></p>
    4843 
    4844 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4845 "Times New Roman"'>a: add magnification region</span></b><span
    4846 style='mso-fareast-font-family:"Times New Roman"'> <o:p></o:p></span></p>
    4847 
    4848 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4849 "Times New Roman"'>Adds a magnification region to the plot and sets the
    4850 magnification amount to x2. This can be edited (or deleted) in the table that
    4851 is shown when the main PWDR tree entry is selected. <o:p></o:p></span></p>
    4852 
    4853 <h4 style='margin-left:.5in'>For line plots with more than one powder pattern: </h4>
    4854 
    4855 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4856 "Times New Roman"'>c: contour on/off</span></b><span style='mso-fareast-font-family:
    4857 "Times New Roman"'><o:p></o:p></span></p>
    4858 
    4859 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4860 "Times New Roman"'>if multiple powder profiles, then a contour plot is shown of
    4861 the observed intensities. All data sets must be the same length as the first
    4862 one to be included in the contour plot. <o:p></o:p></span></p>
    4863 
    4864 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4865 "Times New Roman"'>S: set color Scheme</span></b><span style='mso-fareast-font-family:
    4866 "Times New Roman"'> <o:p></o:p></span></p>
    4867 
    4868 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4869 "Times New Roman"'>Select the color map used for contour plots <o:p></o:p></span></p>
    4870 
    4871 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4872 "Times New Roman"'>m: toggle single/multiple plot</span></b><span
    4873 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    4874 
    4875 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4876 "Times New Roman"'>for multiple powder profiles, this will show only the one
    4877 selected from the data tree. The offset options (below) are not active. <o:p></o:p></span></p>
    4878 
    4879 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4880 "Times New Roman"'>f: select data</span></b><span style='mso-fareast-font-family:
    4881 "Times New Roman"'><o:p></o:p></span></p>
    4882 
    4883 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4884 "Times New Roman"'>Allows only some powder patterns to be plotted, rather than
    4885 all. <o:p></o:p></span></p>
    4886 
    4887 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4888 "Times New Roman"'>+,=: no selection</span></b><span style='mso-fareast-font-family:
    4889 "Times New Roman"'><o:p></o:p></span></p>
    4890 
    4891 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4892 "Times New Roman"'>for multiple powder profiles, only the observed curve is
    4893 shown when this mode is turned on ('+' and '=' do exactly the same thing).<o:p></o:p></span></p>
    4894 
    4895 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4896 "Times New Roman"'>/: normalize</span></b><span style='mso-fareast-font-family:
    4897 "Times New Roman"'><o:p></o:p></span></p>
    4898 
    4899 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4900 "Times New Roman"'>for multiple powder profiles, all diffraction datasets are
    4901 normalized so that the maximum intensity is 1. <o:p></o:p></span></p>
    4902 
    4903 <h4 style='margin-left:.5in'>Offset modes for line plots in waterfall mode
    4904 (multiple patterns only): </h4>
    4905 
    4906 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4907 "Times New Roman"'>l: offset left</span></b><span style='mso-fareast-font-family:
    4908 "Times New Roman"'><o:p></o:p></span></p>
    4909 
    4910 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4911 "Times New Roman"'>for a waterfall plot of multiple powder profiles, increase
    4912 the offset so that later plots are shifted more to the left relative to
    4913 previous plots. <o:p></o:p></span></p>
    4914 
    4915 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4916 "Times New Roman"'>r: offset right</span></b><span style='mso-fareast-font-family:
    4917 "Times New Roman"'><o:p></o:p></span></p>
    4918 
    4919 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4920 "Times New Roman"'>for a waterfall plot of multiple powder profiles, increase
    4921 the offset to the right (or decrease the left offset.) <o:p></o:p></span></p>
    4922 
    4923 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4924 "Times New Roman"'>d,D: offset down</span></b><span style='mso-fareast-font-family:
    4925 "Times New Roman"'><o:p></o:p></span></p>
    4926 
    4927 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4928 "Times New Roman"'>for a waterfall plot of multiple powder profiles, increase
    4929 the offset down. (D does the same as d but to a much larger amount) <o:p></o:p></span></p>
    4930 
    4931 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4932 "Times New Roman"'>u,U: offset up</span></b><span style='mso-fareast-font-family:
    4933 "Times New Roman"'><o:p></o:p></span></p>
    4934 
    4935 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4936 "Times New Roman"'>for a waterfall plot of multiple powder profiles, increase
    4937 the offset up. (U does the same as u but to a much larger amount) <o:p></o:p></span></p>
    4938 
    4939 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4940 "Times New Roman"'>o: reset offset</span></b><span style='mso-fareast-font-family:
    4941 "Times New Roman"'><o:p></o:p></span></p>
    4942 
    4943 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4944 "Times New Roman"'>for a waterfall plot of multiple powder profiles, reset to
    4945 no offset. <o:p></o:p></span></p>
    4946 
    4947 <h4 style='margin-left:.5in'>For contour plots:</h4>
    4948 
    4949 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4950 "Times New Roman"'>d: lower contour max</span></b><span style='mso-fareast-font-family:
    4951 "Times New Roman"'><o:p></o:p></span></p>
    4952 
    4953 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4954 "Times New Roman"'>this lowers the level chosen for the highest contour color. <o:p></o:p></span></p>
    4955 
    4956 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4957 "Times New Roman"'>u: raise contour max</span></b><span style='mso-fareast-font-family:
    4958 "Times New Roman"'><o:p></o:p></span></p>
    4959 
    4960 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4961 "Times New Roman"'>this raises the level chosen for the highest contour color <o:p></o:p></span></p>
    4962 
    4963 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4964 "Times New Roman"'>i: interpolation method</span></b><span style='mso-fareast-font-family:
    4965 "Times New Roman"'><o:p></o:p></span></p>
    4966 
    4967 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4968 "Times New Roman"'>this changes the method used to represent the contours. If
    4969 selected a dialog box appears with all the possible choices. Default is
    4970 ‘nearest’; the other useful choice is ‘bilinear’, this will smooth out the
    4971 contours. <o:p></o:p></span></p>
    4972 
    4973 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4974 "Times New Roman"'>s: color scheme</span></b><span style='mso-fareast-font-family:
    4975 "Times New Roman"'><o:p></o:p></span></p>
    4976 
    4977 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4978 "Times New Roman"'>this changes the color scheme for the contouring. Default is
    4979 ‘Paired’, black/ white options are ‘Greys’ and ‘binary’ (for black on white) or
    4980 ‘gray’ (for white on black). Others can be very colorful (but not useful!) <o:p></o:p></span></p>
    4981 
    4982 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4983 "Times New Roman"'>c: contour off/on</span></b><span style='mso-fareast-font-family:
    4984 "Times New Roman"'><o:p></o:p></span></p>
    4985 
    4986 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4987 "Times New Roman"'>this turns off contouring and returns to a waterfall plot
    4988 with any offsets applied. <o:p></o:p></span></p>
    4989 
    4990 <h4 style='margin-left:.5in'>For display of reflections from magnetic unit
    4991 space groups </h4>
    4992 
    4993 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    4994 "Times New Roman"'>j: show next; reset use flag</span></b><span
    4995 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    4996 
    4997 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4998 "Times New Roman"'>Show the next magnetic space group in the list, clearing the
    4999 &quot;Use&quot; flag for the currently displayed space group. (available from
    5000 Index Unit Cells only). <o:p></o:p></span></p>
    5001 
    5002 <p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    5003 "Times New Roman"'>k: show next</span></b><span style='mso-fareast-font-family:
    5004 "Times New Roman"'><o:p></o:p></span></p>
    5005 
    5006 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5007 "Times New Roman"'>Show the next magnetic space group in the list. The
    5008 &quot;Use&quot; flag for the currently displayed space group is unchanged.
    5009 (available from Index Unit Cells only). <o:p></o:p></span></p>
    5010 
    5011 <h4 style='margin-left:.25in'><a name="PWDR_Comments"><u>Comments</u></a></h4>
    5012 
    5013 <p class=MsoNormal style='margin-left:.5in'>This window shows whatever comment
    5014 lines (preceded by “#”) found when the powder data file was read by GSAS-II. If
    5015 you are lucky, there will be useful information here (e.g. sample name, date
    5016 collected, wavelength used, etc.). If not, this window will be blank. The text
    5017 is read-only.</p>
    5018 
    5019 <h4 style='margin-left:.25in'><a name="PWDR_Limits"><u>Limits</u></a></h4>
    5020 
    5021 <p class=MsoNormal style='margin-left:.5in'>This window shows the limits in
    5022 position to be used in any fitting for this powder pattern. The ‘original’
    5023 values are obtained from the minimum &amp; maximum values in the powder
    5024 pattern. The ‘new’ values determine the range of data that will be used in fitting.
    5025 Units are 2Theta for CW data and time (microsec) for TOF data. </p>
    5026 
    5027 <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    5028 can I do here?<o:p></o:p></span></h5>
    5029 
    5030 <p style='margin-left:.75in'>You can change the &quot;new&quot; values for Tmin
    5031 and Tmax as needed. Change the upper and lower Tmin values by clicking on the
    5032 appropriate vertical line and dragging it to the right or left or by typing
    5033 values into the data window. </p>
    5034 
    5035 <p style='margin-left:.75in'>Menu ‘<b>Edit Limits</b>’ </p>
    5036 
    5037 <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
    5038 "Times New Roman"'>Copy</span></b><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    5039 
    5040 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5041 "Times New Roman"'>this copies the limits shown to other selected powder
    5042 patterns. If used, a dialog box (Copy Parameters) will appear showing the list
    5043 of available powder patterns, you can copy the limits parameters to any or all
    5044 of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the
    5045 copy; ‘Cancel’ to cancel the operation. <o:p></o:p></span></p>
    5046 
    5047 <p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
    5048 "Times New Roman"'>Add Exclude</span></b><span style='mso-fareast-font-family:
    5049 "Times New Roman"'><o:p></o:p></span></p>
    5050 
    5051 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5052 "Times New Roman"'>Select this menu item and click on a data point. A pair of
    5053 magenta lines is drawn to indicate a range that should be excluded. (No green
    5054 solid line with the computed pattern is shown for those data). The magenta
    5055 lines can be dragged, as described below for setting data limits. <o:p></o:p></span></p>
    5056 
    5057 <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    5058 is plotted here?</span></h5>
    5059 
    5060 <p style='margin-left:1.0in'>The plot is the same as for <a href="#PWDR">Powder
    5061 Histograms - type PWDR</a> and the key press commands are all the same.
    5062 However, two vertical lines are displayed, green for the lower Tmin value and
    5063 red for the upper Tmin value. These can be dragged to set limits. </p>
    5064 
    5065 <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    5066 can I do with the plot?</span></h5>
    5067 
    5068 <p style='margin-left:1.0in'>The upper and lower Tmin values can be changed by
    5069 clicking on the appropriate vertical line and dragging it to the right or left.
    5070 </p>
    5071 
    5072 <h4 style='margin-left:.25in'><a name="PWDR_Background"><u><span
    5073 style='mso-fareast-font-family:"Times New Roman"'>Background</span></u></a><u><span
    5074 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></u></h4>
    5075 
    5076 <p class=MsoNormal style='margin-left:.5in'><a name=Background></a><span
    5077 style='mso-fareast-font-family:"Times New Roman"'>This window shows the choice
    5078 of background functions and coefficients to be used in fitting this powder pattern.
    5079 There are three types of contributions available for the background:<o:p></o:p></span></p>
    5080 
    5081 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5082 "Times New Roman"'>1). A continuous empirical function (‘chebyschev’,
    5083 ‘chebyschev-1’, ‘cosine’, ‘lin interpolate’, ‘inv interpolate’ &amp; ‘log
    5084 interpolate’). The latter three select fixed points with spacing that is equal,
    5085 inversely equal or equal on a log scale of the x-coordinate. The set of
    5086 magnitudes at each point then comprise the background variables. All are
    5087 refined when refine is selected. Note that ‘chebyschev-1' is a better choice
    5088 than ‘chebyschev’. <o:p></o:p></span></p>
    5089 
    5090 <p class=MsoNormal style='margin-left:.5in;tab-stops:0in'><span
    5091 style='mso-fareast-font-family:"Times New Roman"'>2). A set of Debye diffuse
    5092 scattering equation terms of the form:<o:p></o:p></span></p>
    5093 
    5094 <p class=MsoNormal style='margin-left:.5in;tab-stops:0in'><!--[if gte msEquation 12]><m:oMathPara><m:oMathParaPr><m:jc
    5095    m:val="left"/></m:oMathParaPr><m:oMath><i style='mso-bidi-font-style:normal'><span
    5096   style='font-family:"Cambria Math",serif;mso-fareast-font-family:"Times New Roman"'><m:r>B</m:r><m:r>=</m:r><m:r>A</m:r></span></i><m:d><m:dPr><span
    5097     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    5098     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    5099     normal'><m:ctrlPr></m:ctrlPr></span></m:dPr><m:e><m:f><m:fPr><m:type m:val="skw"/><span
    5100       style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    5101       mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    5102       normal'><m:ctrlPr></m:ctrlPr></span></m:fPr><m:num><i style='mso-bidi-font-style:
    5103       normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    5104       "Times New Roman"'><m:r>sinQR</m:r></span></i></m:num><m:den><i
    5105       style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
    5106       mso-fareast-font-family:"Times New Roman"'><m:r>QR</m:r></span></i></m:den></m:f></m:e></m:d><m:sSup><m:sSupPr><span
    5107     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    5108     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    5109     normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style:
    5110     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    5111     "Times New Roman"'><m:r>e</m:r></span></i></m:e><m:sup><i style='mso-bidi-font-style:
    5112     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    5113     "Times New Roman"'><m:r>-</m:r><m:r>U</m:r></span></i><m:sSup><m:sSupPr><span
    5114       style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    5115       mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    5116       normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style:
    5117       normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    5118       "Times New Roman"'><m:r>Q</m:r></span></i></m:e><m:sup><i
    5119       style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
    5120       mso-fareast-font-family:"Times New Roman"'><m:r>2</m:r></span></i></m:sup></m:sSup></m:sup></m:sSup></m:oMath></m:oMathPara><![endif]--><![if !msEquation]><span
    5121 style='font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-font-family:
    5122 "Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US;
    5123 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
    5124  id="_x0000_i1025" type="#_x0000_t75" style='width:130.5pt;height:23.25pt'>
    5125  <v:imagedata src="gsasII_files/image001.png" o:title="" chromakey="white"/>
    5126 </v:shape><![endif]--><![if !vml]><img width=174 height=31
    5127 src="gsasII_files/image046.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    5128 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    5129 
    5130 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5131 "Times New Roman"'>where A,R &amp; U are the possible variables and can be
    5132 individually selected as desired; Q = 2π/d.<o:p></o:p></span></p>
    5133 
    5134 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5135 "Times New Roman"'>3). A set of individual Bragg peaks using the pseudo-Voigt
    5136 profile function as their shapes. Their parameters are ‘pos’, ’int’, ‘sig’
    5137 &amp; ‘gam’; each can be selected for refinement. The default values for sig
    5138 &amp; gam (=0.10) are for very sharp peaks, you may adjust them accordingly to
    5139 the kind of peak you are trying to fit before trying to refine them.<o:p></o:p></span></p>
    5140 
    5141 <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    5142 can I do here?<o:p></o:p></span></h5>
    5143 
    5144 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    5145 text-indent:-.25in;mso-list:l23 level1 lfo17'><![if !supportLists]><span
    5146 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    5147 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5148 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:
    5149 normal'>Background</b>’ – <o:p></o:p></span></p>
    5150 
    5151 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5152 auto;text-indent:-.25in;mso-list:l6 level1 lfo19'><![if !supportLists]><span
    5153 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    5154 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    5155 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b><span
    5156 style='mso-fareast-font-family:"Times New Roman"'> – this copies the background
    5157 parameters shown to other selected powder patterns. If used, a dialog box (Copy
    5158 Parameters) will appear showing the list of available powder patterns, you can
    5159 copy the background parameters to any or all of them; select ‘All’ to copy them
    5160 to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the
    5161 operation.<o:p></o:p></span></p>
    5162 
    5163 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5164 auto;text-indent:-.25in;mso-list:l6 level1 lfo19'><![if !supportLists]><span
    5165 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    5166 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    5167 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy
    5168 flags </span></b><span style='mso-fareast-font-family:"Times New Roman"'>– this
    5169 copies only the refinement flags shown to other selected powder patterns. If
    5170 used, a dialog box (Copy Refinement Flags) will appear showing the list of
    5171 available powder patterns, you can copy the refinement flags to any or all of
    5172 them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the
    5173 copy; ‘Cancel’ to cancel the operation.<o:p></o:p></span></p>
    5174 
    5175 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5176 auto;text-indent:-.25in;mso-list:l23 level1 lfo17'><![if !supportLists]><span
    5177 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    5178 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5179 style='mso-fareast-font-family:"Times New Roman"'>You can select a different
    5180 Background function from the pull down tab.<o:p></o:p></span></p>
    5181 
    5182 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5183 auto;text-indent:-.25in;mso-list:l23 level1 lfo17'><![if !supportLists]><span
    5184 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    5185 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5186 style='mso-fareast-font-family:"Times New Roman"'>You can choose to refine/not
    5187 refine the background coefficients.<o:p></o:p></span></p>
    5188 
    5189 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5190 auto;text-indent:-.25in;mso-list:l23 level1 lfo17'><![if !supportLists]><span
    5191 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    5192 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5193 style='mso-fareast-font-family:"Times New Roman"'>You can select the number of
    5194 background coefficients to be used (1-36).<o:p></o:p></span></p>
    5195 
    5196 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5197 auto;text-indent:-.25in;mso-list:l23 level1 lfo17'><![if !supportLists]><span
    5198 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    5199 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5200 style='mso-fareast-font-family:"Times New Roman"'>You can change individual
    5201 background coefficient values. Enter the value then press Enter or click the
    5202 mouse elsewhere in the Background window. This will set the new value.<o:p></o:p></span></p>
    5203 
    5204 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5205 auto;text-indent:-.25in;mso-list:l23 level1 lfo17'><![if !supportLists]><span
    5206 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span
    5207 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5208 style='mso-fareast-font-family:"Times New Roman"'>You can introduce one or more
    5209 Debye scattering terms into the background. For each one you should enter a
    5210 sensible value for ‘R’ – an expected interatomic distance in an amorphous phase
    5211 is appropriate. Select parameters to refine; usually start with the ‘A’
    5212 coefficients.<o:p></o:p></span></p>
    5213 
    5214 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    5215 text-indent:-.25in;mso-list:l23 level1 lfo17'><![if !supportLists]><span
    5216 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>7.<span
    5217 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5218 style='mso-fareast-font-family:"Times New Roman"'>You can introduce single
    5219 Bragg peaks into the background. For each you should specify at least the
    5220 position. Select parameters to refine; usually start with the ‘int’
    5221 coefficients.<o:p></o:p></span></p>
    5222 
    5223 <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    5224 is plotted here?</span></h5>
    5225 
    5226 <p style='margin-left:1.0in'>The plot is the same as for <a href="#PWDR">Powder
    5227 Histograms - type PWDR</a> and the key press commands are largerly the same.
    5228 Specific to this plot are fixed background points. These can be added, deleted
    5229 and moved. Once that is done the background parameters for the selected
    5230 function can be fitted to the fixed points. </p>
    5231 
    5232 <h4 style='margin-left:.25in'><a name="PWDR_Instrument_Parameters"><u><span
    5233 style='mso-fareast-font-family:"Times New Roman"'>Instrument Parameters</span></u></a><u><span
    5234 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></u></h4>
    5235 
    5236 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5237 "Times New Roman"'>This window shows the instrument parameters for the selected
    5238 powder data set. The plot window shows the corresponding resolution curves.
    5239 Solid lines are for the default values (in parentheses), dashed lines from the
    5240 refined values and ‘+’ for individual entries in the ‘<span style='color:#0070C0'>Peak_List</span>’.
    5241 </span><span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    5242 none;text-underline:none'><o:p></o:p></span></span></p>
    5243 
    5244 <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    5245 can I do here?</span><span class=MsoHyperlink><span style='color:#00B0F0;
    5246 text-decoration:none;text-underline:none'><o:p></o:p></span></span></h5>
    5247 
    5248 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    5249 text-indent:-.25in;mso-list:l11 level1 lfo21'><![if !supportLists]><span
    5250 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5251 color:windowtext;text-decoration:none;text-underline:none'><span
    5252 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5253 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    5254 "Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Operations</b>’
    5255 –<span class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5256 text-underline:none'><o:p></o:p></span></span></span></p>
    5257 
    5258 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5259 auto;text-indent:-.25in;mso-list:l17 level2 lfo23;tab-stops:list 1.0in'><![if !supportLists]><span
    5260 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5261 color:windowtext;text-decoration:none;text-underline:none'><span
    5262 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5263 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5264 style='mso-fareast-font-family:"Times New Roman"'>Load profile… </span></b><span
    5265 style='mso-fareast-font-family:"Times New Roman"'>- loads a GSAS-II instrument
    5266 parameter file (name.instprm), replacing the existing instrument parameter
    5267 values. All refinement flags are unset.<span class=MsoHyperlink><b
    5268 style='mso-bidi-font-weight:normal'><span style='color:windowtext;text-decoration:
    5269 none;text-underline:none'><o:p></o:p></span></b></span></span></p>
    5270 
    5271 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5272 auto;text-indent:-.25in;mso-list:l17 level2 lfo23;tab-stops:list 1.0in'><![if !supportLists]><span
    5273 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5274 color:windowtext;text-decoration:none;text-underline:none'><span
    5275 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5276 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5277 style='mso-fareast-font-family:"Times New Roman"'>Save profile… - </span></b><span
    5278 style='mso-fareast-font-family:"Times New Roman"'>saves the current instrument
    5279 parameter values in a simple text file (name.instprm); you will be prompted for
    5280 the file name – do not change the extension. This file may be edited but heed
    5281 the warning to not change the parameter names, the order of the parameter
    5282 records or add new parameter records as this will invalidate the file. You may
    5283 only change the numeric values if necessary. You can change or add comment
    5284 records (begins with ‘#’).<span class=MsoHyperlink><b style='mso-bidi-font-weight:
    5285 normal'><span style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></b></span></span></p>
    5286 
    5287 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5288 auto;text-indent:-.25in;mso-list:l17 level2 lfo23;tab-stops:list 1.0in'><![if !supportLists]><span
    5289 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5290 color:windowtext;text-decoration:none;text-underline:none'><span
    5291 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5292 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5293 style='mso-fareast-font-family:"Times New Roman"'>Reset profile </span></b><span
    5294 style='mso-fareast-font-family:"Times New Roman"'>– resets the values for the
    5295 instrument parameters to the default values shown in parentheses for each
    5296 entry.<span class=MsoHyperlink><b style='mso-bidi-font-weight:normal'><span
    5297 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></b></span></span></p>
    5298 
    5299 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5300 auto;text-indent:-.25in;mso-list:l17 level2 lfo23;tab-stops:list 1.0in'><![if !supportLists]><span
    5301 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5302 color:windowtext;text-decoration:none;text-underline:none'><span
    5303 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5304 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5305 style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b><span
    5306 style='mso-fareast-font-family:"Times New Roman"'> – this copies the instrument
    5307 parameters shown to other selected powder patterns. If used, a dialog box (Copy
    5308 parameters) will appear showing the list of available powder patterns, you can
    5309 copy the instrument parameters to any or all of them; select ‘All’ to copy them
    5310 to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the
    5311 operation. The copy will only work for instrument parameters that are
    5312 commensurate with the one that is shown, e.g. single radiation patterns will
    5313 not be updated from K</span><sub><span style='font-family:Symbol;mso-fareast-font-family:
    5314 "Times New Roman"'>a</span></sub><sub><span style='mso-fareast-font-family:
    5315 "Times New Roman"'>1</span></sub><span style='mso-fareast-font-family:"Times New Roman"'>/K</span><sub><span
    5316 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span
    5317 style='mso-fareast-font-family:"Times New Roman"'>2</span></sub><span
    5318 style='mso-fareast-font-family:"Times New Roman"'> ones.<span
    5319 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5320 text-underline:none'><o:p></o:p></span></span></span></p>
    5321 
    5322 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5323 auto;text-indent:-.25in;mso-list:l17 level2 lfo23;tab-stops:list 1.0in'><![if !supportLists]><span
    5324 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5325 color:windowtext;text-decoration:none;text-underline:none'><span
    5326 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5327 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5328 style='mso-fareast-font-family:"Times New Roman"'>Copy flags </span></b><span
    5329 style='mso-fareast-font-family:"Times New Roman"'>- – this copies the instrument
    5330 parameter refinement flags shown to other selected powder patterns. If used, a
    5331 dialog box (Copy refinement flags) will appear showing the list of available
    5332 powder patterns, you can copy the instrument parameter refinement flags to any
    5333 or all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to
    5334 do the copy; ‘Cancel’ to cancel the operation. The copy will only work for
    5335 instrument parameters that are commensurate with the one that is shown, e.g.
    5336 single radiation patterns will not be updated from K</span><sub><span
    5337 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span
    5338 style='mso-fareast-font-family:"Times New Roman"'>1</span></sub><span
    5339 style='mso-fareast-font-family:"Times New Roman"'>/K</span><sub><span
    5340 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span
    5341 style='mso-fareast-font-family:"Times New Roman"'>2</span></sub><span
    5342 style='mso-fareast-font-family:"Times New Roman"'> ones.<span
    5343 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5344 text-underline:none'><o:p></o:p></span></span></span></p>
    5345 
    5346 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5347 auto;text-indent:-.25in;mso-list:l11 level1 lfo21'><![if !supportLists]><span
    5348 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5349 color:windowtext;text-decoration:none;text-underline:none'><span
    5350 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5351 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    5352 "Times New Roman"'>You can change any of the profile coefficients<span
    5353 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5354 text-underline:none'><o:p></o:p></span></span></span></p>
    5355 
    5356 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    5357 text-indent:-.25in;mso-list:l11 level1 lfo21'><![if !supportLists]><span
    5358 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5359 color:windowtext;text-decoration:none;text-underline:none'><span
    5360 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5361 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    5362 "Times New Roman"'>You can choose to refine any profile coefficients. <b
    5363 style='mso-bidi-font-weight:normal'>NB</b>: In certain circumstances some
    5364 choices are ignored e.g. Zero is not refined during peak fitting. Also some
    5365 choices may lead to unstable refinement, e.g. Lam refinement and lattice
    5366 parameter refinement. Examine the ‘</span><a href="#Covariance"><span
    5367 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
    5368 none;text-underline:none'>Covariance’</span></a><span style='mso-fareast-font-family:
    5369 "Times New Roman"'> display for highly correlated parameters.<span
    5370 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5371 text-underline:none'><o:p></o:p></span></span></span></p>
    5372 
    5373 <h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    5374 is plotted here?</span></h5>
    5375 
    5376 <p style='margin-left:1.0in'>This plot shows the contributions to the powder
    5377 pattern peak widths as delta-Q/Q (=delta-d/d) vs. Q for the Gaussian and
    5378 Lorentzian parts of the profile function, in addition to the overall widths.
    5379 The solid curves are based on the default values of U, V, W, X and Y shown in
    5380 the <a href="#Instrument_Parameters">Instrument Parameters</a> window (shown in
    5381 parentheses; these are the values for the instrument contribution that were set
    5382 when the powder pattern was first read in to GSAS-II.) The dashed values are
    5383 based on the refined values, if different. If individual peak fitting has been
    5384 performed, the values of ‘sig’ &amp; ‘gam’ for those peaks are plotted as ‘+’;
    5385 these are computed from the fitted values of U, V, W, X and Y as well as any
    5386 sig or gam values that are individually refined. </p>
    5387 
    5388 <h4 style='margin-left:.25in'><a name="PWDR_Sample_Parameters"></a><u>Sample
    5389 Parameters</u></h4>
    5390 
    5391 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5392 "Times New Roman"'>This window shows the various sample-dependent parameters
    5393 for the selected powder pattern. The presence of a refine button indicates that
    5394 a parameter can be refined (all others are fixed.) All values shown in this
    5395 window can be edited. Note that the last three parameters (named FreePrm<i>X</i>,
    5396 <i>X</i>=1,2,3) have labels that can be changed. If changed in one histogram,
    5397 the same label is used for all histograms. When a label is changed, the
    5398 Comments tree item for each PWDR histogram is searched for a matching
    5399 &quot;Label=value&quot; pair (differences in letter case between the two label
    5400 strings is ignored). When found, the value is converted to a float and saved as
    5401 the appropriate Sample Parameter. NB: for powder data be sure the correct
    5402 instrument type is selected (<b style='mso-bidi-font-weight:normal'>Debye-Scherrer</b>
    5403 or <b style='mso-bidi-font-weight:normal'>Bragg-Brentano</b>).</span></p>
    5404 
    5405 <h5 style='margin-left:.5in'>What can I do here?</h5>
    5406 
    5407 <p style='margin-left:1.0in'><b>Command</b> Menu items</p>
    5408 
    5409 <p style='margin-left:1.1in'>In this window you can change parameters
    5410 associated with a histogram or set them to be refined. The histogram scale
    5411 factor is usually refined. For <b>Debye-Scherrer</b> mode the &quot;Sample X
    5412 displacement&quot; is also ususally refined but the &quot;Sample Y
    5413 displacement&quot; can only be refined when data are collected over a two-theta
    5414 range that extends to greater than ~140 degrees (typically for CW Neutron).
    5415 Sample absorption should not be refined when all atomic displacement parameters
    5416 (Uiso or Uaniso values) are varied, as the correlation is very high. For <b>Bragg-Brentano</b>,
    5417 &quot;Sample displacement&quot; is usually refined and for low-Z samples
    5418 &quot;Sample transparency&quot; is usually refined. &quot;Surface
    5419 roughness&quot; parameters are not usually refined. Remaining parameters are of
    5420 use for texture or parametric studies and may be changed with the menu commands
    5421 described here. </p>
    5422 
    5423 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-fareast-font-family:
    5424 "Times New Roman"'>Set scale<o:p></o:p></span></p>
    5425 
    5426 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5427 "Times New Roman"'>Rescales a pattern by multiplying by the current scale
