Changeset 5257


Ignore:
Timestamp:
Apr 1, 2022 8:14:22 AM (12 months ago)
Author:
vondreele
Message:

Add '?' to various places & all connect to help pages with text filled in.
Remove Pawley popup - interfered with operation & caused crashes.

Location:
trunk
Files:
5 edited

Legend:

Unmodified
Added
Removed

  • trunk/GSASIIimgGUI.py

    r5175 r5257  
    205205    G2frame.ImageZ = GetImageZ(G2frame,data)
    206206    mainSizer = G2frame.dataWindow.GetSizer()
    207     mainSizer.Add(wx.StaticText(G2frame.dataWindow,
    208         label='Do not change anything here unless you are absolutely sure!'),0)
     207    topSizer = wx.BoxSizer(wx.HORIZONTAL)
     208    topSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Do not change anything here unless you are absolutely sure!'),0)
     209    topSizer.Add((-1,-1),1,wx.EXPAND)
     210    topSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex=G2frame.dataWindow.helpKey))
     211    mainSizer.Add(topSizer,0,wx.EXPAND)
    209212    mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Image size: %d by %d'%(data['size'][0],data['size'][1])),0)
    210213    pixSize = wx.FlexGridSizer(0,4,5,5)
    … …  
    16471650    G2frame.Bind(wx.EVT_MENU, OnIntPDFtool, id=G2G.wxID_IMINTEGPDFTOOL)
    16481651
    1649     mainSizer = G2frame.dataWindow.GetSizer()
     1652    mainSizer = G2frame.dataWindow.GetSizer() 
     1653    topSizer = wx.BoxSizer(wx.HORIZONTAL)
     1654    topSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Image Controls:'))
     1655    topSizer.Add((-1,-1),1,wx.EXPAND)
     1656    topSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex=G2frame.dataWindow.helpKey))
     1657    mainSizer.Add(topSizer,0,wx.EXPAND)
    16501658    mainSizer.Add((5,10),0)   
    16511659    mainSizer.Add(ComboSizer(),0,wx.ALIGN_LEFT)
    … …  
    20822090        G2frame.GetStatusBar().SetStatusText("To add mask: press a,r,s,x,y,p or f on 2D image for arc/ring/spot/xline/yline/polygon/frame",1)
    20832091    mainSizer = G2frame.dataWindow.GetSizer()
     2092    topSizer = wx.BoxSizer(wx.HORIZONTAL)
     2093    topSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Mask Controls:'))
     2094    topSizer.Add((-1,-1),1,wx.EXPAND)
     2095    topSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex=G2frame.dataWindow.helpKey))
     2096    mainSizer.Add(topSizer,0,wx.EXPAND)
    20842097    mainSizer.Add((5,10),0)
    20852098
    … …  
    26712684       
    26722685    mainSizer = G2frame.dataWindow.GetSizer()
     2686    topSizer = wx.BoxSizer(wx.HORIZONTAL)
     2687    topSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Stress/Strain Controls:'))
     2688    topSizer.Add((-1,-1),1,wx.EXPAND)
     2689    topSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex=G2frame.dataWindow.helpKey))
     2690    mainSizer.Add(topSizer,0,wx.EXPAND)
    26732691    mainSizer.Add((5,10),0)
    26742692    mainSizer.Add(SamSizer())

  • trunk/GSASIIphsGUI.py

    r5250 r5257  
    1330213302        # FillPawleyReflectionsGrid executable starts here
    1330313303        G2frame.GetStatusBar().SetStatusText('To delete a Pawley reflection: select row & press Delete',1)                       
    13304         oldSizer = PawleyRefList.GetSizer()
    13305         if oldSizer: oldSizer.Clear()
     13304        # oldSizer = PawleyRefList.GetSizer()
     13305        # if oldSizer: oldSizer.Clear(True)
    1330613306        generalData = data['General']
    1330713307        PawleyPeaks = data['Pawley ref']
    13308         if len(PawleyPeaks) == 0 or not generalData['doPawley']:
    13309             msg = ('Pawley refinement not yet set up. Use the "Pawley setup"'+
    13310                     ' and "Pawley create" menu commands to change this. '+
    13311                     '(Note settings also found on General tab).')
    13312             if not generalData['doPawley']:
    13313                 msg += '\n\nCall Pawley setup?'
    13314             else:
    13315                 msg += '\n\nCall Pawley create?'
    13316             dlg = wx.MessageDialog(G2frame,msg,'Pawley not setup',
    13317                                    wx.YES_NO | wx.ICON_QUESTION)
    13318             try:
    13319                 dlg.CenterOnParent()
    13320                 result = dlg.ShowModal()
    13321                 if result == wx.ID_YES and not generalData['doPawley']:
    13322                     wx.CallAfter(OnPawleySet,None)
    13323                 elif result == wx.ID_YES:
    13324                     wx.CallAfter(OnPawleyLoad,None)
    13325             finally:
    13326                 dlg.Destroy()
    13327         rowLabels = []
    13328         for i in range(len(PawleyPeaks)): rowLabels.append(str(i))
    13329         if generalData['Modulated']:
    13330             colLabels = ['h','k','l','m','mul','d','refine','Fsq(hkl)','sig(Fsq)']
    13331             Types = 5*[wg.GRID_VALUE_LONG,]+[wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_BOOL,]+ \
    13332                 2*[wg.GRID_VALUE_FLOAT+':10,2',]
    13333             pos = [6,7]
    13334         else:   
    13335             colLabels = ['h','k','l','mul','d','refine','Fsq(hkl)','sig(Fsq)']
    13336             Types = 4*[wg.GRID_VALUE_LONG,]+[wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_BOOL,]+ \
    13337                 2*[wg.GRID_VALUE_FLOAT+':10,2',]
    13338             pos = [5,6]
    13339         PawleyTable = G2G.Table(PawleyPeaks,rowLabels=rowLabels,colLabels=colLabels,types=Types)
    13340         G2frame.PawleyRefl.SetTable(PawleyTable, True)
    13341         G2frame.PawleyRefl.Bind(wx.EVT_KEY_DOWN, KeyEditPawleyGrid)                 
    13342         G2frame.PawleyRefl.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, onRefineDClick)
    13343         for r in range(G2frame.PawleyRefl.GetNumberRows()):
    13344             for c in range(G2frame.PawleyRefl.GetNumberCols()):
    13345                 if c in pos:
    13346                     G2frame.PawleyRefl.SetReadOnly(r,c,isReadOnly=False)
    13347                 else:
    13348                     G2frame.PawleyRefl.SetCellStyle(r,c,VERY_LIGHT_GREY,True)
    13349         G2frame.PawleyRefl.SetMargins(0,0)
    13350         G2frame.PawleyRefl.AutoSizeColumns(False)
     13308        # removed because it interfered with normal ops. & crashed GSAS-II
     13309        # if len(PawleyPeaks) == 0 or not generalData['doPawley']:
     13310        #     msg = ('Pawley refinement not yet set up. Use the "Pawley setup"'+
     13311        #             ' and "Pawley create" menu commands to change this. '+
     13312        #             '(Note settings also found on General tab).')
     13313        #     if not generalData['doPawley']:
     13314        #         msg += '\n\nCall Pawley setup?'
     13315        #     else:
     13316        #         msg += '\n\nCall Pawley create?'
     13317        #     dlg = wx.MessageDialog(G2frame,msg,'Pawley not setup',
     13318        #                            wx.YES_NO | wx.ICON_QUESTION)
     13319        #     try:
     13320        #         dlg.CenterOnParent()
     13321        #         result = dlg.ShowModal()
     13322        #         if result == wx.ID_YES and not generalData['doPawley']:
     13323        #             wx.CallAfter(OnPawleySet,None)
     13324        #         elif result == wx.ID_YES:
     13325        #             wx.CallAfter(OnPawleyLoad,None)
     13326        #     finally:
     13327        #         dlg.Destroy()
    1335113328        mainSizer = wx.BoxSizer(wx.VERTICAL)
    1335213329        topSizer = wx.BoxSizer(wx.HORIZONTAL)
    … …  
    1335513332        topSizer.Add(G2G.HelpButton(PawleyRefList,helpIndex=G2frame.dataWindow.helpKey))
    1335613333        mainSizer.Add(topSizer,0,wx.EXPAND)
    13357         mainSizer.Add(G2frame.PawleyRefl)
     13334        rowLabels = []
     13335        if len(PawleyPeaks):           
     13336            for i in range(len(PawleyPeaks)): rowLabels.append(str(i))
     13337            if generalData['Modulated']:
     13338                colLabels = ['h','k','l','m','mul','d','refine','Fsq(hkl)','sig(Fsq)']
     13339                Types = 5*[wg.GRID_VALUE_LONG,]+[wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_BOOL,]+ \
     13340                    2*[wg.GRID_VALUE_FLOAT+':10,2',]
     13341                pos = [6,7]
     13342            else:   
     13343                colLabels = ['h','k','l','mul','d','refine','Fsq(hkl)','sig(Fsq)']
     13344                Types = 4*[wg.GRID_VALUE_LONG,]+[wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_BOOL,]+ \
     13345                    2*[wg.GRID_VALUE_FLOAT+':10,2',]
     13346                pos = [5,6]
     13347            PawleyTable = G2G.Table(PawleyPeaks,rowLabels=rowLabels,colLabels=colLabels,types=Types)
     13348            G2frame.PawleyRefl.SetTable(PawleyTable, True)
     13349            G2frame.PawleyRefl.Bind(wx.EVT_KEY_DOWN, KeyEditPawleyGrid)                 
     13350            G2frame.PawleyRefl.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, onRefineDClick)
     13351            for r in range(G2frame.PawleyRefl.GetNumberRows()):
     13352                for c in range(G2frame.PawleyRefl.GetNumberCols()):
     13353                    if c in pos:
     13354                        G2frame.PawleyRefl.SetReadOnly(r,c,isReadOnly=False)
     13355                    else:
     13356                        G2frame.PawleyRefl.SetCellStyle(r,c,VERY_LIGHT_GREY,True)
     13357            G2frame.PawleyRefl.SetMargins(0,0)
     13358            G2frame.PawleyRefl.AutoSizeColumns(False)
     13359            mainSizer.Add(G2frame.PawleyRefl)
     13360        else:
     13361            mainSizer.Add(wx.StaticText(PawleyRefList,label=' There are no Pawley reflections'))
    1335813362        SetPhaseWindow(PawleyRefList,mainSizer)
    1335913363                   
    … …  
    1342213426        genDlg.Destroy()
    1342313427
    13424         if generalData['doPawley'] and res == wx.ID_OK and (
    13425                 not startPawley or startDmin != generalData['Pawley dmin']):
     13428        if generalData['doPawley'] and res == wx.ID_OK and (not startPawley or startDmin != generalData['Pawley dmin']):
    1342613429            dlg = wx.MessageDialog(G2frame,'Do you want to initialize the Pawley reflections with the settings?','Initialize Pawley?',
    1342713430                wx.YES_NO | wx.ICON_QUESTION)
    … …  
    1354813551                        ref[6+im] /= (Sample['Scale'][0] * Vst * Lorenz * pola * ref[3+im])
    1354913552                    else:
    13550                         ref[6+im] /= (0.02*Sample['Scale'][0] * ref[3+im]*cw[indx])     #why 0.02*cw?