    5428 factor. <o:p></o:p></span></p>
    5429 
    5430 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-fareast-font-family:
    5431 "Times New Roman"'>Load<o:p></o:p></span></p>
    5432 
    5433 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5434 "Times New Roman"'>This loads sample parameters from a previously saved .samprm
    5435 file. <o:p></o:p></span></p>
    5436 
    5437 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-fareast-font-family:
    5438 "Times New Roman"'>Save<o:p></o:p></span></p>
    5439 
    5440 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5441 "Times New Roman"'>This saves the sample parameters to a file with the
    5442 extension ’.samprm’. A file dialog box will appear to ask for the name of the
    5443 file to be written. <o:p></o:p></span></p>
    5444 
    5445 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-fareast-font-family:
    5446 "Times New Roman"'>Copy<o:p></o:p></span></p>
    5447 
    5448 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5449 "Times New Roman"'>This copies the sample parameters shown to other selected
    5450 powder patterns. If used, a dialog box (Copy parameters) will appear showing
    5451 the list of available powder patterns, you can copy the sample parameters to
    5452 any or all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’
    5453 to do the copy; ‘Cancel’ to cancel the operation. <o:p></o:p></span></p>
    5454 
    5455 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-fareast-font-family:
    5456 "Times New Roman"'>Copy selected...<o:p></o:p></span></p>
    5457 
    5458 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5459 "Times New Roman"'>This copies only the sample parameter that are selected to
    5460 other selected powder patterns, but is otherwise similar to &quot;Copy&quot;. <o:p></o:p></span></p>
    5461 
    5462 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-fareast-font-family:
    5463 "Times New Roman"'>Copy flags<o:p></o:p></span></p>
    5464 
    5465 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5466 "Times New Roman"'>This copies the sample parameter refinement flags shown to
    5467 other selected powder patterns. If used, a dialog box (Copy refinement flags)
    5468 will appear showing the list of available powder patterns, you can copy the
    5469 sample parameter refinement flags to any or all of them; select ‘All’ to copy
    5470 them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the
    5471 operation. <o:p></o:p></span></p>
    5472 
    5473 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-fareast-font-family:
    5474 "Times New Roman"'>Set one value<o:p></o:p></span></p>
    5475 
    5476 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5477 "Times New Roman"'>This is used to set a single selected sample parameter for a
    5478 selected set of PWDR histograms. The same value can be used for all histograms
    5479 or a dialog can be used to provide a table where you can set the values
    5480 differently for each of selected histograms. <o:p></o:p></span></p>
    5481 
    5482 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-fareast-font-family:
    5483 "Times New Roman"'>Load all<o:p></o:p></span></p>
    5484 
    5485 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    5486 "Times New Roman"'>Reads a file containing a table of sample parameters and
    5487 copies them to matching PWDR entries. The file will look something like the
    5488 example here: <o:p></o:p></span></p>
    5489 
    5490 <blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><pre style='margin-left:
    5491 .5in'><o:p>&nbsp;</o:p></pre><pre style='margin-left:.5in'>#filename<span style='mso-spacerun:yes'>       </span>temperature pressure ignore-me<span style='mso-spacerun:yes'>  </span>humidity</pre><pre
    5492 style='margin-left:.5in'>LaB6_dc250.tif<span style='mso-spacerun:yes'>      </span>100<span style='mso-spacerun:yes'>          </span>1<span style='mso-spacerun:yes'>      </span>test<span style='mso-spacerun:yes'>       </span>.2</pre><pre
    5493 style='margin-left:.5in'>LaB6_dc300.tif<span style='mso-spacerun:yes'>      </span>150<span style='mso-spacerun:yes'>          </span>1<span style='mso-spacerun:yes'>      </span>test<span style='mso-spacerun:yes'>       </span>.25</pre></blockquote>
    5494 
    5495 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5496 style='mso-fareast-font-family:"Times New Roman"'>Note that the first line(s)
    5497 in the file can be a header, but each header line must start marked with a hash
    5498 (#). A header is not required. &quot;Columns&quot; in the table are separated
    5499 by one or more delimiters (which may be a comma, tab or space). Note that
    5500 columns do not need to be aligned, as long as each entry is spaced by at least
    5501 one delimiter. The first column in the table is used to look up PWDR entries
    5502 where the initial space-delimited string after the PWDR tag (&quot;myfile&quot;
    5503 in &quot;PWRD myfile AZM=180...&quot;) must match the table. Subsequent columns
    5504 can then be mapped to sample parameters or can be ignored, using a dialog
    5505 window. <o:p></o:p></span></p>
    5506 
    5507 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5508 style='mso-fareast-font-family:"Times New Roman"'>Rescale all<o:p></o:p></span></p>
    5509 
    5510 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5511 style='mso-fareast-font-family:"Times New Roman"'>Allows a series of selected
    5512 PWDR histograms to be put on a common scale by integrating them over a specific
    5513 two-theta region and then scaling them so that the integration range will match
    5514 the first pattern. <o:p></o:p></span></p>
    5515 
    5516 <h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    5517 name="PWDR_Peak_List"></a><u>Peak List</u></h4>
    5518 
    5519 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5520 style='mso-fareast-font-family:"Times New Roman"'>The Peak List data tree entry
    5521 is used to fit diffraction peaks at user-supplied positions (not generated from
    5522 a unit cell). Peak positions and intensities may be selected for individual
    5523 refinement. Gaussian (sigma) and Lorentzian (gamma) peak widths may be varied
    5524 individually or the values may be generated from the U,V &amp; W (sigma) and X
    5525 &amp; Y (gamma) values in the Instrument Parameters tree item: If individual
    5526 values are refined, then the value in the table is used. If values are not
    5527 refined, then those determined by U,V &amp; W and/or X &amp; Y are placed in
    5528 the table and are used. Likewise, the background is generated using the
    5529 parameters in the Background data tree entry and the range of data used in the
    5530 fit is set from the Limits tree item. Note that optionally the parameters on
    5531 the Background and in the Instrument Parameters tree items may be refined as
    5532 peak settings are fitted. <o:p></o:p></span></p>
    5533 
    5534 <h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>What
    5535 can I do here?</h5>
    5536 
    5537 <p style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>There
    5538 are three ways to interact with Peak List data tree item: through its menu,
    5539 labeled <b>Peak Fitting</b>, through interaction with the peak list table, and
    5540 through interactions with the plot. </p>
    5541 
    5542 <p style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The
    5543 following interactions are available with the peak table: <o:p></o:p></p>
    5544 
    5545 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5546 style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
    5547 "Times New Roman"'><BL>·</span><span style='mso-fareast-font-family:"Times New Roman"'>
    5548 <span style='mso-spacerun:yes'> </span>You can change individual peak
    5549 coefficient values. Enter the value then press Enter or Tab or click the mouse
    5550 elsewhere in the Peak List window. This will set the new value. <o:p></o:p></span></p>
    5551 
    5552 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5553 style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
    5554 "Times New Roman"'>·</span><span style='mso-fareast-font-family:"Times New Roman"'><span
    5555 style='mso-spacerun:yes'>  </span>You can change the individual refine flags
    5556 either by clicking on the check boxes. <o:p></o:p></span></p>
    5557 
    5558 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5559 style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
    5560 "Times New Roman"'>·</span><span style='mso-fareast-font-family:"Times New Roman"'><span
    5561 style='mso-spacerun:yes'>  </span>You can change all refine flags in a column
    5562 by clicking on a single one and then click on the column label above. The
    5563 entire column should be highlighted in blue. Type ‘y’ to set the refine flags
    5564 or ‘n’ to clear the flags. This can also be done by double-clicking on the
    5565 column label, which brings up a menu. <o:p></o:p></span></p>
    5566 
    5567 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5568 style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
    5569 "Times New Roman"'>·</span><span style='mso-fareast-font-family:"Times New Roman"'><span
    5570 style='mso-spacerun:yes'>  </span>You can delete peaks in the Peak List by
    5571 selecting a row by clicking on the row label to the left (multiple selection of
    5572 rows is allowed). Selected rows will be highlighted in the plot (see below).
    5573 Then press the Delete or backspace key. (Note that peaks can also be deleted
    5574 from the plot, see below.) <o:p></o:p></span></p>
    5575 
    5576 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5577 style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
    5578 "Times New Roman"'>·</span><span style='mso-fareast-font-family:"Times New Roman"'><span
    5579 style='mso-spacerun:yes'>  </span>You can highlight a peak by clicking or
    5580 double-clicking on the row label (to the left) for a peak. The color of the
    5581 line will change from blue to green. </BL><o:p></o:p></span></p>
    5582 
    5583 <p style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The
    5584 <b>Peak Fitting</b> menu contains the following commands:</p>
    5585 
    5586 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5587 style='mso-fareast-font-family:"Times New Roman"'>Set sel. ref flags<o:p></o:p></span></p>
    5588 
    5589 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5590 style='mso-fareast-font-family:"Times New Roman"'>If one or more row of peaks
    5591 are selected by clicking on the peak label to the left, this menu item can be
    5592 used to set the refinement flags for the selected reflections. <o:p></o:p></span></p>
    5593 
    5594 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5595 style='mso-fareast-font-family:"Times New Roman"'>Set all ref flags<o:p></o:p></span></p>
    5596 
    5597 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5598 style='mso-fareast-font-family:"Times New Roman"'>This sets refinement flags
    5599 for all peaks in the table. <o:p></o:p></span></p>
    5600 
    5601 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5602 style='mso-fareast-font-family:"Times New Roman"'>Auto search<o:p></o:p></span></p>
    5603 
    5604 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5605 style='mso-fareast-font-family:"Times New Roman"'>This fills the table with
    5606 peak positions. These are selected based on peak tops that are substantially
    5607 above background. Noisy data will give spurious peaks and small peaks or
    5608 shoulders will not be found. Examine results &amp; modify as needed. <o:p></o:p></span></p>
    5609 
    5610 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5611 style='mso-fareast-font-family:"Times New Roman"'>UnDo<o:p></o:p></span></p>
    5612 
    5613 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5614 style='mso-fareast-font-family:"Times New Roman"'>Resets peak parameters,
    5615 background and instrument parameter values varied in the last peak fitting
    5616 refinement back to their original values. Use this to recover from a failed
    5617 refinement. Note: only one previous refinement is saved, so this cannot be
    5618 pressed twice to return to the refinement before the previous. <o:p></o:p></span></p>
    5619 
    5620 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5621 style='mso-fareast-font-family:"Times New Roman"'>PeakFit<o:p></o:p></span></p>
    5622 
    5623 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5624 style='mso-fareast-font-family:"Times New Roman"'>Performs a least squares fit
    5625 of the peaks in Peak List to the data. Any peak parameters, background
    5626 parameters and instrument parameters with refine checked will be varied in this
    5627 refinement. The refinement will proceed until convergence. We suggest you vary
    5628 the intensity along with the background first (the default), then vary the
    5629 position and instrument parameters after. The order will depend on how poor is
    5630 the initial estimate of the instrument parameters (U, V, W, X, Y &amp; SH/L).
    5631 To determine how to proceed, examine in detail the powder pattern difference
    5632 curve displayed in the GSASII Plots window. If individual peaks show peak
    5633 widths that are widely different, their individual sigma and gamma parameters
    5634 may be refined. If the refinement results in negative peak coefficients, these
    5635 will be highlighted in red. If this happens, you should use the <b>UnDo</b>
    5636 menu item (above) to return to the refinement and reconsider your choice of
    5637 parameters to be varied. <o:p></o:p></span></p>
    5638 
    5639 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5640 style='mso-fareast-font-family:"Times New Roman"'>LSQ one cycle <o:p></o:p></span></p>
    5641 
    5642 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5643 style='mso-fareast-font-family:"Times New Roman"'>Perform a single cycle of
    5644 least squares refinement. This can be used in difficult cases to get a
    5645 refinement started toward convergence. <o:p></o:p></span></p>
    5646 
    5647 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5648 style='mso-fareast-font-family:"Times New Roman"'>Reset sig and gam <o:p></o:p></span></p>
    5649 
    5650 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5651 style='mso-fareast-font-family:"Times New Roman"'>This resets the values of
    5652 sigma and gamma in the table to those computed from the instrument parameters
    5653 U, V, W, X &amp; Y. <o:p></o:p></span></p>
    5654 
    5655 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5656 style='mso-fareast-font-family:"Times New Roman"'>Peak copy<o:p></o:p></span></p>
    5657 
    5658 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5659 style='mso-fareast-font-family:"Times New Roman"'>Copy the current set of peaks
    5660 to other histogram(s) <o:p></o:p></span></p>
    5661 
    5662 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5663 style='mso-fareast-font-family:"Times New Roman"'>Seq PeakFit<o:p></o:p></span></p>
    5664 
    5665 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5666 style='mso-fareast-font-family:"Times New Roman"'>Fit peaks for multiple
    5667 histograms <o:p></o:p></span></p>
    5668 
    5669 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5670 style='mso-fareast-font-family:"Times New Roman"'>Clear peaks<o:p></o:p></span></p>
    5671 
    5672 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5673 style='mso-fareast-font-family:"Times New Roman"'>This removes all the peaks
    5674 from the Peak List. <o:p></o:p></span></p>
    5675 
    5676 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5677 style='mso-fareast-font-family:"Times New Roman"'>Move selected peak<o:p></o:p></span></p>
    5678 
    5679 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5680 style='mso-fareast-font-family:"Times New Roman"'>A peak may be moved using the
    5681 following process: select it in the table by clicking on its label (to left),
    5682 use this menu item. The peak line will then follow movement of the mouse in the
    5683 plot window. Click with the left mouse button to set a new position. Click with
    5684 the right mouse button to delete that peak. Click outside the axes to abort the
    5685 move and return to the previous position. (Note that peak movement is also
    5686 possible with the plot window, see below.) <o:p></o:p></span></p>
    5687 
    5688 <h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5689 style='mso-fareast-font-family:"Times New Roman"'>What is plotted here?</span></h5>
    5690 
    5691 <p style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The
    5692 plot window shows the observed and computed patterns, as well as the background
    5693 and peak positions. Observed points are shown as blue crosses (+) and the
    5694 fitted pattern is shown as a solid green line. The background is shown as a red
    5695 line and the difference curve is shown as a cyan (turquoise) line, below the
    5696 observed and computed pattern. Peak positions are shown as vertical blue lines
    5697 (or green when selected). The upper and lower data limits are shown as red and
    5698 green dashed vertical lines, respectively. </p>
    5699 
    5700 <h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5701 style='mso-fareast-font-family:"Times New Roman"'>What can I do with the plot?</span><o:p></o:p></h5>
    5702 
    5703 <p style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><BL>For
    5704 all actions involving mouse clicks such as those below, be sure that the
    5705 Zoom/Pan buttons are not selected on the Plot window, as the mouse clicks will
    5706 be used for zooming or panning, not the desired action. </p>
    5707 
    5708 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5709 style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
    5710 "Times New Roman"'>·</span><span style='mso-fareast-font-family:"Times New Roman"'><span
    5711 style='mso-spacerun:yes'>  </span>You can add peaks to the Peak list using the
    5712 mouse on the plot by: position the cursor pointer onto a cross for an observed
    5713 point and pressing the left mouse button. The selected peak will be added to
    5714 the Peak List in the appropriate position to keep peaks sorted and a blue
    5715 vertical line will be plotted on that position. We recommend that you begin
    5716 picking peaks from the right side of the pattern; that way the tool tip won’t
    5717 be in your way as you select peaks. <o:p></o:p></span></p>
    5718 
    5719 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5720 style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
    5721 "Times New Roman"'>·</span><span style='mso-fareast-font-family:"Times New Roman"'><span
    5722 style='mso-spacerun:yes'>  </span>You can delete peaks using the mouse on the
    5723 plot by positioning the pointer on the blue line for the peak to be deleted and
    5724 then pressing the right mouse button. The blue line should vanish and the
    5725 corresponding peak will be removed from the Peak List. <o:p></o:p></span></p>
    5726 
    5727 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5728 style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
    5729 "Times New Roman"'>·</span><span style='mso-fareast-font-family:"Times New Roman"'><span
    5730 style='mso-spacerun:yes'>  </span>You can move a Peak List item using the mouse
    5731 on the plot by: position the pointer on the blue line for the peak you wish to
    5732 move and then hold the left mouse button down, dragging the line to the desired
    5733 position. When the mouse button is released, the peak line will be drawn in the
    5734 new position. <o:p></o:p></span></p>
    5735 
    5736 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5737 style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
    5738 "Times New Roman"'>·</span><span style='mso-fareast-font-family:"Times New Roman"'><span
    5739 style='mso-spacerun:yes'>  </span>The fit limits can be changed without
    5740 selecting the Limits item in the data tree from the plot. Change the upper and
    5741 lower Tmin values by clicking on the appropriate vertical line and dragging it
    5742 to the right or left. </BL><o:p></o:p></span></p>
    5743 
    5744 <h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    5745 name="PWDR_Index_Peak_List"></a><u>Index Peak List</u></h4>
    5746 
    5747 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5748 style='mso-fareast-font-family:"Times New Roman"'>This window shows the list of
    5749 peaks that will be used for indexing (see </span><a href="#Unit_Cells_List"><span
    5750 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
    5751 none;text-underline:none'>Unit Cells List</span></a><span style='mso-fareast-font-family:
    5752 "Times New Roman"'>). It must be filled before indexing can proceed. When
    5753 indexing is completed, this display will show the resulting hkl values for
    5754 every indexed reflection along with the calculated d-spacing (‘d-calc’) for the
    5755 selected unit cell in <a href="#Unit_Cells_List"><b>Unit Cells List</b></a>.</span>
    5756 <span style='mso-fareast-font-family:"Times New Roman"'>.<span
    5757 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5758 text-underline:none'><o:p></o:p></span></span></span></p>
    5759 
    5760 <h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5761 style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<span
    5762 class=MsoHyperlink><span style='color:#4F4FFF;text-decoration:none;text-underline:
    5763 none'><o:p></o:p></span></span></span></h5>
    5764 
    5765 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    5766 text-indent:-.25in;mso-list:l29 level1 lfo25;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5767 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5768 color:windowtext;text-decoration:none;text-underline:none'><span
    5769 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5770 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    5771 "Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Operations</b>’
    5772 – <b style='mso-bidi-font-weight:normal'>Load/Reload</b> – loads the peak
    5773 positions &amp; intensities from the </span><a href="#Peak_List"><span
    5774 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
    5775 none;text-underline:none'>Peak List</span></a><span style='mso-fareast-font-family:
    5776 "Times New Roman"'> to make them available for the indexing routine. The d-obs
    5777 is obtained from Bragg’s Law after applying the Zero correction shown on the </span><a
    5778 href="#Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman";
    5779 color:windowtext;text-decoration:none;text-underline:none'>Instrument
    5780 Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'>
    5781 table to the position shown here.<span class=MsoHyperlink><span
    5782 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    5783 
    5784 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    5785 text-indent:-.25in;mso-list:l29 level1 lfo25;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5786 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5787 color:windowtext;text-decoration:none;text-underline:none'><span
    5788 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5789 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    5790 "Times New Roman"'>You may deselect individual peaks from indexing by
    5791 unchecking the corresponding ‘use’ box.<span class=MsoHyperlink><span
    5792 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    5793 
    5794 <h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    5795 name="PWDR_Unit_Cells_List"><u>Unit Cells List</u></a></h4>
    5796 
    5797 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5798 style='mso-fareast-font-family:"Times New Roman"'>This tree item has several
    5799 purposes, it can be used to perform autoindexing and it can be used to show the
    5800 positions of peaks from unit cells which may be results from autoindexing or
    5801 may be entered from a phase or manually. It can be used to refine unit cell
    5802 parameters. It can also be used to search for cells/symmetry settings related
    5803 to a specified unit cell &amp; space group. <o:p></o:p></span></p>
    5804 
    5805 <h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5806 style='mso-fareast-font-family:"Times New Roman"'>What can I do here?</span><span
    5807 class=MsoHyperlink><span style='color:#4F4FFF;text-decoration:none;text-underline:
    5808 none'><o:p></o:p></span></span></h5>
    5809 
    5810 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>For
    5811 autoindexing</b>, the peaks in the <a href="#Index_Peak_List">Index Peak List</a>
    5812 are used. Select one or more Bravais lattice types to use and use the
    5813 &quot;Cell Index/Refine&quot;/&quot;Index Cell&quot; menu command to start
    5814 indexing. Output will appear on the console and a progress bar dialog will
    5815 appear which tracks trial volume. A <b style='mso-bidi-font-weight:normal'>Cancel</b>
    5816 button will terminate indexing; it may need to be pressed more than once to
    5817 fully terminate the indexing process. Console output shows possible solutions
    5818 with a computed <b>M20</b> for each; good solutions are indicated by high <b>M20</b>
    5819 values. <b style='mso-bidi-font-weight:normal'>X20</b> gives number of
    5820 unindexed lines out of the 1<sup>st</sup> 20 lines and <b>Nc</b> gives total
    5821 number of reflections generated for each solution. </p>
    5822 
    5823 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The
    5824 &quot;Copy Cell&quot; menu commnd copies a selected solution to the Unit cell
    5825 values; the Bravais lattice shown for the choice is copied. Press <b
    5826 style='mso-bidi-font-weight:normal'>Show hkl positions</b> to generate the
    5827 allowed reflection positions, which are visually superimposed on the displayed
    5828 powder pattern to visually confirm the indexing. Pay particular attention to
    5829 any unmatched peaks in the pattern. A <b style='mso-bidi-font-weight:normal'>Space
    5830 group</b> can be from the pulldown box to remove reflections based on space
    5831 group extinctions and visually eliminate possiblities. </p>
    5832 
    5833 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    5834 margin-left:1.2in;text-indent:-.25in;mso-list:l28 level1 lfo26;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5835 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    5836 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5837 style='mso-fareast-font-family:"Times New Roman"'>Max Nc/Nobs: – this controls
    5838 the extent of the search for the correct indexing. This may need to be
    5839 increased if an indexing trial terminates too quickly. It rarely needs to be
    5840 changed. <o:p></o:p></span></p>
    5841 
    5842 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    5843 margin-left:1.2in;text-indent:-.25in;mso-list:l28 level1 lfo26;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5844 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    5845 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5846 style='mso-fareast-font-family:"Times New Roman"'>Start Volume: – this sets an
    5847 initial unit cell volume for the indexing. It rarely needs to be changed. <o:p></o:p></span></p>
    5848 
    5849 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    5850 margin-left:1.2in;text-indent:-.25in;mso-list:l28 level1 lfo26;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5851 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    5852 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5853 style='mso-fareast-font-family:"Times New Roman"'>Select &quot;keep&quot; in
    5854 the table for a cell that should be preserved when an additional indexing run
    5855 is tried; all without that are erased before the indexing trial begins. <o:p></o:p></span></p>
    5856 
    5857 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>To
    5858 display a unit cell</b>, optionally with space group extinctions, set a Bravais
    5859 class to determine a unit cell type (see <a href="#Laue_List">list below</a>),
    5860 optionally select a space group (by default the lowest symmetry space group for
    5861 the class is selected) and enter the unit cell contents. Or use the &quot;Cell
    5862 Index/Refine&quot;/&quot;Load Phase&quot; menu command to read this information
    5863 from a phase that has been read into a project or from a file (such as a CIF)
    5864 using the &quot;Cell Index/Refine&quot;/&quot;Import Cell&quot; menu command. </p>
    5865 
    5866 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>For
    5867 symmetry exploration</b>, once a phase/cell has been loaded, use the &quot;Run
    5868 SUBGROUPS&quot;, &quot;Cell Symmetry Search&quot; or &quot;Run
    5869 k-SUBGROUPSMAG&quot; commands from the &quot;Cell Index/Refine&quot; menu.
    5870 These commands look for: subgroups, higher symmetry cells or magnetic
    5871 subgroups, respectively. Also note the &quot;Transform Cell&quot; commnd in
    5872 that menu that can perform namy common lattice transformations, apply a
    5873 user-supplied cell transformation or create a magnetic phase. </p>
    5874 
    5875 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>To
    5876 optimize a cell</b>, to fit the peaks in the <a href="#Index_Peak_List">Index
    5877 Peak List</a>, use the &quot;Cell Index/Refine&quot;/&quot;Refine Cell&quot;
    5878 menu command. The results will be placed in the <b>Indexing Result</b> table
    5879 with ‘<b>use’</b> selected. </p>
    5880 
    5881 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Other</b>:
    5882 The &quot;Make new phase&quot; command creates a new phase from the selected unit
    5883 cell and chosen space group. A dialog box will appear asking for a name for
    5884 this phase. See the new entry under Phases and the new lattice parameters will
    5885 be in the <a href="#General">General </a>window for that phase. </p>
    5886 
    5887 <p style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    5888 name="Laue_List"><b>GSAS-II Laue classes</b> (note that some redundant entries
    5889 are included for convenience.)</a></p>
    5890 
    5891 <span style='mso-bookmark:Laue_List'></span>
    5892 
    5893 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    5894 margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo27;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5895 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    5896 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    5897 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5898 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Cubic:
    5899 Fm3m, Im3m &amp; Pm3m <o:p></o:p></span></p>
    5900 
    5901 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    5902 margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo27;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5903 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    5904 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    5905 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5906 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Rhombohedral:
    5907 R3-H (hexagonal axes) <o:p></o:p></span></p>
    5908 
    5909 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    5910 margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo27;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5911 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    5912 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    5913 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5914 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Hexagonal:
    5915 P6/mmm <o:p></o:p></span></p>
    5916 
    5917 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    5918 margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo27;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5919 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    5920 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    5921 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5922 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Tetragonal:
    5923 I4/mmm, P4/mmm <o:p></o:p></span></p>
    5924 
    5925 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    5926 margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo27;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5927 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    5928 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    5929 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5930 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Orthorhombic:
    5931 Fmmm, Immm, Ammm, Bmmm, Cmmm, Pmmm <o:p></o:p></span></p>
    5932 
    5933 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    5934 margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo27;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5935 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    5936 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    5937 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5938 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Monoclinic:
    5939 I2/m, C2/m, P2/m (b-unique) <o:p></o:p></span></p>
    5940 
    5941 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    5942 margin-left:1.0in;text-indent:-.25in;mso-list:l0 level1 lfo27;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5943 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    5944 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    5945 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5946 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Triclinic:
    5947 P1, C1 <o:p></o:p></span></p>
    5948 
    5949 <h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    5950 name="PWDR_Reflection_Lists"></a><u>Reflection Lists</u></h4>
    5951 
    5952 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5953 style='mso-fareast-font-family:"Times New Roman"'>This window shows the
    5954 reflections for the selected phase (selected by the tab at top) found in this
    5955 powder data set. It is generated by a Rietveld (including Pawley and LeBail)
    5956 refinements. Reflection d-spaces are generated directly from lattice parameters
    5957 but 2θ values will incorporate corrections, such as for sample displacement,
    5958 zero, etc. </span></p>
    5959 
    5960 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5961 style='mso-fareast-font-family:"Times New Roman"'>The indicies (hkl values) for
    5962 reflections can be displayed by letting the mouse rest at the position of a
    5963 reflection in 2-theta, Q, etc. (the vertical position does not matter). After a
    5964 short delay, a &quot;tool tip&quot; will be displayed for any reflections close
    5965 to the lateral mouse position. </span></p>
    5966 
    5967 <h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    5968 style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<span
    5969 class=MsoHyperlink><span style='color:#4F4FFF;text-decoration:none;text-underline:
    5970 none'><o:p></o:p></span></span></span></h5>
    5971 
    5972 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    5973 text-indent:-.25in;mso-list:l18 level1 lfo29;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5974 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5975 color:windowtext;text-decoration:none;text-underline:none'><span
    5976 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5977 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    5978 "Times New Roman"'>Menu<b style='mso-bidi-font-weight:normal'> ‘Reflection
    5979 List’ </b>– <span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    5980 none;text-underline:none'><o:p></o:p></span></span></span></p>
    5981 
    5982 <p class=MsoListParagraphCxSpLast style='margin-left:1.25in;mso-add-space:auto;
    5983 text-indent:-.25in;mso-list:l18 level2 lfo29;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    5984 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5985 color:windowtext;text-decoration:none;text-underline:none'><span
    5986 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5987 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    5988 "Times New Roman"'>Select phase – if there is more than one phase; you can
    5989 select another phase; the window title will show which phase is shown. <span
    5990 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5991 text-underline:none'><o:p></o:p></span></span></span></p>
     4500<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     4501"Times New Roman"'>[<a href="gsasII-pwdr.html">see separate page</a>]<o:p></o:p></span></p>
    59924502
    59934503<h2 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
     
    60094519available a green ring is shown for F-observed, a blue ring for F-calculated
    60104520and a central disk for <span style='font-family:"Calibri",sans-serif'>Δ</span>F
    6011 (green for Fo&gt;Fc and red for Fo&lt;Fc).</p>
     4521(green for <span class=SpellE>Fo</span>&gt;Fc and red for <span class=SpellE>Fo</span>&lt;Fc).</p>
    60124522
    60134523<h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
     
    60154525
    60164526<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    6017 text-indent:-.25in;mso-list:l1 level1 lfo31;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4527text-indent:-.25in;mso-list:l1 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    60184528style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    6019 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    6020 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Change
    6021 the scale</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    6022 move the slider, the rings will change their radius accordingly.<o:p></o:p></span></p>
     4529style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4530dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4531"Times New Roman"'>Change the scale</span></b><span style='mso-fareast-font-family:
     4532"Times New Roman"'> – move the slider, the rings will change their radius
     4533accordingly.<o:p></o:p></span></p>
    60234534
    60244535<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    6025 auto;text-indent:-.25in;mso-list:l1 level1 lfo31;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4536auto;text-indent:-.25in;mso-list:l1 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    60264537style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    6027 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    6028 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select
    6029 the zone</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    6030 select between 100, 010 or 001; plot axes will be labeled accordingly.<o:p></o:p></span></p>
     4538style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4539dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4540"Times New Roman"'>Select the zone</span></b><span style='mso-fareast-font-family:
     4541"Times New Roman"'> – select between 100, 010 or 001; plot axes will be labeled
     4542accordingly.<o:p></o:p></span></p>
    60314543
    60324544<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    6033 auto;text-indent:-.25in;mso-list:l1 level1 lfo31;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4545auto;text-indent:-.25in;mso-list:l1 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    60344546style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    6035 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    6036 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select
    6037 plot type</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    6038 the choices are either F or F<sup>2</sup>, </span><span style='font-family:
    6039 "Calibri",sans-serif;mso-fareast-font-family:"Times New Roman"'>Δ</span><span
     4547style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4548dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4549"Times New Roman"'>Select plot type</span></b><span style='mso-fareast-font-family:
     4550"Times New Roman"'> – the choices are either F or F<sup>2</sup>, </span><span
     4551style='font-family:"Calibri",sans-serif;mso-fareast-font-family:"Times New Roman"'>Δ</span><span
    60404552style='mso-fareast-font-family:"Times New Roman"'>F<sup>2</sup>/</span><span
    60414553style='font-family:"Calibri",sans-serif;mso-fareast-font-family:"Times New Roman"'>σ(F<sup>2</sup>)</span><span
     