     13553                        ref[6+im] /= (Sample['Scale'][0] * ref[3+im]*cw[indx])
    1355113554                except IndexError:
    13552                     pass
     13555                    ref[6+im] = 0.0
    1355313556        finally:
    1355413557            wx.EndBusyCursor()
    … …  
    1366013663        oldSizer = MapPeakList.GetSizer()
    1366113664        if oldSizer: oldSizer.Clear()
     13665        mainSizer = wx.BoxSizer(wx.VERTICAL)
     13666        topSizer = wx.BoxSizer(wx.HORIZONTAL)
     13667        topSizer.Add(wx.StaticText(MapPeakList,label='Fourier map peak positions for %s:'%data['General']['Name']),0,WACV)
     13668        topSizer.Add((-1,-1),1,wx.EXPAND)
     13669        topSizer.Add(G2G.HelpButton(MapPeakList,helpIndex=G2frame.dataWindow.helpKey))
     13670        mainSizer.Add(topSizer,0,wx.EXPAND)
    1366213671        if 'Map Peaks' in data:
    13663             mainSizer = wx.BoxSizer(wx.VERTICAL)
    13664             topSizer = wx.BoxSizer(wx.HORIZONTAL)
    13665             topSizer.Add(wx.StaticText(MapPeakList,label='Fourier map peak positions for %s:'%data['General']['Name']),0,WACV)
    13666             topSizer.Add((-1,-1),1,wx.EXPAND)
    13667             topSizer.Add(G2G.HelpButton(MapPeakList,helpIndex=G2frame.dataWindow.helpKey))
    13668             mainSizer.Add(topSizer,0,wx.EXPAND)
    1366913672            G2frame.GetStatusBar().SetStatusText('Double click any column heading to sort',1)
    1367013673            mapPeaks = data['Map Peaks']                       
    … …  
    1368213685            MapPeaks.AutoSizeColumns(False)
    1368313686            mainSizer.Add(MapPeaks)
    13684             SetPhaseWindow(MapPeakList,mainSizer)
     13687        else:
     13688            mainSizer.Add(wx.StaticText(MapPeakList,label=' Map peak list is empty'))
     13689        SetPhaseWindow(MapPeakList,mainSizer)
    1368513690                   
    1368613691    def OnPeaksMove(event):

  • trunk/help/gsasII-phase.html

    r5250 r5257  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele, Robert B.</o:LastAuthor>
    27   <o:Revision>43</o:Revision>
    28   <o:TotalTime>7209</o:TotalTime>
     27  <o:Revision>48</o:Revision>
     28  <o:TotalTime>7295</o:TotalTime>
    2929  <o:Created>2021-06-20T02:30:00Z</o:Created>
    30   <o:LastSaved>2022-03-24T14:35:00Z</o:LastSaved>
     30  <o:LastSaved>2022-03-31T21:35:00Z</o:LastSaved>
    3131  <o:Pages>1</o:Pages>
    32   <o:Words>10313</o:Words>
    33   <o:Characters>58786</o:Characters>
     32  <o:Words>10342</o:Words>
     33  <o:Characters>58951</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    35   <o:Lines>489</o:Lines>
    36   <o:Paragraphs>137</o:Paragraphs>
    37   <o:CharactersWithSpaces>68962</o:CharactersWithSpaces>
     35  <o:Lines>491</o:Lines>
     36  <o:Paragraphs>138</o:Paragraphs>
     37  <o:CharactersWithSpaces>69155</o:CharactersWithSpaces>
    3838  <o:Version>16.00</o:Version>
    3939 </o:DocumentProperties>
    … …  
    4949 <w:WordDocument>
    5050  <w:Zoom>148</w:Zoom>
    51   <w:SpellingState>Clean</w:SpellingState>
    52   <w:GrammarState>Clean</w:GrammarState>
    5351  <w:TrackMoves>false</w:TrackMoves>
    5452  <w:TrackFormatting/>
    … …  
    953951        mso-font-kerning:14.0pt;}
    954952a:link, span.MsoHyperlink
    955         {mso-style-priority:99;
     953        {mso-style-noshow:yes;
     954        mso-style-priority:99;
    956955        color:blue;
    957956        text-decoration:underline;
    … …  
    13071306        font-family:"Times New Roman",serif;
    13081307        mso-fareast-font-family:"Times New Roman";}
    1309 span.SpellE
    1310         {mso-style-name:"";
    1311         mso-spl-e:yes;}
    1312 span.GramE
    1313         {mso-style-name:"";
    1314         mso-gram-e:yes;}
    13151308.MsoChpDefault
    13161309        {mso-style-type:export-only;
    … …  
    18761869
    18771870<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1878 is where to find help on the Phase Tree items in GSAS-II. Note that the window
    1879 displayed for this page has multiple tabs. The help information is broken down
    1880 by tab section. <o:p></o:p></span></p>
     1871is where to find help on the Phase Tree items in GSAS-II. Note that the window displayed
     1872for this page has multiple tabs. The help information is broken down by tab
     1873section. <o:p></o:p></span></p>
    18811874
    18821875<h2 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'><a
    … …  
    19021895phase. It also has the controls for Pawley intensity extraction and for
    19031896computing Fourier maps for this phase. It can also has the controls for Monte
    1904 Carlo/Simulated Annealing for solving structures with flexible rigid molecular <span
    1905 class=GramE>bodies..</span> <span class=MsoHyperlink><span style='color:windowtext;
    1906 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
     1897Carlo/Simulated Annealing for solving structures with flexible rigid molecular
     1898bodies.. <span class=MsoHyperlink><span style='color:windowtext;text-decoration:
     1899none;text-underline:none'><o:p></o:p></span></span></span></p>
    19071900
    19081901<h5 style='margin-left:.5in'>What can I do here?</h5>
    … …  
    19431936style='mso-fareast-font-family:"Times New Roman"'>This performs a charge
    19441937flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution
    1945 using the method of <span class=SpellE>Oszlanyi</span> &amp; <span
    1946 class=SpellE>Suto</span> (Acta <span class=SpellE>Cryst</span>. A60, 134-141,
    1947 2004). You will need to select a source for the reflection set and perhaps
    1948 select an element for normalization by its form factor, a resolution limit
    1949 (usually 0.5</span><span style='font-family:"Calibri",sans-serif;mso-fareast-font-family:
    1950 "Times New Roman"'>Å</span><span style='mso-fareast-font-family:"Times New Roman"'>)
    1951 and a charge flip threshold (usually 0.1); these are found near the bottom of
    1952 the <b style='mso-bidi-font-weight:normal'>General</b> window. There are also
    1953 Test HKLs to show the progress in phasing with charge flipping cycles. They
    1954 show the generally chaotic phase behavior before a solution is found; after
    1955 that the phases are essentially fixed. No use is made of this information; it
    1956 is just for your edification. A progress bar showing the charge flip residual
    1957 is shown while the charge flip is in operation. When the residual is no longer
    1958 decreasing (be patient – it doesn’t necessarily fall continuously), press the <b
    1959 style='mso-bidi-font-weight:normal'>Cancel</b> button to stop the charge
    1960 flipping, otherwise it will stop at 10000 cycles. The resulting map will be
    1961 positioned to properly place symmetry operators (NB: depends on the quality of
    1962 the resulting phases; the map could be still offset by a few steps), searched
    1963 for peaks and the display shifts to <b style='mso-bidi-font-weight:normal'>Map
    1964 peaks</b> to show them.<b><o:p></o:p></b></span></p>
     1938using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You
     1939will need to select a source for the reflection set and perhaps select an
     1940element for normalization by its form factor, a resolution limit (usually 0.5</span><span
     1941style='font-family:"Calibri",sans-serif;mso-fareast-font-family:"Times New Roman"'>Å</span><span
     1942style='mso-fareast-font-family:"Times New Roman"'>) and a charge flip threshold
     1943(usually 0.1); these are found near the bottom of the <b style='mso-bidi-font-weight:
     1944normal'>General</b> window. There are also Test HKLs to show the progress in
     1945phasing with charge flipping cycles. They show the generally chaotic phase
     1946behavior before a solution is found; after that the phases are essentially
     1947fixed. No use is made of this information; it is just for your edification. A
     1948progress bar showing the charge flip residual is shown while the charge flip is
     1949in operation. When the residual is no longer decreasing (be patient – it
     1950doesn’t necessarily fall continuously), press the <b style='mso-bidi-font-weight:
     1951normal'>Cancel</b> button to stop the charge flipping, otherwise it will stop
     1952at 10000 cycles. The resulting map will be positioned to properly place
     1953symmetry operators (NB: depends on the quality of the resulting phases; the map
     1954could be still offset by a few steps), searched for peaks and the display
     1955shifts to <b style='mso-bidi-font-weight:normal'>Map peaks</b> to show them.<b><o:p></o:p></b></span></p>
    19651956
    19661957<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
    … …  
    20041995style='mso-fareast-font-family:"Times New Roman"'>Transform </span></b><span
    20051996style='mso-fareast-font-family:"Times New Roman"'>- This allows for a change in
    2006 axes, <span class=GramE>symmetry</span> or unit cell. It is also used to create
    2007 a magnetic phase from a chemical (nuclear) phase. One important transformation
    2008 that can be done here is for Origin 1 settings to Origin 2 (<a
    2009 href="#_Origin_1_-&gt;">described below</a>).<b><o:p></o:p></b></span></p>
     1997axes, symmetry or unit cell. It is also used to create a magnetic phase from a
     1998chemical (nuclear) phase. One important transformation that can be done here is
     1999for Origin 1 settings to Origin 2 (<a href="#_Origin_1_-&gt;">described below</a>).<b><o:p></o:p></b></span></p>
    20102000
    20112001<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
    … …  
    20152005</span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Compare
    20162006– </span></b><span style='mso-fareast-font-family:"Times New Roman"'>Compares
    2017 idealized <span class=SpellE>polyhedra</span> (tetrahedron &amp; octahedron) to
    2018 those obtained from a Reverse Monte Carlo run in RMCProfile.<b><o:p></o:p></b></span></p>
     2007idealized polyhedra (tetrahedron &amp; octahedron) to those obtained from a
     2008Reverse Monte Carlo run in RMCProfile.<b><o:p></o:p></b></span></p>
    20192009
    20202010<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
    … …  
    20362026style='mso-fareast-font-family:"Times New Roman"'>Protein quality</span></b><span
    20372027style='mso-fareast-font-family:"Times New Roman"'> – evaluate protein quality
    2038 by python versions of <span class=SpellE>errat</span> &amp; errat2 codes by <span
    2039 class=SpellE>Colovos</span>, C. &amp; <span class=SpellE>Yeates</span>, T.O. Protein
    2040 Science 2, 1511-1519 (1991).<b><o:p></o:p></b></span></p>
     2028by python versions of errat &amp; errat2 codes by Colovos, C. &amp; Yeates,
     2029T.O. Protein Science 2, 1511-1519 (1991).<b><o:p></o:p></b></span></p>
    20412030
    20422031<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
    … …  
    20622051</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    20632052style='mso-fareast-font-family:"Times New Roman"'>Phase name</span></b><span
    2064 style='mso-fareast-font-family:"Times New Roman"'> – this is the name assigned
    2065 to this phase. It can be changed at any time.<span class=MsoHyperlink><span
     2053style='mso-fareast-font-family:"Times New Roman"'> – this is the name assigned to
     2054this phase. It can be changed at any time.<span class=MsoHyperlink><span
    20662055style='color:windowtext'><o:p></o:p></span></span></span></p>
    20672056
    … …  
    20872076the phase is initialized; it can be changed later. Be careful about the impact
    20882077on Atom site symmetry and multiplicity if you do. GSAS-II will recognize any
    2089 legal space group symbol using the short Hermann-<span class=SpellE>Mauguin</span>
    2090 forms; put a space between the axial fields (<span class=GramE>e.g.</span> ‘F d
    2091 3 m’ not ‘Fd3m’; ‘F d 3 m’ is understood as well as ‘F d -3 m’). For space
    2092 groups with a choice of origin (<span class=GramE>e.g.</span> F d 3 m), GSAS-II
    2093 always uses the 2<sup>nd</sup> setting where the center of inversion is located
    2094 at the origin. The choice of space group will set the available unit cell
    2095 parameters.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
     2078legal space group symbol using the short Hermann-Mauguin forms; put a space
     2079between the axial fields (e.g. ‘F d 3 m’ not ‘Fd3m’; ‘F d 3 m’ is understood as
     2080well as ‘F d -3 m’). For space groups with a choice of origin (e.g. F d 3 m),
     2081GSAS-II always uses the 2<sup>nd</sup> setting where the center of inversion is
     2082located at the origin. The choice of space group will set the available unit
     2083cell parameters.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    20962084
    20972085<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
    … …  
    21982186 <v:imagedata src="gsasII-phase_files/image001.png" o:title="" chromakey="white"/>
    21992187</v:shape><![endif]--><![if !vml]><img width=335 height=19
    2200 src="gsasII-phase_files/image049.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><br>
     2188src="gsasII-phase_files/image002.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><br>
    22012189<span style='font-family:"Cambria Math",serif;mso-fareast-font-family:"Times New Roman";
    22022190mso-bidi-font-style:italic'>A0-A5 correspond to the reciprocal metric tensor
    … …  
    22242212table is shown next on the General page; you may select the isotope (only
    22252213relevant for neutron diffraction experiments). The density (just above the
    2226 Elements) is computed depending on this choice, the unit cell volume and the
    2227 atom fractions/site multiplicities in the entries on the Atoms page.<span
     2214Elements) is computed depending on this choice, the unit cell volume and the atom
     2215fractions/site multiplicities in the entries on the Atoms page.<span
    22282216class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    22292217
    … …  
    22572245style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    22582246style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Pawley
    2259 <span class=SpellE>dmin</span></span></b><span style='mso-fareast-font-family:
    2260 "Times New Roman"'> – This is the minimum d-spacing to be used in a Pawley
    2261 refinement. <b style='mso-bidi-font-weight:normal'>NB:</b> be sure to set this
    2262 to match the minimum d-spacing indicated by the powder pattern limits (see <b
     2247dmin</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – This
     2248is the minimum d-spacing to be used in a Pawley refinement. <b
     2249style='mso-bidi-font-weight:normal'>NB:</b> be sure to set this to match the
     2250minimum d-spacing indicated by the powder pattern limits (see <b
    22632251style='mso-bidi-font-weight:normal'>Limits</b> for the powder data set).</span></p>
    22642252
    … …  
    22692257style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    22702258</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    2271 style='mso-fareast-font-family:"Times New Roman"'>Pawley <span class=SpellE>dmax</span></span></b><span
     2259style='mso-fareast-font-family:"Times New Roman"'>Pawley dmax</span></b><span
    22722260style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'> –
    22732261This is the maximum d-spacing for reflections in a Pawley refinement. It is
    … …  
    22842272style='mso-fareast-font-family:"Times New Roman"'>Pawley neg. wt.</span></b><span
    22852273style='mso-fareast-font-family:"Times New Roman"'> – This is the weight for a
    2286 penalty function applied during a Pawley refinement on resulting negative intensities.
    2287 Use with caution; initially try very small values (<span class=GramE>e.g.</span>
    2288 .01). A value of zero means no penalty is applied.<span class=MsoHyperlink><span
     2274penalty function applied during a Pawley refinement on resulting negative
     2275intensities. Use with caution; initially try very small values (e.g. .01). A
     2276value of zero means no penalty is applied.<span class=MsoHyperlink><span
    22892277style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    22902278
    … …  
    22952283style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    22962284</span></span></span></span><![endif]><span style='mso-fareast-font-family:
    2297 "Times New Roman"'>Fourier map controls are shown next on the General page.