    60514563
    60524564<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    6053 text-indent:-.25in;mso-list:l1 level1 lfo31;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4565text-indent:-.25in;mso-list:l1 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    60544566style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    6055 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    6056 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select
    6057 layer </span></b><span style='mso-fareast-font-family:"Times New Roman"'>– move
    6058 the slider for upper layers for the selected zone.<o:p></o:p></span></p>
     4567style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4568dir=LTR></span><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     4569"Times New Roman"'>Select layer </span></b><span style='mso-fareast-font-family:
     4570"Times New Roman"'>– move the slider for upper layers for the selected zone.<o:p></o:p></span></p>
    60594571
    60604572<h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
     
    60734585
    60744586<p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>A
    6075 PDF entry is created from a <a href="#PWDR">powder histogram (PWDR entry)</a>
     4587PDF entry is created from a <a href="gsasII-pwdr.html#PWDR">powder histogram (PWDR entry)</a>
    60764588using the <b>Setup PDFs</b> entry in the <a href="#Calculate_menu">Calculate
    60774589menu</a>. The main PDF data tree item displays the same window as the PDF
     
    60914603
    60924604<p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The
    6093 Optimize PDF button can be used to refine the values of the &quot;Flat
    6094 Bkg&quot;, &quot;Background ratio&quot; and &quot;Ruland width&quot; parameters
    6095 to best agree with the -4*pi*r line that is plotted for r &lt; Rmin. Rmin
    6096 should be set to a distance below the shortest expected interatomic distance
    6097 for the material. </p>
     4605Optimize PDF button can be used to refine the values of the &quot;Flat <span
     4606class=SpellE>Bkg</span>&quot;, &quot;Background ratio&quot; and &quot;Ruland
     4607width&quot; parameters to best agree with the -4*pi*r line that is plotted for
     4608r &lt; <span class=SpellE>Rmin</span>. <span class=SpellE>Rmin</span> should be
     4609set to a distance below the shortest expected interatomic distance for the
     4610material. </p>
    60984611
    60994612<h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>What
     
    61014614
    61024615<p style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The
    6103 PDF parameters can be changed, triggering recomputation of the <a
    6104 href="#PDF_I_Q">I(Q)</a>, <a href="#PDF_S_Q">S(Q)</a>, <a href="#PDF_F_Q">F(Q)</a>
    6105 and <a href="#PDF_G_R">G(R) functions</a>. Available menu commands are: </p>
     4616PDF parameters can be changed, triggering <span class=SpellE>recomputation</span>
     4617of the <a href="#PDF_I_Q">I(Q)</a>, <a href="#PDF_S_Q">S(Q)</a>, <a
     4618href="#PDF_F_Q">F(Q)</a> and <a href="#PDF_G_R">G(R) functions</a>. Available
     4619menu commands are: </p>
    61064620
    61074621<p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
     
    61174631
    61184632<p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6119 style='mso-fareast-font-family:"Times New Roman"'>Removes a previously-entered
     4633style='mso-fareast-font-family:"Times New Roman"'>Removes a <span class=GramE>previously-entered</span>
    61204634element from the chemical formula. <o:p></o:p></span></p>
    61214635
     
    61474661style='mso-fareast-font-family:"Times New Roman"'>Recomputes the PDF for the
    61484662current entry. This is usually done automatically when values are changed, but
    6149 if not this can be forced with this menu item. <o:p></o:p></span></p>
     4663if <span class=GramE>not</span> this can be forced with this menu item. <o:p></o:p></span></p>
    61504664
    61514665<p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
     
    61544668<p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    61554669style='mso-fareast-font-family:"Times New Roman"'>Recomputes the PDFs for all
    6156 selected PDF entries. This is usually done after Copy Controls is used. By
    6157 default PDFs are optimized to reduce the low G(r) region, but this can be
    6158 turned off. <o:p></o:p></span></p>
     4670selected PDF entries. This is usually done after Copy Controls is used. By <span
     4671class=GramE>default</span> PDFs are optimized to reduce the low G(r) region,
     4672but this can be turned off. <o:p></o:p></span></p>
    61594673
    61604674<h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
     
    63124826window shows whatever comment lines found in a “metadata” file when the image
    63134827data file was read by GSAS-II. If you are lucky, there will be useful
    6314 information here (e.g. sample name, date collected, wavelength used, etc.). If
    6315 not, this window will be blank. The text is read-only.</p>
     4828information here (<span class=GramE>e.g.</span> sample name, date collected,
     4829wavelength used, etc.). If not, this window will be blank. The text is
     4830read-only.</p>
    63164831
    63174832<h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>Image
     
    63244839
    63254840<p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>Menu
    6326 command for this window are used to perform calibration (fitting the
    6327 calibration values from a diffraction pattern image taken with a calibrant) and
    6328 for integration. Other menu commands allow the values on the window to be saved
    6329 to a file, read from a file or copied to other images. The &quot;Xfer
    6330 Angles&quot; menu command scales the current integration range for other images
    6331 located at different detector distances. <span class=MsoHyperlink><span
    6332 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></p>
     4841command for this window <span class=GramE>are</span> used to perform
     4842calibration (fitting the calibration values from a diffraction pattern image
     4843taken with a calibrant) and for integration. Other menu commands allow the
     4844values on the window to be saved to a file, read from a file or copied to other
     4845images. The &quot;Xfer Angles&quot; menu command scales the current integration
     4846range for other images located at different detector distances. <span
     4847class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
     4848text-underline:none'><o:p></o:p></span></span></p>
    63334849
    63344850<h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
     
    63384854style='mso-fareast-font-family:"Times New Roman"'>Image masks are used
    63394855designate areas of an image that should not be included in the integration,
    6340 typically used due to detector irregularities, shadows of the beamstop,
    6341 single-crystal peaks from a mounting, etc. Masks can be created with a menu
    6342 command or with keyboard/mouse shortcuts. There are five types of masks:<o:p></o:p></span></p>
     4856typically used due to detector irregularities, shadows of the <span
     4857class=SpellE>beamstop</span>, single-crystal peaks from a mounting, etc. Masks
     4858can be created with a menu command or with keyboard/mouse shortcuts. There are
     4859five types of masks:<o:p></o:p></span></p>
    63434860
    63444861<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6345 margin-left:1.0in;text-indent:-.25in;mso-list:l27 level1 lfo32;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4862margin-left:1.0in;text-indent:-.25in;mso-list:l27 level1 lfo20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    63464863style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    6347 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6348 style='mso-fareast-font-family:"Times New Roman"'>Spot masks: occlude a circle
    6349 with a selected center and diameter in image coordinates (mm). <o:p></o:p></span></p>
     4864style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4865dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Spot
     4866masks: occlude a circle with a selected center and diameter in image
     4867coordinates (mm). <o:p></o:p></span></p>
    63504868
    63514869<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6352 margin-left:1.0in;text-indent:-.25in;mso-list:l27 level1 lfo32;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4870margin-left:1.0in;text-indent:-.25in;mso-list:l27 level1 lfo20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    63534871style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    6354 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6355 style='mso-fareast-font-family:"Times New Roman"'>Ring masks: occludes a
    6356 specific Bragg reflection (a ring placed relative to the image center). The
    6357 location and thickness of the ring are specified in degrees 2-theta. <o:p></o:p></span></p>
     4872style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4873dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Ring
     4874masks: occludes a specific Bragg reflection (a ring placed relative to the
     4875image center). The location and thickness of the ring are specified in degrees
     48762-theta. <o:p></o:p></span></p>
    63584877
    63594878<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6360 margin-left:1.0in;text-indent:-.25in;mso-list:l27 level1 lfo32;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4879margin-left:1.0in;text-indent:-.25in;mso-list:l27 level1 lfo20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    63614880style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    6362 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6363 style='mso-fareast-font-family:"Times New Roman"'>Arc masks: occlude a section
    6364 of a Bragg reflection, similar to a ring mask, except that in addition to the
    6365 location and thickness of the ring, the mask has a starting and ending
    6366 azimuthal angle. <o:p></o:p></span></p>
     4881style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4882dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Arc
     4883masks: occlude a section of a Bragg reflection, <span class=GramE>similar to</span>
     4884a ring mask, except that in addition to the location and thickness of the ring,
     4885the mask has a starting and ending azimuthal angle. <o:p></o:p></span></p>
    63674886
    63684887<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6369 margin-left:1.0in;text-indent:-.25in;mso-list:l27 level1 lfo32;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4888margin-left:1.0in;text-indent:-.25in;mso-list:l27 level1 lfo20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    63704889style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    6371 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6372 style='mso-fareast-font-family:"Times New Roman"'>Polygon masks: occlude an
    6373 arbitary region created by line segments joining a series of points specified
    6374 in image coordinates (mm). Pixels inside the polygon mask are not used for
    6375 integration. <o:p></o:p></span></p>
     4890style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4891dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Polygon
     4892masks: occlude an <span class=SpellE>arbitary</span> region created by line
     4893segments joining a series of points specified in image coordinates (mm). Pixels
     4894inside the polygon mask are not used for integration. <o:p></o:p></span></p>
    63764895
    63774896<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6378 margin-left:1.0in;text-indent:-.25in;mso-list:l27 level1 lfo32;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4897margin-left:1.0in;text-indent:-.25in;mso-list:l27 level1 lfo20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    63794898style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    6380 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6381 style='mso-fareast-font-family:"Times New Roman"'>The Frame mask: occludes an
    6382 arbitary region created by line segments joining a series of points specified
    6383 in image coordinates (mm). Typically a point is placed near each corner of the
    6384 image. Only pixels inside the frame mask are used for integration. Only one
    6385 frame mask can be defined. <o:p></o:p></span></p>
     4899style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4900dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>The
     4901Frame mask: occludes an <span class=SpellE>arbitary</span> region created by
     4902line segments joining a series of points specified in image coordinates (mm). <span
     4903class=GramE>Typically</span> a point is placed near each corner of the image.
     4904Only pixels inside the frame mask are used for integration. Only one frame mask
     4905can be defined. <o:p></o:p></span></p>
    63864906
    63874907<h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>What
     
    63974917
    63984918<p style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The
    6399 image is shown, as described above. Note that The frame mask, if defined, is
    6400 displayed in green, while the other types of masks are shown in red.</p>
     4919image is shown, as described above. Note that <span class=GramE>The</span>
     4920frame mask, if defined, is displayed in green, while the other types of masks
     4921are shown in red.</p>
    64014922
    64024923<h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>What
     
    64044925
    64054926<p style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>There
    6406 are menu commands to create masks as well as keyboard shortcuts. If a menu
    6407 command is used, then use left and right mouse clicks as described below. </p>
     4927are menu commands to create masks as well as keyboard shortcuts. If a menu command
     4928is used, then use left and right mouse clicks as described below. </p>
    64084929
    64094930<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6410 margin-left:1.5in;text-indent:-.25in;mso-list:l22 level1 lfo33;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4931margin-left:1.5in;text-indent:-.25in;mso-list:l22 level1 lfo21;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    64114932style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    6412 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6413 style='mso-fareast-font-family:"Times New Roman"'>Spot masks: <o:p></o:p></span></p>
     4933style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4934dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Spot
     4935masks: <o:p></o:p></span></p>
    64144936
    64154937<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Create
     
    64194941
    64204942<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6421 margin-left:2.2in;text-indent:-.25in;mso-list:l22 level2 lfo33;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4943margin-left:2.2in;text-indent:-.25in;mso-list:l22 level2 lfo21;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    64224944style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:"Courier New";
    64234945mso-fareast-font-family:"Courier New"'><span style='mso-list:Ignore'>o<span
    6424 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6425 style='mso-fareast-font-family:"Times New Roman"'>Press the 's' key and then
    6426 left-click successively on multiple locations for spot masks. Press the 's' key
    6427 again or <a href="#Mac_rightclick">right-click*</a> to stop adding spot masks. <o:p></o:p></span></p>
     4946style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp; </span></span></span><![endif]><span
     4947dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Press
     4948the 's' key and then <span class=GramE>left-click</span> successively on
     4949multiple locations for spot masks. Press the 's' key again or <a
     4950href="#Mac_rightclick">right-click*</a> to stop adding spot masks. <o:p></o:p></span></p>
    64284951
    64294952<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6430 margin-left:2.2in;text-indent:-.25in;mso-list:l22 level2 lfo33;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4953margin-left:2.2in;text-indent:-.25in;mso-list:l22 level2 lfo21;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    64314954style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:"Courier New";
    64324955mso-fareast-font-family:"Courier New"'><span style='mso-list:Ignore'>o<span
    6433 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6434 style='mso-fareast-font-family:"Times New Roman"'>Alternately, move the mouse
    6435 to the position for a new spot mask and press the 't' key. (Note that this can
    6436 be used while the plot is in Zoom or Pan mode.) <o:p></o:p></span></p>
     4956style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp; </span></span></span><![endif]><span
     4957dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Alternately,
     4958move the mouse to the position for a new spot mask and press the 't' key. (Note
     4959that this can be used while the plot is in Zoom or Pan mode.) <o:p></o:p></span></p>
    64374960
    64384961<p style='margin-left:1.95in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The
    6439 default size for newly-created spot masks is determined by the <tt><span
    6440 style='font-size:10.0pt'>Spot_mask_diameter</span></tt> <a href="#Preferences">configuration
    6441 variable</a> or 1.0 mm, if not specified. </p>
     4962default size for <span class=GramE>newly-created</span> spot masks is
     4963determined by the <span class=SpellE><tt><span style='font-size:10.0pt'>Spot_mask_diameter</span></tt></span>
     4964<a href="#Preferences">configuration variable</a> or 1.0 mm, if not specified. </p>
    64424965
    64434966<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Edit
    6444 Spot mask location</b> by left-clicking inside or on the edge the of the mask
    6445 and then drag the spot mask to a new location. </p>
     4967Spot mask location</b> by <span class=GramE>left-clicking</span> inside or on
     4968the edge the of the mask and then drag the spot mask to a new location. </p>
    64464969
    64474970<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Edit
     
    64504973
    64514974<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6452 margin-left:1.5in;text-indent:-.25in;mso-list:l22 level1 lfo33;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     4975margin-left:1.5in;text-indent:-.25in;mso-list:l22 level1 lfo21;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    64534976style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    6454 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6455 style='mso-fareast-font-family:"Times New Roman"'>Ring masks: <o:p></o:p></span></p>
     4977style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     4978dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Ring
     4979masks: <o:p></o:p></span></p>
    64564980
    64574981<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Create
     
    64614985
    64624986<p style='margin-left:1.95in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The
    6463 default thickness for newly-created ring masks is determined by the <tt><span
    6464 style='font-size:10.0pt'>Ring_mask_thickness</span></tt> <a href="#Preferences">configuration
    6465 variable</a> or 0.1 degrees (2theta) if not specified. </p>
     4987default thickness for <span class=GramE>newly-created</span> ring masks is
     4988determined by the <span class=SpellE><tt><span style='font-size:10.0pt'>Ring_mask_thickness</span></tt></span>
     4989<a href="#Preferences">configuration variable</a> or 0.1 degrees (2theta) if
     4990not specified. </p>
    64664991
    64674992<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Edit
    6468 Ring mask location</b> by left-clicking on either the inner or outer circle and
    6469 drag the circle to the new radius. </p>
     4993Ring mask location</b> by <span class=GramE>left-clicking</span> on either the
     4994inner or outer circle and drag the circle to the new radius. </p>
    64704995
    64714996<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Edit
    64724997Ring mask thickness</b> by <a href="#Mac_rightclick">right-clicking*</a> either
    6473 on the inner or outer circle and drag the the circle change spacing between the
    6474 inner and outer circle. </p>
     4998on the inner or outer circle and drag the <span class=SpellE>the</span> circle
     4999change spacing between the inner and outer circle. </p>
    64755000
    64765001<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6477 margin-left:1.5in;text-indent:-.25in;mso-list:l22 level1 lfo33;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     5002margin-left:1.5in;text-indent:-.25in;mso-list:l22 level1 lfo21;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    64785003style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    6479 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6480 style='mso-fareast-font-family:"Times New Roman"'>Arc masks: occludes a section
    6481 of a Bragg reflection, similar to a ring mask, except that in addition to the
    6482 location and thickness of the ring, the mask has a starting and ending
    6483 azimuthal angle. <o:p></o:p></span></p>
     5004style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     5005dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Arc
     5006masks: occludes a section of a Bragg reflection, <span class=GramE>similar to</span>
     5007a ring mask, except that in addition to the location and thickness of the ring,
     5008the mask has a starting and ending azimuthal angle. <o:p></o:p></span></p>
    64845009
    64855010<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Create
     
    64895014
    64905015<p style='margin-left:1.95in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The
    6491 default size for newly-created ring masks is determined by <a
    6492 href="#Preferences">configuration variables</a><br>
    6493 thickness: <tt><span style='font-size:10.0pt'>Ring_mask_thickness</span></tt>
     5016default size for <span class=GramE>newly-created</span> ring masks is
     5017determined by <a href="#Preferences">configuration variables</a><br>
     5018thickness: <span class=SpellE><tt><span style='font-size:10.0pt'>Ring_mask_thickness</span></tt></span>
    64945019(0.1 degrees 2theta if not specified) and <br>
    6495 azimuthal range: <tt><span style='font-size:10.0pt'>Arc_mask_azimuth</span></tt>
     5020azimuthal range: <span class=SpellE><tt><span style='font-size:10.0pt'>Arc_mask_azimuth</span></tt></span>
    64965021(10.0 degrees if not specified.) </p>
    64975022
    64985023<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Edit
    6499 Arc mask location</b> by left-clicking on either the inner or outer circle and
    6500 drag the circle to the new radius. Alternately, left-click on the upper or
    6501 lower arc limit (the straight lines) and drag them to rotate the center of the
    6502 arc azimuthal range to a new position. </p>
     5024Arc mask location</b> by <span class=GramE>left-clicking</span> on either the
     5025inner or outer circle and drag the circle to the new radius. Alternately, <span
     5026class=GramE>left-click</span> on the upper or lower arc limit (the straight
     5027lines) and drag them to rotate the center of the arc azimuthal range to a new
     5028position. </p>
    65035029
    65045030<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Edit
    65055031Arc mask thickness or range</b> by <a href="#Mac_rightclick">right-clicking*</a>
    6506 either on the inner or outer circle and drag the the circle change spacing
    6507 between the inner and outer circle. Alternately, <a href="#Mac_rightclick">right-click*</a>
    6508 on the upper or lower arc limit (the straight lines) and drag them to change
    6509 the arc azimuthal range. </p>
     5032either on the inner or outer circle and drag the <span class=SpellE>the</span>
     5033circle change spacing between the inner and outer circle. Alternately, <a
     5034href="#Mac_rightclick">right-click*</a> on the upper or lower arc limit (the
     5035straight lines) and drag them to change the arc azimuthal range. </p>
    65105036
    65115037<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6512 margin-left:1.5in;text-indent:-.25in;mso-list:l22 level1 lfo33;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     5038margin-left:1.5in;text-indent:-.25in;mso-list:l22 level1 lfo21;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    65135039style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    6514 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6515 style='mso-fareast-font-family:"Times New Roman"'>Polygon masks: occludes an
    6516 arbitary region created by line segments joining a series of points specified
    6517 in image coordinates (mm). Pixels inside the polygon mask are not used for
    6518 integration. <o:p></o:p></span></p>
     5040style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     5041dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>Polygon
     5042masks: occludes an <span class=SpellE>arbitary</span> region created by line
     5043segments joining a series of points specified in image coordinates (mm). Pixels
     5044inside the polygon mask are not used for integration. <o:p></o:p></span></p>
    65195045
    65205046<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Create
    6521 Polygon masks</b> with a menu command and then by left-clicking successively on
    6522 the vertices of the polygon shape surrounding pixels to be excluded. After the
    6523 last point is defined, <a href="#Mac_rightclick">right-click*</a> anywhere to
    6524 close the mask. Alternately, press the 'p' key and then left-click, as before,
    6525 to define the mask and <a href="#Mac_rightclick">right-click*</a> anywhere to
    6526 close the mask. </p>
     5047Polygon masks</b> with a menu command and then by <span class=GramE>left-clicking</span>
     5048successively on the vertices of the polygon shape surrounding pixels to be
     5049excluded. After the last point is defined, <a href="#Mac_rightclick">right-click*</a>
     5050anywhere to close the mask. Alternately, press the 'p' key and then left-click,
     5051as before, to define the mask and <a href="#Mac_rightclick">right-click*</a>
     5052anywhere to close the mask. </p>
    65275053
    65285054<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Edit
    6529 Polygon mask</b> by left-clicking on any point at a vertex in the polygon mask
    6530 and drag that point to a new position. If the vertex is dragged to the same
    6531 position as any other vertex in the mask the dragged point is deleted. </p>
     5055Polygon mask</b> by <span class=GramE>left-clicking</span> on any point at a
     5056vertex in the polygon mask and drag that point to a new position. If the vertex
     5057is dragged to the same position as any other vertex in the mask the dragged
     5058point is deleted. </p>
    65325059
    65335060<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Add
     