    2298 Single crystal data or a completed Rietveld or Pawley refinement is required
    2299 before a Fourier map can be computed. Select the desired type of map, the
    2300 source of the reflection set and the map resolution desired. The peak cutoff is
    2301 defined as a percentage of the maximum and defines the lowest level considered
    2302 in the peak search.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
     2285"Times New Roman"'>Fourier map controls are shown next on the General page. Single
     2286crystal data or a completed Rietveld or Pawley refinement is required before a
     2287Fourier map can be computed. Select the desired type of map, the source of the
     2288reflection set and the map resolution desired. The peak cutoff is defined as a
     2289percentage of the maximum and defines the lowest level considered in the peak
     2290search.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    23032291
    23042292<p class=MsoListParagraphCxSpMiddle style='margin-left:73.2pt;mso-add-space:
    … …  
    23192307</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    23202308style='mso-fareast-font-family:"Times New Roman"'>Reflection sets </span></b><span
    2321 style='mso-fareast-font-family:"Times New Roman"'>– This is the source of structure
    2322 factors to be used in a charge flip calculation. These may be either a single
    2323 crystal data set, or structure factors extracted from a powder pattern via a
    2324 Pawley or LeBail refinement or a Rietveld refinement.<span class=MsoHyperlink><span
    2325 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
     2309style='mso-fareast-font-family:"Times New Roman"'>– This is the source of
     2310structure factors to be used in a charge flip calculation. These may be either
     2311a single crystal data set, or structure factors extracted from a powder pattern
     2312via a Pawley or LeBail refinement or a Rietveld refinement.<span
     2313class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
     2314text-underline:none'><o:p></o:p></span></span></span></p>
    23262315
    23272316<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
    … …  
    23322321</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    23332322style='mso-fareast-font-family:"Times New Roman"'>Normalizing element </span></b><span
    2334 style='mso-fareast-font-family:"Times New Roman"'>– This is an element form
    2335 factor chosen to normalize the structure factors before charge flipping. <b
     2323style='mso-fareast-font-family:"Times New Roman"'>– This is an element form factor
     2324chosen to normalize the structure factors before charge flipping. <b
    23362325style='mso-bidi-font-weight:normal'>None</b> (the default) can be selected from
    23372326the lower right of the Periodic Table display shown when this is selected.<span
    … …  
    23792368style='mso-fareast-font-family:"Times New Roman"'>Test HKLs</span></b><span
    23802369style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'> –
    2381 plot of phases for selected <span class=SpellE>hkls</span> are shown at end of
    2382 charge flipping run. Just for you to look at.</span><span style='mso-fareast-font-family:
    2383 "Times New Roman"'><o:p></o:p></span></p>
     2370plot of phases for selected hkls are shown at end of charge flipping run. Just
     2371for you to look at.</span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    23842372
    23852373<p class=MsoListParagraphCxSpMiddle style='margin-left:73.2pt;mso-add-space:
    … …  
    23982386This is the source of structure factors to be used in a charge flip
    23992387calculation. These may be either a single crystal data set, or structure
    2400 factors extracted from a powder pattern via a Pawley or <span class=SpellE>Lebail</span>
    2401 refinement or a Rietveld refinement.<o:p></o:p></span></p>
     2388factors extracted from a powder pattern via a Pawley or Lebail refinement or a
     2389Rietveld refinement.<o:p></o:p></span></p>
    24022390
    24032391<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
    … …  
    24692457point in the structure does not contain a center of symmetry. Origin 1 places
    24702458the origin at the highest symmetry setting while Origin 2 places the origin at
    2471 a center of symmetry (creating a -<span class=GramE>x,-</span>y,-z symmetry
    2472 operator, which means that reflection phases can only be 0 or π.) GSAS-II
    2473 requires use of the Origin 2 settings because computations are much faster and
    2474 simpler without complex structure factors. Alas, the literature contains <span
    2475 class=GramE>a number of</span> structures reported in Origin 1, where the
    2476 origin choice may not be clearly communicated. (The CIF standard does not
    2477 require that origin choice be indicated.) When a structure is imported that
    2478 uses any of the space groups where an origin choice is possible, a message is
    2479 shown in GSAS-II notifying the user that they must confirm that the origin
    2480 choice is correct and then provides the opportunity to change origins. <o:p></o:p></span></p>
     2459a center of symmetry (creating a -x,-y,-z symmetry operator, which means that
     2460reflection phases can only be 0 or π.) GSAS-II requires use of the Origin 2
     2461settings because computations are much faster and simpler without complex structure
     2462factors. Alas, the literature contains a number of structures reported in
     2463Origin 1, where the origin choice may not be clearly communicated. (The CIF
     2464standard does not require that origin choice be indicated.) When a structure is
     2465imported that uses any of the space groups where an origin choice is possible,
     2466a message is shown in GSAS-II notifying the user that they must confirm that
     2467the origin choice is correct and then provides the opportunity to change
     2468origins. <o:p></o:p></span></p>
    24812469
    24822470<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
    … …  
    25062494 <tr style='mso-yfti-irow:2'>
    25072495  <td style='padding:.75pt .75pt .75pt .75pt'>
    2508   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    2509   "Times New Roman"'>Ti</span></span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     2496  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Ti<o:p></o:p></span></p>
    25102497  </td>
    25112498  <td style='padding:.75pt .75pt .75pt .75pt'>
    … …  
    25602547 <tr style='mso-yfti-irow:2'>
    25612548  <td style='padding:.75pt .75pt .75pt .75pt'>
    2562   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    2563   "Times New Roman"'>Ti</span></span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     2549  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Ti<o:p></o:p></span></p>
    25642550  </td>
    25652551  <td style='padding:.75pt .75pt .75pt .75pt'>
    … …  
    25912577<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
    25922578style='mso-fareast-font-family:"Times New Roman";color:white;mso-color-alt:
    2593 windowtext'>where the origin is shifted by (0,1/</span><span class=GramE><span
    2594 style='mso-fareast-font-family:"Times New Roman"'>4,-</span></span><span
    2595 style='mso-fareast-font-family:"Times New Roman"'>1/8). <o:p></o:p></span></p>
     2579windowtext'>where the origin is shifted by (0,1/4,-1/8). </span><span
     2580style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    25962581
    25972582<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
    … …  
    26092594</v:shape><![endif]--><![if !vml]><img width=322 height=190
    26102595src="gsasII_files/wrong.png" align=right v:shapes="Picture_x0020_3"><![endif]><span
    2611 style='mso-fareast-font-family:"Times New Roman"'>GSAS-II always uses the symmetry
    2612 operators for Origin 2; if the structure is input incorrectly with the
    2613 coordinates set for Origin 1, there are several <span class=GramE>fairly
    2614 obvious</span> signs of problems: (1) the site symmetries and multiplicities
    2615 are wrong, often giving an incorrect chemical formula, (2) the interatomic
    2616 distances are incorrect, and (3) a plot of the structure is improbable. In this
    2617 case incorrect multiplicities gives rise to a density of 7.9 g/cc, double the
    2618 correct value. Impossible interatomic distances of 1.88Å for <span
    2619 class=SpellE><span class=GramE>Ti-Ti</span></span>, and 1.39Å for <span
    2620 class=SpellE>Ti</span>-O are seen. The unit cell contents with the wrong space
    2621 group operators <span class=GramE>is</span> shown to the right. <o:p></o:p></span></p>
     2596style='mso-fareast-font-family:"Times New Roman"'>GSAS-II always uses the
     2597symmetry operators for Origin 2; if the structure is input incorrectly with the
     2598coordinates set for Origin 1, there are several fairly obvious signs of
     2599problems: (1) the site symmetries and multiplicities are wrong, often giving an
     2600incorrect chemical formula, (2) the interatomic distances are incorrect, and
     2601(3) a plot of the structure is improbable. In this case incorrect
     2602multiplicities gives rise to a density of 7.9 g/cc, double the correct value.
     2603Impossible interatomic distances of 1.88Å for Ti-Ti, and 1.39Å for Ti-O are
     2604seen. The unit cell contents with the wrong space group operators is shown to
     2605the right. <o:p></o:p></span></p>
    26222606
    26232607<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
    26242608style='mso-fareast-font-family:"Times New Roman"'>With coordinates that match
    2625 the space group operations, the correct <span class=SpellE>Ti</span>-O
    2626 distances are 1.92Å and 1.97Å and the shortest <span class=SpellE>Ti-Ti</span>
    2627 distance is 3.0Å. (Note that interatomic distances can be computed in GSAS-II
    2628 using the Phase Atoms tab and the Compute/&quot;Show Distances &amp;
    2629 Angles&quot; menu item.) <o:p></o:p></span></p>
     2609the space group operations, the correct Ti-O distances are 1.92Å and 1.97Å and
     2610the shortest Ti-Ti distance is 3.0Å. (Note that interatomic distances can be
     2611computed in GSAS-II using the Phase Atoms tab and the Compute/&quot;Show
     2612Distances &amp; Angles&quot; menu item.) <o:p></o:p></span></p>
    26302613
    26312614<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
    … …  
    26722655<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
    26732656HAP parameters include: the phase fraction; the sample contributions to peak
    2674 broadening: <span class=SpellE>microstrain</span> and crystallite size; a
    2675 LeBail intensity extraction flag; hydrostatic/elastic strain shifts to lattice
    2676 parameters; corrections to peak intensities due to experimental effects
    2677 (preferred orientation, <span class=GramE>extinction</span> and disordered
    2678 solvents).</p>
     2657broadening: microstrain and crystallite size; a LeBail intensity extraction
     2658flag; hydrostatic/elastic strain shifts to lattice parameters; corrections to
     2659peak intensities due to experimental effects (preferred orientation, extinction
     2660and disordered solvents).</p>
    26792661
    26802662<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'>For
    2681 single crystal data, the only parameters are scale, <span class=GramE>extinction</span>
    2682 and disordered solvent. There is no Sample Parameters histogram scale factor.</p>
     2663single crystal data, the only parameters are scale, extinction and disordered
     2664solvent. There is no Sample Parameters histogram scale factor.</p>
    26832665
    26842666<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
    … …  
    27222704
    27232705<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
    2724 style='mso-fareast-font-family:"Times New Roman"'>Used for single crystal <span
    2725 class=GramE>data:</span> relates F<sup>2</sup><sub>obs</sub> to F<sup>2</sup><sub>calc</sub>.<o:p></o:p></span></p>
     2706style='mso-fareast-font-family:"Times New Roman"'>Used for single crystal data:
     2707relates F<sup>2</sup><sub>obs</sub> to F<sup>2</sup><sub>calc</sub>.<o:p></o:p></span></p>
    27262708
    27272709<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
    … …  
    27312713<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
    27322714style='mso-fareast-font-family:"Times New Roman"'>is computed from size
    2733 factor(s) in microns (<span class=SpellE>μm</span> = 10<sup>-6</sup> m), with
    2734 the Scherrer constant assumed as unity. Sizes can be computed in three ways:
    2735 isotropic, <span class=GramE>uniaxial</span> and ellipsoidal. In isotropic
    2736 broadening, crystallites are assumed to average as uniform in all directions
    2737 and a single size value is supplied; with uniaxial broadening, a preferred
    2738 direction (as a crystallographic axis, such as 0,0,1 is supplied) -- note that
    2739 for most crystal systems only one axis makes sense -- and two size parameters
    2740 are defined, one for along the axis and one for in the perpendicular plane;
    2741 with ellipsoidal, six terms are used to define a broadening tensor that has
    2742 arbitrary orientation -- this model may require constraints and is seldom
    2743 needed. Note that size broadening is usually Lorentzian, which corresponds to a
    2744 <span class=SpellE>LGmix</span> value of 1.0; if this value is between 0. and
    2745 1., both Gaussian and Lorentz size broadening is modeled and a value of 0.0 is
    2746 pure Gaussian. Values less than 0. or greater than 1. make no physical sense.