    65375064
    65385065<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    6539 margin-left:1.5in;text-indent:-.25in;mso-list:l22 level1 lfo33;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
     5066margin-left:1.5in;text-indent:-.25in;mso-list:l22 level1 lfo21;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    65405067style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    6541 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6542 style='mso-fareast-font-family:"Times New Roman"'>The Frame mask: occludes an
    6543 arbitary region created by line segments joining a series of points specified
    6544 in image coordinates (mm). Typically a point is placed near each corner of the
    6545 image. Only pixels inside the frame mask are used for integration. Only one
    6546 frame mask can be defined. <o:p></o:p></span></p>
     5068style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     5069dir=LTR></span><span style='mso-fareast-font-family:"Times New Roman"'>The
     5070Frame mask: occludes an <span class=SpellE>arbitary</span> region created by
     5071line segments joining a series of points specified in image coordinates (mm). <span
     5072class=GramE>Typically</span> a point is placed near each corner of the image.
     5073Only pixels inside the frame mask are used for integration. Only one frame mask
     5074can be defined. <o:p></o:p></span></p>
    65475075
    65485076<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Create
    6549 a Frame mask</b> with a menu command and then by left-clicking successively on
    6550 the vertices of a polygon. After the last point is defined, <a
     5077a Frame mask</b> with a menu command and then by <span class=GramE>left-clicking</span>
     5078successively on the vertices of a polygon. After the last point is defined, <a
    65515079href="#Mac_rightclick">right-click*</a> anywhere to close the frame mask.
    65525080Alternately, press the 'f' key and then left-click, as before, to define the
     
    65565084
    65575085<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Edit
    6558 the Frame mask</b> by left-clicking on any point at a vertex in the frame mask
    6559 and drag that point to a new position. If the vertex is dragged to the same
    6560 position as any other vertex in the mask the dragged point is deleted. </p>
     5086the Frame mask</b> by <span class=GramE>left-clicking</span> on any point at a
     5087vertex in the frame mask and drag that point to a new position. If the vertex
     5088is dragged to the same position as any other vertex in the mask the dragged
     5089point is deleted. </p>
    65615090
    65625091<p style='margin-left:1.75in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b>Add
     
    66015130
    66025131<div class=MsoNormal align=center style='text-align:center;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6603 style='mso-fareast-font-family:"Times New Roman"'>
    6604 
    6605 <hr size=2 width="100%" align=center>
     5132style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     5133
     5134<hr size=3 width="100%" align=center>
    66065135
    66075136</span></div>
    66085137
    66095138<div class=MsoNormal align=center style='text-align:center;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6610 style='mso-fareast-font-family:"Times New Roman"'>
    6611 
    6612 <hr size=2 width="100%" align=center>
     5139style='mso-fareast-font-family:"Times New Roman";mso-no-proof:yes'>
     5140
     5141<hr size=3 width="100%" align=center>
    66135142
    66145143</span></div>
     
    66195148
    66205149<p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6621 style='mso-fareast-font-family:"Times New Roman"'>When a phase is selected from
    6622 the <a href="#Data_tree"><span style='color:windowtext;text-decoration:none;
    6623 text-underline:none'>data tree</span></a>, parameters are shown for that
    6624 selected phase in a tabbed window. Clicking on each tab raises the windows
    6625 listed below. Each tab is identified by the underlined phrase in the following:</span><span
    6626 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    6627 text-underline:none'><o:p></o:p></span></span></p>
    6628 
    6629 <h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    6630 name=General>General Phase Parameters</a></h4>
    6631 
    6632 <span style='mso-bookmark:General'></span>
    6633 
    6634 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6635 style='mso-fareast-font-family:"Times New Roman"'>This gives overall parameters
    6636 describing the phase such as the name, space group, the unit cell parameters
    6637 and overall parameters for the atom present in the phase. It also has the
    6638 controls for Pawley intensity extraction and for computing Fourier maps for
    6639 this phase. It can also be used to compute new structures based on the unit
    6640 cell and atom poistions. <span class=MsoHyperlink><span style='color:windowtext;
    6641 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    6642 
    6643 <h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6644 style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<span
    6645 class=MsoHyperlink><span style='color:#4F4FFF;text-decoration:none;text-underline:
    6646 none'><o:p></o:p></span></span></span></h5>
    6647 
    6648 <p class=MsoListParagraph style='margin-left:1.0in;mso-add-space:auto;
    6649 text-indent:-.25in;mso-list:l2 level1 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6650 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    6651 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    6652 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:
    6653 normal'>Compute’</b> – The compute menu shows computations that are possible
    6654 for this phase. </span></p>
    6655 
    6656 <p class=MsoNormal style='margin-left:1.5in;mso-add-space:auto;text-indent:
    6657 -.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6658 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    6659 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b><span
    6660 style='mso-fareast-font-family:"Times New Roman"'>Fourier maps</span></b><span
    6661 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    6662 
    6663 <p class=MsoNormal style='margin-left:.5in;mso-add-space:auto;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6664 style='mso-fareast-font-family:"Times New Roman"'>compute Fourier maps according
    6665 to the controls set at bottom of General page.<o:p></o:p></span></p>
    6666 
    6667 <p class=MsoNormal style='margin-left:1.5in;mso-add-space:auto;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    6668 style='mso-fareast-font-family:"Times New Roman"'>Search maps</span></b><span
    6669 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    6670 
    6671 <p class=MsoNormal style='margin-left:.5in;mso-add-space:auto;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6672 style='mso-fareast-font-family:"Times New Roman"'>search the computed Fourier
    6673 map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this
    6674 procedure; they will be printed on the console and will be shown in the ‘<a
    6675 href="Map_peaks">Map peaks</a>’ page. This page will immediately be shown and
    6676 the peaks will be shown on the structure drawing for this phase as white 3-D
    6677 crosses.<o:p></o:p></span></p>
    6678 
    6679 <p class=MsoNormal style='margin-left:1.5in;mso-add-space:auto;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    6680 style='mso-fareast-font-family:"Times New Roman"'>Charge flipping </span></b><span
    6681 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    6682 
    6683 <p class=MsoNormal style='margin-left:.5in;mso-add-space:auto;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6684 style='mso-fareast-font-family:"Times New Roman"'>This performs a charge
    6685 flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution
    6686 using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You
    6687 will need to select a source for the reflection set and perhaps select an
    6688 element for normalization by its form factor, a resolution limit (usually 0.5A)
    6689 and a charge flip threshold (usually 0.1); these are found at the bottom of the
    6690 <b style='mso-bidi-font-weight:normal'>General</b> window. A progress bar
    6691 showing the charge flip residual is shown while the charge flip is in
    6692 operation. When the residual is no longer decreasing (be patient – it doesn’t
    6693 necessarily fall continuously), press the <b style='mso-bidi-font-weight:normal'>Cancel</b>
    6694 button to stop the charge flipping. The resulting map will be positioned to
    6695 properly place symmetry operators (NB: depends on the quality of the resulting
    6696 phases), searched for peaks and the display shifts to <b style='mso-bidi-font-weight:
    6697 normal'>Map peaks</b> to show them.<o:p></o:p></span></p>
    6698 
    6699 <p class=MsoNormal style='margin-left:1.5in;mso-add-space:auto;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    6700 style='mso-fareast-font-family:"Times New Roman"'>Clear map </span></b><span
    6701 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    6702 
    6703 <p class=MsoNormal style='margin-left:.5in;mso-add-space:auto;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6704 style='mso-fareast-font-family:"Times New Roman"'>This clears any
    6705 Fourier/charge flip map from memory; the Fourier map controls are also cleared.<o:p></o:p></span></p>
    6706 
    6707 <p class=MsoNormal style='margin-left:1.5in;mso-add-space:auto;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    6708 style='mso-fareast-font-family:"Times New Roman"'>Transform</span></b><span
    6709 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    6710 
    6711 <p class=MsoNormal style='margin-left:.5in;mso-add-space:auto;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6712 style='mso-fareast-font-family:"Times New Roman"'>This allows for a change in
    6713 axes, symmetry or unit cell. It is also used to create a magnetic phase from a
    6714 chemical (nuclear) phase. One important transformation that can be done here is
    6715 for Origin 1 settings to Origin 2 (<a href="#Origin1">described below</a>) <o:p></o:p></span></p>
    6716 
    6717 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    6718 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    6719 text-underline:none'><o:p>&nbsp;</o:p></span></span></p>
    6720 
    6721 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    6722 text-indent:-.25in;mso-list:l2 level1 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6723 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6724 color:windowtext;text-decoration:none;text-underline:none'><span
    6725 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6726 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    6727 "Times New Roman"'>The items in the upper part of the General page that can be changed
    6728 are Phase name, Phase type, Space group, unit cell parameters &amp; refine
    6729 flag. These are described in turn:<span class=MsoHyperlink><span
    6730 style='color:windowtext'><o:p></o:p></span></span></span></p>
    6731 
    6732 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    6733 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6734 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6735 color:windowtext;text-decoration:none;text-underline:none'><span
    6736 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6737 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    6738 style='mso-fareast-font-family:"Times New Roman"'>Phase name</span></b><span
    6739 style='mso-fareast-font-family:"Times New Roman"'> – this is the name assigned to
    6740 this phase. It should only be changed when the phase is initialized or
    6741 imported.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    6742 
    6743 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    6744 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6745 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6746 color:windowtext;text-decoration:none;text-underline:none'><span
    6747 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6748 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    6749 style='mso-fareast-font-family:"Times New Roman"'>Phase type – </span></b><span
    6750 style='mso-fareast-font-family:"Times New Roman"'>this can only be set when
    6751 there are no atoms in the Atoms page for this phase. Select it when the phase
    6752 is initialized.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    6753 
    6754 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    6755 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6756 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6757 color:windowtext;text-decoration:none;text-underline:none'><span
    6758 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6759 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    6760 style='mso-fareast-font-family:"Times New Roman"'>Space group</span></b><span
    6761 style='mso-fareast-font-family:"Times New Roman"'> – this should be set when the
    6762 phase is initialized; it can be changed later. Be careful about the impact on
    6763 Atom site symmetry and multiplicity if you do. GSAS-II will recognize any legal
    6764 space group symbol using the short Hermann-Mauguin forms; put a space between
    6765 the axial fields (e.g. ‘F d 3 m’ not ‘Fd3m’). For space groups with a choice of
    6766 origin (e.g. F d 3 m), GSAS-II always uses the 2<sup>nd</sup> setting where the
    6767 center of inversion is located at the origin. The choice of space group will
    6768 set the available unit cell parameters.<span class=MsoHyperlink><span
    6769 style='color:windowtext'><o:p></o:p></span></span></span></p>
    6770 
    6771 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    6772 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6773 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    6774 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    6775 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Refine
    6776 unit cell</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    6777 set this flag to refine the unit cell parameters in a Rietveld or Pawley
    6778 refinement. The actual parameters refined are the symmetry allowed terms (A<sub>0</sub>-A<sub>5</sub>)
    6779 in the expression</span><i style='mso-bidi-font-style:normal'><span
    6780 style='font-family:"Cambria Math",serif;mso-fareast-font-family:"Times New Roman"'><br>
    6781 </span></i><!--[if gte msEquation 12]><m:oMathPara><m:oMath><m:sSup><m:sSupPr><span
    6782     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    6783     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    6784     normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style:
    6785     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6786     "Times New Roman"'><m:r>d</m:r></span></i></m:e><m:sup><i style='mso-bidi-font-style:
    6787     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6788     "Times New Roman"'><m:r>*2</m:r></span></i></m:sup></m:sSup><i
    6789   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
    6790   mso-fareast-font-family:"Times New Roman"'><m:r>=</m:r></span></i><m:sSub><m:sSubPr><span
    6791     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    6792     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    6793     normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style:
    6794     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6795     "Times New Roman"'><m:r>A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style:
    6796     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6797     "Times New Roman"'><m:r>0</m:r></span></i></m:sub></m:sSub><m:sSup><m:sSupPr><span
    6798     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    6799     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    6800     normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style:
    6801     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6802     "Times New Roman"'><m:r>h</m:r></span></i></m:e><m:sup><i style='mso-bidi-font-style:
    6803     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6804     "Times New Roman"'><m:r>2</m:r></span></i></m:sup></m:sSup><i
    6805   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
    6806   mso-fareast-font-family:"Times New Roman"'><m:r>+</m:r></span></i><m:sSub><m:sSubPr><span
    6807     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    6808     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    6809     normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style:
    6810     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6811     "Times New Roman"'><m:r>A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style:
    6812     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6813     "Times New Roman"'><m:r>1</m:r></span></i></m:sub></m:sSub><m:sSup><m:sSupPr><span
    6814     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    6815     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    6816     normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style:
    6817     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6818     "Times New Roman"'><m:r>k</m:r></span></i></m:e><m:sup><i style='mso-bidi-font-style:
    6819     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6820     "Times New Roman"'><m:r>2</m:r></span></i></m:sup></m:sSup><i
    6821   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
    6822   mso-fareast-font-family:"Times New Roman"'><m:r>+</m:r></span></i><m:sSub><m:sSubPr><span
    6823     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    6824     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    6825     normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style:
    6826     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6827     "Times New Roman"'><m:r>A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style:
    6828     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6829     "Times New Roman"'><m:r>2</m:r></span></i></m:sub></m:sSub><m:sSup><m:sSupPr><span
    6830     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    6831     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    6832     normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style:
    6833     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6834     "Times New Roman"'><m:r>l</m:r></span></i></m:e><m:sup><i style='mso-bidi-font-style:
    6835     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6836     "Times New Roman"'><m:r>2</m:r></span></i></m:sup></m:sSup><i
    6837   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
    6838   mso-fareast-font-family:"Times New Roman"'><m:r>+</m:r></span></i><m:sSub><m:sSubPr><span
    6839     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    6840     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    6841     normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style:
    6842     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6843     "Times New Roman"'><m:r>A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style:
    6844     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6845     "Times New Roman"'><m:r>3</m:r></span></i></m:sub></m:sSub><i
    6846   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
    6847   mso-fareast-font-family:"Times New Roman"'><m:r>h</m:r><m:r>k</m:r><m:r>+</m:r></span></i><m:sSub><m:sSubPr><span
    6848     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    6849     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    6850     normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style:
    6851     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6852     "Times New Roman"'><m:r>A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style:
    6853     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6854     "Times New Roman"'><m:r>4</m:r></span></i></m:sub></m:sSub><i
    6855   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
    6856   mso-fareast-font-family:"Times New Roman"'><m:r>h</m:r><m:r>l</m:r><m:r>+</m:r></span></i><m:sSub><m:sSubPr><span
    6857     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    6858     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    6859     normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style:
    6860     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6861     "Times New Roman"'><m:r>A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style:
    6862     normal'><span style='font-family:"Cambria Math",serif;mso-fareast-font-family:
    6863     "Times New Roman"'><m:r>5</m:r></span></i></m:sub></m:sSub><i
    6864   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
    6865   mso-fareast-font-family:"Times New Roman"'><m:r>kl</m:r></span></i></m:oMath></m:oMathPara><![endif]--><![if !msEquation]><span
    6866 style='font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-font-family:
    6867 "Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US;
    6868 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
    6869  id="_x0000_i1025" type="#_x0000_t75" style='width:251.25pt;height:14.25pt'>
    6870  <v:imagedata src="gsasII_files/image003.png" o:title="" chromakey="white"/>
    6871 </v:shape><![endif]--><![if !vml]><img width=335 height=19
    6872 src="gsasII_files/image048.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
    6873 
    6874 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    6875 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6876 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6877 color:windowtext;text-decoration:none;text-underline:none'><span
    6878 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6879 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    6880 style='mso-fareast-font-family:"Times New Roman"'>a, b, c, alpha, beta, gamma</span></b><span
    6881 style='mso-fareast-font-family:"Times New Roman"'> – lattice parameters; only
    6882 those permitted by the space group are shown. The volume<span
    6883 style='mso-spacerun:yes'>  </span>is computed from the values entered.</span><span
    6884 class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></p>
    6885 
    6886 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    6887 auto;text-indent:-.25in;mso-list:l2 level1 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6888 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6889 color:windowtext;text-decoration:none;text-underline:none'><span
    6890 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6891 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    6892 "Times New Roman"'>If there are entries in the Atoms page then the Elements
    6893 table is shown next on the General page; you may select the isotope (only relevant
    6894 for neutron diffraction experiments). The density (just above the Elements) is
    6895 computed depending on this choice, the unit cell volume and the atom
    6896 fractions/site multiplicities in the entries on the Atoms page.<span
    6897 class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    6898 
    6899 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    6900 auto;text-indent:-.25in;mso-list:l2 level1 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6901 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6902 color:windowtext;text-decoration:none;text-underline:none'><span
    6903 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6904 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    6905 "Times New Roman"'>Next are the Pawley controls.<span class=MsoHyperlink><span
    6906 style='color:windowtext'><o:p></o:p></span></span></span></p>
    6907 
    6908 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    6909 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6910 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6911 color:windowtext;text-decoration:none;text-underline:none'><span
    6912 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6913 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    6914 style='mso-fareast-font-family:"Times New Roman"'>Do Pawley refinement?</span></b><span
    6915 style='mso-fareast-font-family:"Times New Roman"'> – This must be chosen to
    6916 perform a Pawley refinement as opposed to a Rietveld refinement for this phase.
    6917 <b style='mso-bidi-font-weight:normal'>NB:</b> you probably should clear the <b
    6918 style='mso-bidi-font-weight:normal'>Histogram scale factor</b> refinement flag
    6919 (found in <b style='mso-bidi-font-weight:normal'>Sample parameters</b> for the
    6920 powder data set) as it cannot be refined simultaneously with the Pawley
    6921 reflection intensities.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    6922 
    6923 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    6924 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6925 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6926 color:windowtext;text-decoration:none;text-underline:none'><span
    6927 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6928 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    6929 style='mso-fareast-font-family:"Times New Roman"'>Pawley dmin</span></b><span
    6930 style='mso-fareast-font-family:"Times New Roman"'> – This is the minimum
    6931 d-spacing to be used in a Pawley refinement. <b style='mso-bidi-font-weight:
    6932 normal'>NB:</b> be sure to set this to match the minimum d-spacing indicated by
    6933 the powder pattern limits (see <b style='mso-bidi-font-weight:normal'>Limits</b>
    6934 for the powder data set).<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    6935 
    6936 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    6937 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6938 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6939 color:windowtext;text-decoration:none;text-underline:none'><span
    6940 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6941 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    6942 style='mso-fareast-font-family:"Times New Roman"'>Pawley neg. wt.</span></b><span
    6943 style='mso-fareast-font-family:"Times New Roman"'> – This is the weight for a
    6944 penalty function applied during a Pawley refinement on resulting negative
    6945 intensities. Use with caution; initially try very small values (e.g. .01). A
    6946 value of zero means no penalty is applied.<span class=MsoHyperlink><span
    6947 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    6948 
    6949 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    6950 auto;text-indent:-.25in;mso-list:l2 level1 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6951 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6952 color:windowtext;text-decoration:none;text-underline:none'><span
    6953 style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6954 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    6955 "Times New Roman"'>Fourier map controls are shown next on the General page. A
    6956 completed Rietveld or Pawley refinement is required before a Fourier map can be
    6957 computed. Select the desired type of map, the source of the reflection set and
    6958 the map resolution desired. The peak cutoff is defined as a percentage of the
    6959 maximum and defines the lowest level considered in the peak search.<span
    6960 class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    6961 
    6962 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    6963 auto;text-indent:-.25in;mso-list:l2 level1 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6964 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6965 color:windowtext;text-decoration:none;text-underline:none'><span
    6966 style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6967 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
    6968 "Times New Roman"'>Charge flip controls are below the Fourier map controls.<span
    6969 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    6970 text-underline:none'><o:p></o:p></span></span></span></p>
    6971 
    6972 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    6973 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6974 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6975 color:windowtext;text-decoration:none;text-underline:none'><span
    6976 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6977 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    6978 style='mso-fareast-font-family:"Times New Roman"'>Reflection set from</span></b><span
    6979 style='mso-fareast-font-family:"Times New Roman"'> – This is the source of
    6980 structure factors to be used in a charge flip calculation. These may be either
    6981 a single crystal data set, or structure factors extracted from a powder pattern
    6982 via a Pawley refinement or a Rietveld refinement.<span class=MsoHyperlink><span
    6983 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    6984 
    6985 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    6986 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    6987 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    6988 color:windowtext;text-decoration:none;text-underline:none'><span
    6989 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6990 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    6991 style='mso-fareast-font-family:"Times New Roman"'>Normalizing element </span></b><span
    6992 style='mso-fareast-font-family:"Times New Roman"'>– This is an element form
    6993 factor chosen to normalize the structure factors before charge flipping. <b
    6994 style='mso-bidi-font-weight:normal'>None</b> (the default) can be selected from
    6995 the lower right of the Periodic Table display shown when this is selected.<span
    6996 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    6997 text-underline:none'><o:p></o:p></span></span></span></p>
    6998 
    6999 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    7000 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7001 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    7002 color:windowtext;text-decoration:none;text-underline:none'><span
    7003 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7004 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    7005 style='mso-fareast-font-family:"Times New Roman"'>Resolution </span></b><span
    7006 style='mso-fareast-font-family:"Times New Roman"'>– This is the resolution of
    7007 the charge flip map; default is 0.5A. The set of reflections is expanded to a
    7008 full sphere and zero filled to this resolution limit; this suite of reflections
    7009 is then used for charge flipping.<span class=MsoHyperlink><span
    7010 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    7011 
    7012 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    7013 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7014 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    7015 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    7016 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>k-Factor</span></b><span
    7017 style='mso-fareast-font-family:"Times New Roman"'> – This is the threshold on
    7018 the density map, all densities below this are charge flipped.</span></p>
    7019 
    7020 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    7021 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7022 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    7023 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    7024 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>k-Max</span></b><span
    7025 style='mso-fareast-font-family:"Times New Roman"'> – This is an upper threshold
    7026 on the density may; all densities above this are charge flipped. In this way
    7027 the “uranium solution” problem is avoided. Use k-Max = 10-12 for equal atom
    7028 problems and larger for heavy atom ones.<o:p></o:p></span></p>
    7029 
    7030 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    7031 auto;text-indent:-.25in;mso-list:l2 level1 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7032 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>7.<span
    7033 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    7034 style='mso-fareast-font-family:"Times New Roman"'>Monte Carlo/Simulated
    7035 Annealing controls are at the bottom of the window. (Future capability &amp;
    7036 under development).<o:p></o:p></span></p>
    7037 
    7038 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    7039 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7040 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    7041 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    7042 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Reflection
    7043 set from</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    7044 This is the source of structure factors to be used in a charge flip
    7045 calculation. These may be either a single crystal data set, or structure
    7046 factors extracted from a powder pattern via a Pawley refinement or a Rietveld
    7047 refinement.<o:p></o:p></span></p>
    7048 