    2747 Typical sensitivity is to no more than 4 <span class=SpellE>μm</span>; beyond
    2748 that the particles are effectively infinite for a diffraction experiment.<o:p></o:p></span></p>
    2749 
    2750 <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
    2751 class=SpellE><b><span style='mso-fareast-font-family:"Times New Roman"'>Microstrain</span></b></span><b><span
    2752 style='mso-fareast-font-family:"Times New Roman"'> peak broadening </span></b><span
     2715factor(s) in microns (μm = 10<sup>-6</sup> m), with the Scherrer constant
     2716assumed as unity. Sizes can be computed in three ways: isotropic, uniaxial and
     2717ellipsoidal. In isotropic broadening, crystallites are assumed to average as
     2718uniform in all directions and a single size value is supplied; with uniaxial
     2719broadening, a preferred direction (as a crystallographic axis, such as 0,0,1 is
     2720supplied) -- note that for most crystal systems only one axis makes sense --
     2721and two size parameters are defined, one for along the axis and one for in the
     2722perpendicular plane; with ellipsoidal, six terms are used to define a
     2723broadening tensor that has arbitrary orientation -- this model may require
     2724constraints and is seldom needed. Note that size broadening is usually
     2725Lorentzian, which corresponds to a LGmix value of 1.0; if this value is between
     27260. and 1., both Gaussian and Lorentz size broadening is modeled and a value of
     27270.0 is pure Gaussian. Values less than 0. or greater than 1. make no physical sense.
     2728Typical sensitivity is to no more than 4 μm; beyond that the particles are
     2729effectively infinite for a diffraction experiment.<o:p></o:p></span></p>
     2730
     2731<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
     2732style='mso-fareast-font-family:"Times New Roman"'>Microstrain peak broadening </span></b><span
    27532733style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    27542734
    27552735<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
    27562736style='mso-fareast-font-family:"Times New Roman"'>is computed as unitless
    2757 fraction of <span class=SpellE>Δd</span>/d (or equivalently ΔQ/Q) times 10<sup>6</sup>.
    2758 <span class=SpellE>Microstrain</span> can be represented in three ways:
    2759 isotropic, <span class=GramE>uniaxial</span> and generalized. In isotropic
    2760 broadening, <span class=SpellE>microstrain</span> broadening assumed to be the
    2761 same in all crystallographic directions and a single value is supplied; with
    2762 uniaxial broadening, a preferred direction (as a crystallographic axis, such as
    2763 0,0,1) is supplied -- note that for most crystal systems only one axis makes
    2764 sense -- and two <span class=SpellE>microstrain</span> parameters are defined,
    2765 one for along the axis and one for in the perpendicular plane; with
    2766 generalized, the Nicole Popa/Peter Stephens second-order expansion model is
    2767 used and the number of terms will depend on the crystal system. It is typically
    2768 possible to refine all terms when significant anisotropic strain broadening is
    2769 present. Note that <span class=SpellE>microstrain</span> broadening is usually
    2770 Lorentzian, which corresponds to a <span class=SpellE>LGmix</span> value of
    2771 1.0; if this value is between 0. and 1., both Gaussian and Lorentz broadening
    2772 is modeled and a value of 0.0 is pure Gaussian. Values less than 0. or greater
    2773 than 1. make no physical sense. Typical <span class=SpellE>microstrain</span>
    2774 is ~1000.<o:p></o:p></span></p>
     2737fraction of Δd/d (or equivalently ΔQ/Q) times 10<sup>6</sup>. Microstrain can
     2738be represented in three ways: isotropic, uniaxial and generalized. In isotropic
     2739broadening, microstrain broadening assumed to be the same in all
     2740crystallographic directions and a single value is supplied; with uniaxial
     2741broadening, a preferred direction (as a crystallographic axis, such as 0,0,1)
     2742is supplied -- note that for most crystal systems only one axis makes sense --
     2743and two microstrain parameters are defined, one for along the axis and one for
     2744in the perpendicular plane; with generalized, the Nicole Popa/Peter Stephens
     2745second-order expansion model is used and the number of terms will depend on the
     2746crystal system. It is typically possible to refine all terms when significant
     2747anisotropic strain broadening is present. Note that microstrain broadening is usually
     2748Lorentzian, which corresponds to a LGmix value of 1.0; if this value is between
     27490. and 1., both Gaussian and Lorentz broadening is modeled and a value of 0.0
     2750is pure Gaussian. Values less than 0. or greater than 1. make no physical
     2751sense. Typical microstrain is ~1000.<o:p></o:p></span></p>
    27752752
    27762753<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
    … …  
    27982775model is possible with the &quot;<u><span style='color:blue'><a href="#Texture">Texture</a></span></u>&quot;
    27992776tab (which usually requires multiple histograms at different sample
    2800 orientations or detector settings). The approaches available here are March-<span
    2801 class=SpellE>Dollase</span>, which requires a definition of a unique axis (in
     2777orientations or detector settings). The approaches available here are
     2778March-Dollase, which requires a definition of a unique axis (in
    28022779crystallographic coordinates) and the relative amount of excess or depletion of
    28032780crystallites in that direction; or Spherical Harmonics, where the selection of
    … …  
    28192796
    28202797<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
    2821 style='mso-fareast-font-family:"Times New Roman"'>Disordered solvent – <span
    2822 class=SpellE>Babinet</span> A &amp; B</span></b><span style='mso-fareast-font-family:
    2823 "Times New Roman"'><o:p></o:p></span></p>
     2798style='mso-fareast-font-family:"Times New Roman"'>Disordered solvent – Babinet
     2799A &amp; B</span></b><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    28242800
    28252801<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
    2826 style='mso-fareast-font-family:"Times New Roman"'>This correction, using the <span
    2827 class=SpellE>Babinet</span> model, is typically used to treat scattering from
    2828 solvent that is not well-ordered in protein structures. It probably makes no
    2829 sense in most any other application. <o:p></o:p></span></p>
     2802style='mso-fareast-font-family:"Times New Roman"'>This correction, using the
     2803Babinet model, is typically used to treat scattering from solvent that is not
     2804well-ordered in protein structures. It probably makes no sense in most any
     2805other application. <o:p></o:p></span></p>
    28302806
    28312807<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
    … …  
    28532829style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    28542830style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    2855 style='mso-fareast-font-family:"Times New Roman"'>The plot selection items allow
    2856 for three dimensional representations of the <span class=SpellE>microstrain</span>
    2857 or crystallite size distributions (which are spheres for isotropic treatments);
    2858 preferred orientation can be plotted as a Psi scan (a plot of relative
    2859 crystallite abundance for a particular reflection as a function of azimuthal
    2860 angle) or as an inverse pole figure (which shows a stereographic projection of
    2861 the probability distribution for different reciprocal lattice directions as
    2862 viewed down the sample cylinder axis). For no texture/preferred orientation
    2863 this figure would be flat = 1.0.<o:p></o:p></span></p>
     2831style='mso-fareast-font-family:"Times New Roman"'>The plot selection items
     2832allow for three dimensional representations of the microstrain or crystallite
     2833size distributions (which are spheres for isotropic treatments); preferred
     2834orientation can be plotted as a Psi scan (a plot of relative crystallite abundance
     2835for a particular reflection as a function of azimuthal angle) or as an inverse
     2836pole figure (which shows a stereographic projection of the probability
     2837distribution for different reciprocal lattice directions as viewed down the
     2838sample cylinder axis). For no texture/preferred orientation this figure would
     2839be flat = 1.0.<o:p></o:p></span></p>
    28642840
    28652841<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
    … …  
    29422918style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    29432919</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Double
    2944 left <span class=GramE>click</span> a Type column heading</b>: a dialog box is
    2945 shown that allows you to select all atoms with that type. <span
    2946 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    2947 color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></p>
     2920left click a Type column heading</b>: a dialog box is shown that allows you to
     2921select all atoms with that type. <span class=MsoHyperlink><span
     2922style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
     2923none;text-underline:none'><o:p></o:p></span></span></p>
    29482924
    29492925<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    29682944the mouse (<b style='mso-bidi-font-weight:normal'>Alt</b> ignored, <b
    29692945style='mso-bidi-font-weight:normal'>Shift</b> &amp; <b style='mso-bidi-font-weight:
    2970 normal'>Ctrl</b> allow selection of multiple <span class=GramE>cells</span> but
    2971 no use is made of them). An individual data item can be cut/pasted anywhere
    2972 including from/to another document. Bad entries are rejected (yellow
    2973 background). If any entry is changed, press <b style='mso-bidi-font-weight:
    2974 normal'>Enter</b> key or select another atom entry to apply the change.<span
    2975 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    2976 text-underline:none'><o:p></o:p></span></span></span></p>
     2946normal'>Ctrl</b> allow selection of multiple cells but no use is made of them).