    7049 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    7050 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7051 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    7052 color:windowtext;text-decoration:none;text-underline:none'><span
    7053 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7054 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    7055 style='mso-fareast-font-family:"Times New Roman"'>d-min </span></b><span
    7056 style='mso-fareast-font-family:"Times New Roman"'>- This restricts the set of
    7057 reflections to be used in the MC/SA run.</span><span class=MsoHyperlink><span
    7058 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></p>
    7059 
    7060 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    7061 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7062 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    7063 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    7064 class=MsoHyperlink><b style='mso-bidi-font-weight:normal'><span
    7065 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
    7066 none;text-underline:none'>MC/SA algorithm</span></b></span><span
    7067 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    7068 color:windowtext;text-decoration:none;text-underline:none'> – This selects the
    7069 type of jump to be used for each MC/SA trial.</span></span></p>
    7070 
    7071 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    7072 auto;text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7073 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    7074 color:windowtext;text-decoration:none;text-underline:none'><span
    7075 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7076 </span></span></span></span><![endif]><span class=MsoHyperlink><b
    7077 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman";
    7078 color:windowtext;text-decoration:none;text-underline:none'>Annealing schedule</span></b></span><span
    7079 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    7080 color:windowtext;text-decoration:none;text-underline:none'> – This selects the
    7081 beginning MC/SA “temperature”, final “temperature”, slope and number of trials
    7082 at each step.<o:p></o:p></span></span></p>
    7083 
    7084 <p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto;
    7085 text-indent:-.25in;mso-list:l2 level2 lfo35;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7086 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    7087 color:windowtext;text-decoration:none;text-underline:none'><span
    7088 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7089 </span></span></span></span><![endif]><span class=MsoHyperlink><b
    7090 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman";
    7091 color:windowtext;text-decoration:none;text-underline:none'>A-jump &amp; B-jump</span></b></span><span
    7092 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    7093 color:windowtext;text-decoration:none;text-underline:none'> – If the “Tremayne”
    7094 algorithm is chosen these determine the jump components for each trial.<o:p></o:p></span></span></p>
    7095 
    7096 <h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    7097 name=Origin1></a>Origin 1 -&gt; Origin 2 Transformations</h5>
    7098 
    7099 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7100 style='mso-fareast-font-family:"Times New Roman"'>An important transformation
    7101 may be needed in certain cases when space groups that two alternate origin
    7102 settings (<a
    7103 href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#GSASIIspc.spg2origins">listed
    7104 here</a>). These are centrosymmetric space groups where the highest symmetry
    7105 point in the structure does not contain a center of symmetry. Origin 1 places
    7106 the origin at the highest symmetry setting while Origin 2 places the origin at
    7107 a center of symmetry (creating a -x,-y,-z symmetry operator, which means that
    7108 reflection phases can only be 0 or π.) GSAS-II requires use of the Origin 2
    7109 settings because computations are much faster and simpler without complex
    7110 structure factors. Alas, the literature contains a number of structures
    7111 reported in Origin 1, where the origin choice may not be clearly communicated.
    7112 (The CIF standard does not require that origin choice be indicated.) When a
    7113 structure is imported that uses any of the space groups where an origin choice
    7114 is possible, a message is shown in GSAS-II notifying the user that they must
    7115 confirm that the origin choice is correct. <o:p></o:p></span></p>
    7116 
    7117 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    7118 style='mso-fareast-font-family:"Times New Roman"'>Example:</span></b><span
    7119 style='mso-fareast-font-family:"Times New Roman"'> An example of what can go
    7120 wrong is illustrated with the structure of anatase. The space group is <i>I</i>
    7121 4<sub>1</sub>/<i>a m d</i>. In Origin 1 the coordinates are: <o:p></o:p></span></p>
    7122 
    7123 <table class=MsoNormalTable border=0 cellpadding=0 style='mso-cellspacing:1.5pt;
    7124  margin-left:3.0in;mso-yfti-tbllook:1184'>
    7125  <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
    7126   <td colspan=4 style='padding:.75pt .75pt .75pt .75pt'>
    7127   <p class=MsoNormal align=center style='text-align:center'><b><span
    7128   style='mso-fareast-font-family:"Times New Roman"'>Origin 1<o:p></o:p></span></b></p>
    7129   </td>
    7130  </tr>
    7131  <tr style='mso-yfti-irow:1'>
    7132   <td style='padding:.75pt .75pt .75pt .75pt'>
    7133   <p class=MsoNormal align=center style='text-align:center'><b><span
    7134   style='mso-fareast-font-family:"Times New Roman"'>atom<o:p></o:p></span></b></p>
    7135   </td>
    7136   <td colspan=3 style='padding:.75pt .75pt .75pt .75pt'>
    7137   <p class=MsoNormal align=center style='text-align:center'><b><span
    7138   style='mso-fareast-font-family:"Times New Roman"'>coordinates<o:p></o:p></span></b></p>
    7139   </td>
    7140  </tr>
    7141  <tr style='mso-yfti-irow:2'>
    7142   <td style='padding:.75pt .75pt .75pt .75pt'>
    7143   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Ti<o:p></o:p></span></p>
    7144   </td>
    7145   <td style='padding:.75pt .75pt .75pt .75pt'>
    7146   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>0<o:p></o:p></span></p>
    7147   </td>
    7148   <td style='padding:.75pt .75pt .75pt .75pt'>
    7149   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>0<o:p></o:p></span></p>
    7150   </td>
    7151   <td style='padding:.75pt .75pt .75pt .75pt'>
    7152   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>0<o:p></o:p></span></p>
    7153   </td>
    7154  </tr>
    7155  <tr style='mso-yfti-irow:3;mso-yfti-lastrow:yes'>
    7156   <td style='padding:.75pt .75pt .75pt .75pt'>
    7157   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>O<o:p></o:p></span></p>
    7158   </td>
    7159   <td style='padding:.75pt .75pt .75pt .75pt'>
    7160   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>0<o:p></o:p></span></p>
    7161   </td>
    7162   <td style='padding:.75pt .75pt .75pt .75pt'>
    7163   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>0<o:p></o:p></span></p>
    7164   </td>
    7165   <td style='padding:.75pt .75pt .75pt .75pt'>
    7166   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>0.208<o:p></o:p></span></p>
    7167   </td>
    7168  </tr>
    7169 </table>
    7170 
    7171 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7172 style='mso-fareast-font-family:"Times New Roman";color:white;mso-color-alt:
    7173 windowtext'>and in Origin 2 the coordinates are: </span><span style='mso-fareast-font-family:
    7174 "Times New Roman"'><o:p></o:p></span></p>
    7175 
    7176 <table class=MsoNormalTable border=0 cellpadding=0 style='mso-cellspacing:1.5pt;
    7177  margin-left:3.0in;mso-yfti-tbllook:1184'>
    7178  <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
    7179   <td colspan=4 style='padding:.75pt .75pt .75pt .75pt'>
    7180   <p class=MsoNormal align=center style='text-align:center'><b><span
    7181   style='mso-fareast-font-family:"Times New Roman"'>Origin 2<o:p></o:p></span></b></p>
    7182   </td>
    7183  </tr>
    7184  <tr style='mso-yfti-irow:1'>
    7185   <td style='padding:.75pt .75pt .75pt .75pt'>
    7186   <p class=MsoNormal align=center style='text-align:center'><b><span
    7187   style='mso-fareast-font-family:"Times New Roman"'>atom<o:p></o:p></span></b></p>
    7188   </td>
    7189   <td colspan=3 style='padding:.75pt .75pt .75pt .75pt'>
    7190   <p class=MsoNormal align=center style='text-align:center'><b><span
    7191   style='mso-fareast-font-family:"Times New Roman"'>coordinates<o:p></o:p></span></b></p>
    7192   </td>
    7193  </tr>
    7194  <tr style='mso-yfti-irow:2'>
    7195   <td style='padding:.75pt .75pt .75pt .75pt'>
    7196   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Ti<o:p></o:p></span></p>
    7197   </td>
    7198   <td style='padding:.75pt .75pt .75pt .75pt'>
    7199   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>0<o:p></o:p></span></p>
    7200   </td>
    7201   <td style='padding:.75pt .75pt .75pt .75pt'>
    7202   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1/4<o:p></o:p></span></p>
    7203   </td>
    7204   <td style='padding:.75pt .75pt .75pt .75pt'>
    7205   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>-1/8<o:p></o:p></span></p>
    7206   </td>
    7207  </tr>
    7208  <tr style='mso-yfti-irow:3;mso-yfti-lastrow:yes'>
    7209   <td style='padding:.75pt .75pt .75pt .75pt'>
    7210   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>O<o:p></o:p></span></p>
    7211   </td>
    7212   <td style='padding:.75pt .75pt .75pt .75pt'>
    7213   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>0<o:p></o:p></span></p>
    7214   </td>
    7215   <td style='padding:.75pt .75pt .75pt .75pt'>
    7216   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1/4<o:p></o:p></span></p>
    7217   </td>
    7218   <td style='padding:.75pt .75pt .75pt .75pt'>
    7219   <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>0.083<o:p></o:p></span></p>
    7220   </td>
    7221  </tr>
    7222 </table>
    7223 
    7224 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7225 style='mso-fareast-font-family:"Times New Roman";color:white;mso-color-alt:
    7226 windowtext'>where the origin is shifted by (0,0.25,-0.125). </span><span
    7227 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    7228 
    7229 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><!--[if gte vml 1]><v:shape
    7230  id="Picture_x0020_3" o:spid="_x0000_s1027" type="#_x0000_t75" style='position:absolute;
    7231  left:0;text-align:left;margin-left:190.3pt;margin-top:0;width:241.5pt;
    7232  height:142.5pt;z-index:251658752;visibility:visible;mso-wrap-style:square;
    7233  mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:0;
    7234  mso-wrap-distance-top:0;mso-wrap-distance-right:0;mso-wrap-distance-bottom:0;
    7235  mso-position-horizontal:right;mso-position-horizontal-relative:text;
    7236  mso-position-vertical:absolute;mso-position-vertical-relative:line;
    7237  mso-width-percent:0;mso-height-percent:0;mso-width-relative:page;
    7238  mso-height-relative:page' o:allowoverlap="f">
    7239  <v:imagedata src="gsasII_files/wrong.png"/>
    7240  <w:wrap type="square" anchory="line"/>
    7241 </v:shape><![endif]--><![if !vml]><img width=322 height=190
    7242 src="gsasII_files/wrong.png" align=right v:shapes="Picture_x0020_3"><![endif]><span
    7243 style='mso-fareast-font-family:"Times New Roman"'>Since GSAS-II always the
    7244 symmetry operators for Origin 2, if structure is input incorrectly with the
    7245 coordinates set for Origin 1, there are several fairly obvious signs of
    7246 problems: (1) the site symmetries and multiplicities are wrong, often giving an
    7247 incorrect chemical formula, (2) the interatomic distances are incorrect, and
    7248 (3) a plot of the structure is improbable. In this case incorrect
    7249 multiplicities gives rise to a density of 7.9 g/cc, double the correct value.
    7250 Impossible interatomic distances of 1.88Å for Ti-Ti, and 1.39Å for Ti-O are
    7251 seen. The unit cell contents with the wrong space group operators is shown to
    7252 the right. <o:p></o:p></span></p>
    7253 
    7254 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7255 style='mso-fareast-font-family:"Times New Roman"'>With coordinates that match
    7256 the space group operations, the correct Ti-O distances are 1.92Å and 1.97Å and
    7257 the shortest Ti-Ti distance is 3.0Å. (Note that interatomic distances can be
    7258 computed in GSAS-II using the Phase Atoms tab and the Compute/&quot;Show
    7259 Distances &amp; Angles&quot; menu item.) <o:p></o:p></span></p>
    7260 
    7261 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><!--[if gte vml 1]><v:shape
    7262  id="Picture_x0020_4" o:spid="_x0000_s1026" type="#_x0000_t75" style='position:absolute;
    7263  left:0;text-align:left;margin-left:221.8pt;margin-top:0;width:273pt;height:339.75pt;
    7264  z-index:251659776;visibility:visible;mso-wrap-style:square;
    7265  mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:0;
    7266  mso-wrap-distance-top:0;mso-wrap-distance-right:0;mso-wrap-distance-bottom:0;
    7267  mso-position-horizontal:right;mso-position-horizontal-relative:text;
    7268  mso-position-vertical:absolute;mso-position-vertical-relative:line;
    7269  mso-width-percent:0;mso-height-percent:0;mso-width-relative:page;
    7270  mso-height-relative:page' o:allowoverlap="f">
    7271  <v:imagedata src="gsasII_files/xform.png"/>
    7272  <w:wrap type="square" anchory="line"/>
    7273 </v:shape><![endif]--><![if !vml]><img width=364 height=1
    7274 src="gsasII_files/xform.png" align=right v:shapes="Picture_x0020_4"><![endif]><b><span
    7275 style='mso-fareast-font-family:"Times New Roman"'>Transform Origin:</span></b><span
    7276 style='mso-fareast-font-family:"Times New Roman"'> To transform a space group
    7277 setting from Origin setting 1 to 2, use the Transform option in the Compute
    7278 menu and then select the last option in the &quot;Common transformations&quot;
    7279 pulldown menu, which will be setting 1-&gt;2 for space groups where both
    7280 origins are available, as shown to the right. The transformation matrix will be
    7281 set to the identity and the &quot;V&quot; vector will have the required origin
    7282 shift loaded. Press OK. The changes can be seen by selecting the Atoms tab. </span></p>
    7283 
    7284 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7285 style='mso-fareast-font-family:"Times New Roman"'><br clear=right
    7286 style='mso-special-character:line-break'>
    7287 <o:p></o:p></span></p>
    7288 
    7289 <h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    7290 name=Data></a><u>Data</u></h4>
    7291 
    7292 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>This
    7293 tab serves several purposes. It is used to link histograms to the selected
    7294 phase and it allows the values and refinement flags to be set for the
    7295 parameters that are defined for each histogram-phase pair, labeled as HAP
    7296 parameters. [Note that some GSAS-II parameters are defined for each phase
    7297 (atomic positions, for example), other parameters are defined for each histogram
    7298 (scale factors and instrumental constants, for example) but the HAP parameters
    7299 have values for each histogram in each phase.] It can also be used to show a
    7300 graphical representation of an HAP parameter set.</p>
    7301 
    7302 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The
    7303 HAP parameters include: the phase fraction; the sample contribution to peak
    7304 broadening: microstrain and crystallite size; a LeBail intensity extraction
    7305 flag; hydrostatic/elastic strain shifts to lattice parameters; corrections to
    7306 peak intensities due to experimental effects (preferred orientation, extinction
    7307 and disordered solvents).</p>
    7308 
    7309 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    7310 style='mso-fareast-font-family:"Times New Roman"'>Use flag</span></b><span
    7311 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    7312 
    7313 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7314 style='mso-fareast-font-family:"Times New Roman"'>When the Use flag is
    7315 selected, the currently selected phase is used to compute intensities as a
    7316 contribution to the selected histogram (single-crystal histograms can have only
    7317 one phase; powder histograms can have any number of associated phases). When
    7318 not set, the phase is not present in the selected histogram. <o:p></o:p></span></p>
    7319 
    7320 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    7321 style='mso-fareast-font-family:"Times New Roman"'>Phase fraction</span></b><span
    7322 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    7323 
    7324 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7325 style='mso-fareast-font-family:"Times New Roman"'>used in powder histograms: a
    7326 multiplier that determines the relative amount of the selected phase to a
    7327 histogram. Note that when the histogram scale factor is varied, these values
    7328 are on a relative scale. Conventional practice it to vary the scale factor and
    7329 to not vary the phase fraction for one phase in a histogram. Do not refine the
    7330 scale factor and all phase fractions unless a constraint is defined so the
    7331 phase fractions add to 1. <o:p></o:p></span></p>
    7332 
    7333 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    7334 style='mso-fareast-font-family:"Times New Roman"'>Crystallite size peak
    7335 broadening</span></b><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    7336 
    7337 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7338 style='mso-fareast-font-family:"Times New Roman"'>is computed from size
    7339 factor(s) in microns (10<sup>-6</sup> m), with the Scherrer constant assumed as
    7340 unity. Sizes can be computed in three ways: isotropic, uniaxial and
    7341 ellipsoidal. In isotropic broadening, crystallites are assumed to average as
    7342 uniform in all directions and a single size value is supplied; with uniaxial
    7343 broadening, a preferred direction (as a crystallographic axis, such as 0,0,1 is
    7344 supplied) -- note that for most crystal systems only one axis makes sense --
    7345 and two size parameters are defined, one for along the axis and one for in the
    7346 perpendicular plane; with ellipsoidal, six terms are used to define a
    7347 broadening tensor that has arbitrary orientation -- this model may require
    7348 constraints and is seldomly needed. Note that size broadening is usually
    7349 Lorentzian, which corresponds to a LGmix value of 1.0; if this value is between
    7350 0. and 1., both Gaussian and Lorentz size broadening is modeled and a value of
    7351 0.0 is pure Gaussian. Values less than 0. or greater than 1. make no physical
    7352 sense. <o:p></o:p></span></p>
    7353 
    7354 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    7355 style='mso-fareast-font-family:"Times New Roman"'>Microstrain peak broadening </span></b><span
    7356 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    7357 
    7358 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7359 style='mso-fareast-font-family:"Times New Roman"'>is computed as unitless
    7360 fraction of delta d-space/d-space (or equivalently delta-Q/Q) times 10<sup>6</sup>.
    7361 Microstrain can be computed in three ways: isotropic, uniaxial and generalized.
    7362 In isotropic broadening, microstrain broadening assumed to be the same in all
    7363 crystallographic directions and a single value is supplied; with uniaxial
    7364 broadening, a preferred direction (as a crystallographic axis, such as 0,0,1)
    7365 is supplied -- note that for most crystal systems only one axis makes sense --
    7366 and two microstrain parameters are defined, one for along the axis and one for
    7367 in the perpendicular plane; with generalized, the Peter Stephens second-order
    7368 expansion model is used and the number of terms will depend on the crystal
    7369 system. It is typically possible to refine all terms when significant
    7370 anisotropic strain broadening is present. Note that microstrain broadening is
    7371 usually Lorentzian, which corresponds to a LGmix value of 1.0; if this value is
    7372 between 0. and 1., both Gaussian and Lorentz broadening is modeled and a value
    7373 of 0.0 is pure Gaussian. Values less than 0. or greater than 1. make no
    7374 physical sense. <o:p></o:p></span></p>
    7375 
    7376 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    7377 style='mso-fareast-font-family:"Times New Roman"'>LeBail intensity extraction </span></b><span
    7378 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    7379 
    7380 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7381 style='mso-fareast-font-family:"Times New Roman"'>When this is selected,
    7382 intensities are set to values that are best-fit using the LeBail intensity
    7383 determination method rather than are computed from the atomic information for
    7384 the phase. <o:p></o:p></span></p>
    7385 
    7386 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    7387 style='mso-fareast-font-family:"Times New Roman"'>Hydrostatic/elastic strain</span></b><span
    7388 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    7389 
    7390 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7391 style='mso-fareast-font-family:"Times New Roman"'>shifts the lattice constants
    7392 for the contribution of a phase into a histogram (powder diffraction only). The
    7393 values are added to the <a
    7394 href="http://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#gsasiilattice-unit-cells">reciprocal
    7395 lattice parameter tensor terms</a>. They must be refined in sequential
    7396 refinements or where the lattice constants are slightly different in different
    7397 histograms (as an example see the <a
    7398 href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWCombined/Combined%20refinement.htm">Combined
    7399 X-ray/CW-neutron refinement of PbSO4 tutorial</a>. <o:p></o:p></span></p>
    7400 
    7401 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    7402 name="Preferred_orientation"><b><span style='mso-fareast-font-family:"Times New Roman"'>Preferred
    7403 orientation</span></b></a><span style='mso-bookmark:Preferred_orientation'></span><span
    7404 style='mso-fareast-font-family:"Times New Roman"'> <o:p></o:p></span></p>
    7405 
    7406 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    7407 "Times New Roman"'>is treated in one of two ways. Intensity corrections can be
    7408 added to the model here or a full texture model is possible with the &quot;<u><span
    7409 style='color:blue'><a href="#Texture">Texture</a></span></u>&quot; tab (which
    7410 usually requires multiple histograms at different sample or detector settings).
    7411 The approaches available here are March-Dollase, which requires a definition of
    7412 a unique axis (in crystallographic coordinates) and the relative amount of
    7413 excess or depletion of crystallites in that direction; or Spherical Harmonics,
    7414 where the selection of an order determines the shape of the probability surface
    7415 (which is always constrained to match the symmetry of the crystal system). <o:p></o:p></span></p>
    7416 
    7417 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    7418 style='mso-fareast-font-family:"Times New Roman"'>Extinction </span></b><span
    7419 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    7420 
    7421 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7422 style='mso-fareast-font-family:"Times New Roman"'>can occur when
    7423 crystals/crystallites have minimal mosaic character, which results in lowering
    7424 of diffraction intensities for the most intense reflections. This is not
    7425 commonly seen in powder diffraction. <o:p></o:p></span></p>
    7426 
    7427 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span
    7428 style='mso-fareast-font-family:"Times New Roman"'>Disordered solvent</span></b><span
    7429 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    7430 
    7431 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7432 style='mso-fareast-font-family:"Times New Roman"'>This correction, using the
    7433 Babinet model, is typically used to treat scattering from water that is not
    7434 well-ordered in protein structures. It probably makes no sense in any other
    7435 application. <o:p></o:p></span></p>
    7436 
    7437 <h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7438 style='mso-fareast-font-family:"Times New Roman"'>What can I do here?</span></h5>
    7439 
    7440 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    7441 margin-left:.5in;text-indent:-.25in;mso-list:l26 level1 lfo36;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7442 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    7443 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    7444 style='mso-fareast-font-family:"Times New Roman"'>In this tab, menu items allow
    7445 copying values or refinement flags to histograms/phases and selection of which
    7446 histograms are used in the current phase. <o:p></o:p></span></p>
    7447 
    7448 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    7449 margin-left:.5in;text-indent:-.25in;mso-list:l26 level1 lfo36;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7450 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    7451 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    7452 style='mso-fareast-font-family:"Times New Roman"'>The plot selection items
    7453 allow for three dimensional representations of the microstrain or crystallite
    7454 size distributions (which are spheres for isotropic treatments); preferred
    7455 orientation can be plotted as a Psi scan (a plot of relative crystallite
    7456 abundance for a particular reflection as a function of azimuthal angle) or as
    7457 an inverse pole figure (which shows in a stereographic projection the
    7458 probability distribution for different reciprocal lattice directions for a
    7459 particular sample orientation). <o:p></o:p></span></p>
    7460 
    7461 <h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a
    7462 name=Atoms></a><u>Atoms</u><span class=MsoHyperlink><span style='font-size:
    7463 12.0pt;font-family:"Times New Roman",serif;color:#4F4FFF;font-style:normal;
    7464 text-decoration:none;text-underline:none'><o:p></o:p></span></span></h4>
    7465 
    7466 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>This
    7467 is the table of parameters for the atoms in this crystal structure model. The
    7468 menu controls allow manipulation of the values, refinement flags as well as
    7469 initiate calculations of geometrical values (distances &amp; angles) among the
    7470 atoms.</p>
    7471 
    7472 <h5 style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span
    7473 style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<span
    7474 class=MsoHyperlink><span style='color:#4F4FFF;text-decoration:none;text-underline:
    7475 none'><o:p></o:p></span></span></span></h5>
    7476 
    7477 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    7478 text-indent:-.25in;mso-list:l5 level1 lfo38;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7479 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    7480 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>1.
    7481 Atom selection from table - These are controlled by the mouse and the
    7482 Shift/Ctrl/Alt keys. Note that for most purposes (one exception is atom
    7483 reordering which requires an Alt-Left-click on the rows), selection of any cell
    7484 for an atom will work equivalently with selection of the entire row:</p>
    7485 
    7486 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    7487 auto;text-indent:-.25in;mso-list:l5 level2 lfo38;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7488 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    7489 color:windowtext;text-decoration:none;text-underline:none'><span
    7490 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7491 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    7492 style='mso-fareast-font-family:"Times New Roman"'>Left Mouse Button (LMB)</span></b><span
    7493 style='mso-fareast-font-family:"Times New Roman"'> – on a row number selects
    7494 the atom.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    7495 none;text-underline:none'><o:p></o:p></span></span></span></p>
    7496 
    7497 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    7498 auto;text-indent:-.25in;mso-list:l5 level2 lfo38;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span
    7499 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    7500 color:windowtext;text-decoration:none;text-underline:none'><span
    7501 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7502 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    7503 style='mso-fareast-font-family:"Times New Roman"'>Shift LMB</span></b><span
    7504 style='mso-fareast-font-family:"Times New Roman"'> – on a row number selects
    7505 all atoms from last selection to the selected row (or top is none previously
    7506 selected).<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    7507 none;text-underline:none'><o:p></o:p></span></span></span></p>
    7508 
    7509 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    7510 auto;text-indent:-.25in;mso-list:l5 level2 lfo38;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>&l