     2947An individual data item can be cut/pasted anywhere including from/to another
     2948document. Bad entries are rejected (yellow background). If any entry is
     2949changed, press <b style='mso-bidi-font-weight:normal'>Enter</b> key or select
     2950another atom entry to apply the change.<span class=MsoHyperlink><span
     2951style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    29772952
    29782953<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    30162991color:windowtext;text-decoration:none;text-underline:none'><span
    30172992style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3018 </span></span></span></span><![endif]><span class=SpellE><span class=GramE><b
    3019 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>x,y</span></b></span><b
    3020 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>,z</span></b></span><span
     2993</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
     2994style='mso-fareast-font-family:"Times New Roman"'>x,y,z</span></b><span
    30212995style='mso-fareast-font-family:"Times New Roman"'> – change atom coordinate.
    3022 Fractions (<span class=GramE>e.g.</span> 1/3, 1/4) are allowed.<span
    3023 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    3024 text-underline:none'><o:p></o:p></span></span></span></p>
     2996Fractions (e.g. 1/3, 1/4) are allowed.<span class=MsoHyperlink><span
     2997style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    30252998
    30262999<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    30293002color:windowtext;text-decoration:none;text-underline:none'><span
    30303003style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3031 </span></span></span></span><![endif]><span class=SpellE><span class=GramE><b
    3032 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>frac,Uiso</span></b></span><b
    3033 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>,Uij</span></b></span><span
    3034 style='mso-fareast-font-family:"Times New Roman"'> – change these values;
    3035 fractions (e.g. 1/3, 1/4) are allowed.<span class=MsoHyperlink><span
    3036 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
     3004</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
     3005style='mso-fareast-font-family:"Times New Roman"'>frac,Uiso,Uij</span></b><span
     3006style='mso-fareast-font-family:"Times New Roman"'> – change these values; fractions
     3007(e.g. 1/3, 1/4) are allowed.<span class=MsoHyperlink><span style='color:windowtext;
     3008text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    30373009
    30383010<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    30443016style='mso-fareast-font-family:"Times New Roman"'>I/A</span></b><span
    30453017style='mso-fareast-font-family:"Times New Roman"'> – select one of <b
    3046 style='mso-bidi-font-weight:normal'>I</b>(<span class=SpellE>sotropic</span>)
    3047 or <b style='mso-bidi-font-weight:normal'>A</b>(<span class=SpellE>nisotropic</span>);
    3048 the <span class=SpellE><b style='mso-bidi-font-weight:normal'>Uiso</b></span><b
    3049 style='mso-bidi-font-weight:normal'>/<span class=SpellE>Uij</span></b> entries
    3050 will change appropriately. <span class=MsoHyperlink><span style='color:windowtext;
    3051 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
     3018style='mso-bidi-font-weight:normal'>I</b>(sotropic) or <b style='mso-bidi-font-weight:
     3019normal'>A</b>(nisotropic); the <b style='mso-bidi-font-weight:normal'>Uiso/Uij</b>
     3020entries will change appropriately. <span class=MsoHyperlink><span
     3021style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    30523022
    30533023<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    30793049appears with a list of atom parameter names; select one to apply to all
    30803050selected atoms. <b style='mso-bidi-font-weight:normal'>Name</b> will rename
    3081 selected atoms according to position in table (e.g. <span class=GramE>Na(</span>1)
    3082 for Na atom as 1<sup>st</sup> atom in list in row ‘0’). <b style='mso-bidi-font-weight:
    3083 normal'>Type</b> will give periodic table popup; selected element valence will
    3084 be used for all selected atoms and atoms names will be changed. <b
    3085 style='mso-bidi-font-weight:normal'>I/A</b> will give popup with choices to be
    3086 used for all selected atoms. <span class=SpellE><span class=GramE><b
    3087 style='mso-bidi-font-weight:normal'>x,y</b></span><b style='mso-bidi-font-weight:
    3088 normal'>,z</b></span> will give popup for shift to be applied to the parameter
    3089 for all selected atoms. <span class=SpellE><b style='mso-bidi-font-weight:normal'>Uiso</b></span>
    3090 and <b style='mso-bidi-font-weight:normal'>frac</b> will give popup for new value
    3091 to be used for all selected atoms. </p>
     3051selected atoms according to position in table (e.g. Na(1) for Na atom as 1<sup>st</sup>
     3052atom in list in row ‘0’). <b style='mso-bidi-font-weight:normal'>Type</b> will
     3053give periodic table popup; selected element valence will be used for all
     3054selected atoms and atoms names will be changed. <b style='mso-bidi-font-weight:
     3055normal'>I/A</b> will give popup with choices to be used for all selected atoms.
     3056<b style='mso-bidi-font-weight:normal'>x,y,z</b> will give popup for shift to
     3057be applied to the parameter for all selected atoms. <b style='mso-bidi-font-weight:
     3058normal'>Uiso</b> and <b style='mso-bidi-font-weight:normal'>frac</b> will give
     3059popup for new value to be used for all selected atoms. </p>
    30923060
    30933061<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    … …  
    31083076style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    31093077style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b
    3110 style='mso-bidi-font-weight:normal'>Insert atom</b> – insert an H atom (name= <span
    3111 class=SpellE>Unk</span>) at 0,0,0 before the selected atom, it is also drawn as
    3112 an H atom in the structure plot (small white ball).</p>
     3078style='mso-bidi-font-weight:normal'>Insert atom</b> – insert an H atom (name=
     3079Unk) at 0,0,0 before the selected atom, it is also drawn as an H atom in the
     3080structure plot (small white ball).</p>
    31133081
    31143082<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    … …  
    31173085style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b
    31183086style='mso-bidi-font-weight:normal'>Insert viewpoint</b> – insert an H atom
    3119 (name= <span class=SpellE>Unk</span>) before the selected atom with coordinates
    3120 matching the location of the viewpoint, it is also drawn as an H atom in the
    3121 structure plot.</p>
     3087(name= Unk) before the selected atom with coordinates matching the location of
     3088the viewpoint, it is also drawn as an H atom in the structure plot.</p>
    31223089
    31233090<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    … …  
    31653132style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    31663133style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3167 style='mso-bidi-font-weight:normal'>Append atom</b> – add an H atom (name= <span
    3168 class=SpellE>Unk</span>) at 0,0,0 to the end of the atom table, it is also
    3169 drawn as an H atom in the structure plot.</p>
     3134style='mso-bidi-font-weight:normal'>Append atom</b> – add an H atom (name= Unk)
     3135at 0,0,0 to the end of the atom table, it is also drawn as an H atom in the
     3136structure plot.</p>
    31703137
    31713138<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    31743141style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    31753142style='mso-bidi-font-weight:normal'>Append viewpoint</b> – add an H atom (name=
    3176 <span class=SpellE>Unk</span>) to the end of the atom table with coordinates
    3177 matching the location of the viewpoint, it is drawn as an H atom in the
    3178 structure plot.</p>
     3143Unk) to the end of the atom table with coordinates matching the location of the
     3144viewpoint, it is drawn as an H atom in the structure plot.</p>
    31793145
    31803146<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    32123178style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    32133179style='mso-bidi-font-weight:normal'>Reimport atoms </b>– from any importable
    3214 phase file (<span class=GramE>e.g.</span> <span class=SpellE>cif</span>, <span
    3215 class=SpellE>gpx</span>)</p>
     3180phase file (e.g. cif, gpx)</p>
    32163181
    32173182<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    32263191style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    32273192style='mso-bidi-font-weight:normal'>Show Distances &amp; Angles – </b>compute
    3228 distances and angles with <span class=SpellE>esds</span> (if possible) for
    3229 selected atoms. A popup dialog box will appear with distance angle controls.
    3230 NB: if atoms have been added or their type changed, you may need to do a <b
    3231 style='mso-bidi-font-weight:normal'>Reset</b> of this dialog box before
    3232 proceeding.</p>
     3193distances and angles with esds (if possible) for selected atoms. A popup dialog
     3194box will appear with distance angle controls. NB: if atoms have been added or
     3195their type changed, you may need to do a <b style='mso-bidi-font-weight:normal'>Reset</b>
     3196of this dialog box before proceeding.</p>
    32333197
    32343198<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    32363200style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    32373201style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3238 style='mso-bidi-font-weight:normal'>Save Distances &amp; Angles –</b> same as
    3239 a. but reports result to a file with extension <span class=GramE>“.<span
    3240 class=SpellE>disagl</span></span>”.</p>
     3202style='mso-bidi-font-weight:normal'>Save Distances &amp; Angles –</b> same as a.
     3203but reports result to a file with extension “.disagl”.</p>
    32413204
    32423205<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    33113274in/out) <o:p></o:p></span></p>
    33123275
    3313 <p class=MsoNormal style='margin-left:1.25in'><span class=SpellE><b><span
    3314 style='mso-fareast-font-family:"Times New Roman"'>Shift+Left</span></b></span><b><span
    3315 style='mso-fareast-font-family:"Times New Roman"'> Click</span></b><span
    3316 style='mso-fareast-font-family:"Times New Roman"'>: <o:p></o:p></span></p>
     3276<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
     3277"Times New Roman"'>Shift+Left Click</span></b><span style='mso-fareast-font-family:
     3278"Times New Roman"'>: <o:p></o:p></span></p>
    33173279
    33183280<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    … …  
    33243286this way. <o:p></o:p></span></p>
    33253287
    3326 <p class=MsoNormal style='margin-left:1.25in'><span class=SpellE><b><span
    3327 style='mso-fareast-font-family:"Times New Roman"'>Shift+Right</span></b></span><b><span
    3328 style='mso-fareast-font-family:"Times New Roman"'> click</span></b><span
    3329 style='mso-fareast-font-family:"Times New Roman"'>: <o:p></o:p></span></p>
     3288<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
     3289"Times New Roman"'>Shift+Right click</span></b><span style='mso-fareast-font-family:
     3290"Times New Roman"'>: <o:p></o:p></span></p>
    33303291
    33313292<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    33323293"Times New Roman"'>Holding down the shift key while clicking on an atom with
    33333294the right mouse button causes the atom to be selected if previously unselected
    3334 and unselected if previously selected. Any previously selected atoms will be <span
    3335 class=GramE>continue</span> to be selected so shift-right click can be used to
    3336 add atoms to the selection list. If two atoms are overlapped in the current
    3337 view, then the top-most atom will usually be selected. Only atoms in the
    3338 asymmetric unit can be selected from the plot in this way. (On a Mac, <span
    3339 class=SpellE>control+mouse</span> click is an alternate way to do this.) <o:p></o:p></span></p>
     3295and unselected if previously selected. Any previously selected atoms will be
     3296continue to be selected so shift-right click can be used to add atoms to the
     3297selection list. If two atoms are overlapped in the current view, then the
     3298top-most atom will usually be selected. Only atoms in the asymmetric unit can
     3299be selected from the plot in this way. (On a Mac, control+mouse click is an
     3300alternate way to do this.) <o:p></o:p></span></p>
    33403301
    33413302<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
    … …  
    33763337<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    33773338"Times New Roman"'>Pressing the “k” key cycles through the possible slice
    3378 contouring options (none, lines, colors, <span class=SpellE>lines+colors</span>)<o:p></o:p></span></p>
     3339contouring options (none, lines, colors, lines+colors)<o:p></o:p></span></p>
    33793340
    33803341<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
    … …  
    33913352
    33923353<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3393 "Times New Roman"'>Pressing the “<span class=GramE>-“ key</span> steps the
    3394 viewpoint in negative drawing z-direction (toward from viewer). If structure is
    3395 incommensurate, “-” steps the structure and map through the 4<sup>th</sup>
    3396 dimension (-tau).<o:p></o:p></span></p>
     3354"Times New Roman"'>Pressing the “-“ key steps the viewpoint in negative drawing
     3355z-direction (toward from viewer). If structure is incommensurate, “-” steps the
     3356structure and map through the 4<sup>th</sup> dimension (-tau).<o:p></o:p></span></p>
    33973357
    33983358<h4 style='margin-left:.25in'><a name="Phase-Draw_Options"><u>Draw Options</u></a></h4>
    … …  
    34013361
    34023362<p class=MsoNormal style='margin-left:.75in'>The Draw Options window provides
    3403 access to <span class=GramE>a number of</span> items that control how the
    3404 structure is displayed. If a map is available (Fourier of charge flipping), one
    3405 can display a 10<span style='font-family:"Calibri",sans-serif'>Å</span>x10<span
    3406 style='font-family:"Calibri",sans-serif'>Å</span> contoured slice centered at
    3407 the viewpoint. Contouring done as lines, colors or lines &amp; colors combined.
    3408 3-D contouring is also available as green (red for negative density) map grid
    3409 points. One can also draw individual or stack of <span class=SpellE>hkl</span>
    3410 planes across unit cell.</p>
     3363access to a number of items that control how the structure is displayed. If a
     3364map is available (Fourier of charge flipping), one can display a 10<span
     3365style='font-family:"Calibri",sans-serif'>Å</span>x10<span style='font-family:
     3366"Calibri",sans-serif'>Å</span> contoured slice centered at the viewpoint.
     3367Contouring done as lines, colors or lines &amp; colors combined. 3-D contouring
     3368is also available as green (red for negative density) map grid points. One can
     3369also draw individual or stack of hkl planes across unit cell.</p>
    34113370
    34123371<h5 style='margin-left:.5in'>What is drawn here?</h5>
    … …  
    34283387<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
    34293388gives a list of the atoms and bonds that are to be rendered as lines, van der
    3430 Waals radii balls, sticks, balls &amp; sticks, ellipsoids &amp; sticks or <span
    3431 class=SpellE>polyhedra</span>. There are four menus for this tab; Edit allows
    3432 modification of the list of atoms to be rendered, Compute gives some options
    3433 for geometric characterization of selected atoms, Restraints allows definition
    3434 of 4 different types of restraints on the structure and Rigid body allows
    3435 selection of atoms that form a previously defined rigid body.</p>
     3389Waals radii balls, sticks, balls &amp; sticks, ellipsoids &amp; sticks or
     3390polyhedra. There are four menus for this tab; Edit allows modification of the
     3391list of atoms to be rendered, Compute gives some options for geometric characterization
     3392of selected atoms, Restraints allows definition of 4 different types of
     3393restraints on the structure and Rigid body allows selection of atoms that form
     3394a previously defined rigid body.</p>
    34363395
    34373396<h5 style='margin-left:.5in'>What can I do here?</h5>
    … …  
    34683427style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    34693428style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3470 style='mso-bidi-font-weight:normal'>Double left <span class=GramE>click</span>
    3471 a Name, Type and <span class=SpellE>Sym</span> Op column heading</b>: a dialog
    3472 box is shown that allows you to select all atoms with that characteristic. For
    3473 example, selecting the Type column will show all the atom types; your choice
    3474 will then cause all those atoms to be selected.</p>
     3429style='mso-bidi-font-weight:normal'>Double left click a Name, Type and Sym Op
     3430column heading</b>: a dialog box is shown that allows you to select all atoms
     3431with that characteristic. For example, selecting the Type column will show all
     3432the atom types; your choice will then cause all those atoms to be selected.</p>
    34753433
    34763434<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    34783436style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    34793437style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3480 style='mso-bidi-font-weight:normal'>Double left <span class=GramE>click</span>
    3481 a Style, Label or Color column</b>: a dialog box is shown that allows you to
    3482 select a rendering option for all the atoms. For Color a color choice dialog is
    3483 displayed that covers the entire color spectrum. Choose a color by any of the
    3484 means available, press the “Add to Custom Colors”, select that color in the
    3485 Custom colors display and then press OK. <b style='mso-bidi-font-weight:normal'>NB</b>:
    3486 selecting Color will make all atoms have the same color and for Style “blank”
    3487 means the atoms aren’t rendered and thus the drawing will not show any atoms or
    3488 bonds!</p>
     3438style='mso-bidi-font-weight:normal'>Double left click a Style, Label or Color
     3439column</b>: a dialog box is shown that allows you to select a rendering option
     3440for all the atoms. For Color a color choice dialog is displayed that covers the
     3441entire color spectrum. Choose a color by any of the means available, press the
     3442“Add to Custom Colors”, select that color in the Custom colors display and then
     3443press OK. <b style='mso-bidi-font-weight:normal'>NB</b>: selecting Color will
     3444make all atoms have the same color and for Style “blank” means the atoms aren’t
     3445rendered and thus the drawing will not show any atoms or bonds!</p>
    34893446
    34903447<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    34953452operations that can be performed on your selected atoms. You must select one or
    34963453more atoms before using any of the menu items. Most of these items can also be
    3497 accessed by selecting one or more atoms and <span class=GramE>right-clicking</span>
    3498 the mouse.</p>
     3454accessed by selecting one or more atoms and right-clicking the mouse.</p>
    34993455
    35003456<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    35103466style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    35113467style='mso-bidi-font-weight:normal'>Atom label</b> – select the item to be
    3512 shown as a label for each atom in selection. The choices <span class=GramE>are:</span>
    3513 none, type, name or number. (NB: atom labelling slows drawing response time).</p>
     3468shown as a label for each atom in selection. The choices are: none, type, name
     3469or number. (NB: atom labelling slows drawing response time).</p>
    35143470
    35153471<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    35403496style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    35413497style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    3542 </span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    3543 normal'>View point</b></span> – position the plot view point to the first atom
    3544 in the selection.</p>
     3498</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>View
     3499point</b> – position the plot view point to the first atom in the selection.</p>
    35453500
    35463501<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    35593514symmetry operator and unit cell translation selected via a dialog display.
    35603515Duplicate atom positions are not retained. Any anisotropic thermal displacement
    3561 parameters (<span class=SpellE>Uij</span>) will be transformed as appropriate.</p>
     3516parameters (Uij) will be transformed as appropriate.</p>
    35623517
    35633518<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    35763531draw atoms</b> – apply a symmetry operator and unit cell translation to the set
    35773532of selected atoms; they will be changed in place. Any anisotropic thermal
    3578 displacement parameters (<span class=SpellE>Uij</span>) will be transformed as
    3579 appropriate.</p>
     3533displacement parameters (Uij) will be transformed as appropriate.</p>
    35803534
    35813535<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    36123566style='mso-bidi-font-weight:normal'>Create void map </b>– by using a grid of
    36133567probe positions, locate points outside of normal contact distances within a
    3614 structure. Result is a mesh of small blue points in structural voids (<span
    3615 class=GramE>e.g.</span> possible locations of missing water molecules).</p>
     3568structure. Result is a mesh of small blue points in structural voids (e.g.
     3569possible locations of missing water molecules).</p>
    36163570
    36173571<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    36213575style='mso-bidi-font-weight:normal'>Delete atoms</b> – clear the entire draw
    36223576atom table; it is then refilled from the Atoms table. You should do this
    3623 operation after any changes in the Atoms table, <span class=GramE>e.g.</span>
    3624 by a structure refinement.</p>
     3577operation after any changes in the Atoms table, e.g. by a structure refinement.</p>
    36253578
    36263579<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    36543607style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    36553608style='mso-bidi-font-weight:normal'>View pt. dist.</b> - this calculates
    3656 distance from <span class=GramE>view-point</span> to all selected draw atoms;
    3657 result is given on the console window.</p>
     3609distance from view-point to all selected draw atoms; result is given on the
     3610console window.</p>
    36583611
    36593612<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    36683621for the calculated value if a current variance-covariance matrix is available.
    36693622The result is shown on the console window; it may be cut &amp; pasted to
    3670 another application (<span class=GramE>e.g.</span> Microsoft Word).</p>
     3623another application (e.g. Microsoft Word).</p>
    36713624
    36723625<p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto;
    … …  
    36763629style='mso-bidi-font-weight:normal'>Best plane</b> – when 4 or more atoms are
    36773630selected, a best plane is determined for them. The result is shown on the
    3678 console window; it may be cut &amp; pasted to another application (<span
    3679 class=GramE>e.g.</span> Microsoft Word). Shown are the atom coordinates
    3680 transformed to Cartesian best plane coordinates where the largest range is over
    3681 the X-axis and the smallest is over the Z-axis with the origin at the
    3682 unweighted center of the selection. Root mean square displacements along each
    3683 axis for the best plane are also listed. The Z-axis RMS value indicates the
    3684 flatness of the proposed plane. <b style='mso-bidi-font-weight:normal'>NB</b>:
    3685 if you select (<span class=GramE>e.g.</span> all) atoms then Best plane will
    3686 give Cartesian coordinates for these atoms with respect to a coordinate system
    3687 where the X-axis is along the longest axis of the atom grouping and the Z-axis
    3688 is along the shortest distance. The origin is at the unweighted center of the
    3689 selected atoms.</p>
     3631console window; it may be cut &amp; pasted to another application (e.g.
     3632Microsoft Word). Shown are the atom coordinates transformed to Cartesian best
     3633plane coordinates where the largest range is over the X-axis and the smallest
     3634is over the Z-axis with the origin at the unweighted center of the selection.
     3635Root mean square displacements along each axis for the best plane are also
     3636listed. The Z-axis RMS value indicates the flatness of the proposed plane. <b
     3637style='mso-bidi-font-weight:normal'>NB</b>: if you select (e.g. all) atoms then
     3638Best plane will give Cartesian coordinates for these atoms with respect to a
     3639coordinate system where the X-axis is along the longest axis of the atom grouping
     3640and the Z-axis is along the shortest distance. The origin is at the unweighted
     3641center of the selected atoms.</p>
    36903642
    36913643<p class=MsoNormal style='margin-left:58.5pt'>7. Menu ‘<b>Restraints’</b> –
    … …  
    36963648restraint</b> – for selected atom pair (A-B).</p>
    36973649
    3698 <p class=MsoNormal style='margin-left:1.5in;text-indent:-.25in'><span
    3699 class=SpellE>b.</span> <b>Add angle restraint</b> – for selected atom triple
    3700 (A-B-C)</p>
     3650<p class=MsoNormal style='margin-left:1.5in;text-indent:-.25in'>b. <b>Add angle
     3651restraint</b> – for selected atom triple (A-B-C)</p>
    37013652
    37023653<p class=MsoNormal style='margin-left:1.5in;text-indent:-.25in'>c. <b>Add plane
    … …  
    37573708in/out) <o:p></o:p></span></p>
    37583709
    3759 <p class=MsoNormal style='margin-left:1.25in'><span class=SpellE><b><span
    3760 style='mso-fareast-font-family:"Times New Roman"'>Shift+Left</span></b></span><b><span
    3761 style='mso-fareast-font-family:"Times New Roman"'> Click</span></b><span
    3762 style='mso-fareast-font-family:"Times New Roman"'>: <o:p></o:p></span></p>
     3710<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
     3711"Times New Roman"'>Shift+Left Click</span></b><span style='mso-fareast-font-family:
     3712"Times New Roman"'>: <o:p></o:p></span></p>
    37633713
    37643714<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    … …  
    37703720this way. <o:p></o:p></span></p>
    37713721
    3772 <p class=MsoNormal style='margin-left:1.25in'><span class=SpellE><b><span
    3773 style='mso-fareast-font-family:"Times New Roman"'>Shift+Right</span></b></span><b><span
    3774 style='mso-fareast-font-family:"Times New Roman"'> click</span></b><span
    3775 style='mso-fareast-font-family:"Times New Roman"'>: <o:p></o:p></span></p>
     3722<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
     3723"Times New Roman"'>Shift+Right click</span></b><span style='mso-fareast-font-family:
     3724"Times New Roman"'>: <o:p></o:p></span></p>
    37763725
    37773726<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    37783727"Times New Roman"'>Holding down the shift key while clicking on an atom with
    37793728the right mouse button causes the atom to be selected if previously unselected
    3780 and unselected if previously selected. Any previously selected atoms will be <span
    3781 class=GramE>continue</span> to be selected so shift-right click can be used to
    3782 add atoms to the selection list. If two atoms are overlapped in the current
    3783 view, then the top-most atom will usually be selected. Only atoms in the
    3784 asymmetric unit can be selected from the plot in this way. (On a Mac, <span
    3785 class=SpellE>control+mouse</span> click is an alternate way to do this.) <o:p></o:p></span></p>
     3729and unselected if previously selected. Any previously selected atoms will be
     3730continue to be selected so shift-right click can be used to add atoms to the
     3731selection list. If two atoms are overlapped in the current view, then the
     3732top-most atom will usually be selected. Only atoms in the asymmetric unit can
     3733be selected from the plot in this way. (On a Mac, control+mouse click is an
     3734alternate way to do this.) <o:p></o:p></span></p>
    37863735
    37873736<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
    … …  
    38143763<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    38153764"Times New Roman"'>Pressing the “s” key brings up a (large) selection of color
    3816 schemes for the slice contours. Default – “</span><span class=SpellE>RdYlGn</span><span
    3817 style='mso-fareast-font-family:"Times New Roman"'>” (Green – positive, red –
    3818 negative &amp; yellow – zero).<o:p></o:p></span></p>
     3765schemes for the slice contours. Default – “</span>RdYlGn<span style='mso-fareast-font-family:
     3766"Times New Roman"'>” (Green – positive, red – negative &amp; yellow – zero).<o:p></o:p></span></p>
    38193767
    38203768<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
    … …  
    38233771<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    38243772"Times New Roman"'>Pressing the “k” key cycles through the possible slice
    3825 contouring options (none, lines, colors, <span class=SpellE>lines+colors</span>)<o:p></o:p></span></p>
     3773contouring options (none, lines, colors, lines+colors)<o:p></o:p></span></p>
    38263774
    38273775<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
    … …  
    38323780a movie file of the change in the structure along the 4<sup>th</sup> dimension
    38333781(tau). Movie controls are found in the GSAS-II <a href="#Preferences">Configuration
    3834 Variables</a>. Requires the <span class=SpellE>imageio</span> python package be
    3835 available for import – it is not normally available in the GSAS-II version of
    3836 python.<o:p></o:p></span></p>
     3782Variables</a>. Requires the imageio python package be available for import – it
     3783is not normally available in the GSAS-II version of python.<o:p></o:p></span></p>
    38373784
    38383785<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
    … …  
    38483795
    38493796<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3850 "Times New Roman"'>Pressing the “<span class=GramE>-“ key</span> steps the
    3851 viewpoint in negative drawing z-direction (away from viewer). If structure is
    3852 incommensurate, “-” steps the structure and map through the 4<sup>th</sup>
    3853 dimension (-tau).<o:p></o:p></span></p>
     3797"Times New Roman"'>Pressing the “-“ key steps the viewpoint in negative drawing
     3798z-direction (away from viewer). If structure is incommensurate, “-” steps the
     3799structure and map through the 4<sup>th</sup> dimension (-tau).<o:p></o:p></span></p>
    38543800
    38553801<h4 style='margin-left:.25in'><a name="Phase-RB_Models">RB Models</a></h4>
    … …  
    39003846in/out) <o:p></o:p></span></p>
    39013847
    3902 <p style='margin-left:1.0in'>When a rigid body is being inserted into a structure,
    3903 both the rigid body and the crystal structure are displayed. It is useful to
    3904 plan for this by preselecting the atoms in the Draw Atoms list and to have
    3905 atoms displayed as &quot;Sticks&quot; or &quot;Ball-and-Sticks.&quot; The rigid
    3906 body will be displayed as &quot;Ball-and-Sticks<span class=GramE>&quot;</span>
    3907 but bonds will be in green. Use of the Alt key causes the above mouse movements
    3908 to reposition the rigid body rather than change the view of the crystal
    3909 structure:</p>
    3910 
    3911 <p class=MsoNormal style='margin-left:1.25in'><span class=SpellE><b><span
    3912 style='mso-fareast-font-family:"Times New Roman"'>Alt+Left</span></b></span><b><span
    3913 style='mso-fareast-font-family:"Times New Roman"'> drag</span></b><span
    3914 style='mso-fareast-font-family:"Times New Roman"'>: <o:p></o:p></span></p>
     3848<p style='margin-left:1.0in'>When a rigid body is being inserted into a
     3849structure, both the rigid body and the crystal structure are displayed. It is
     3850useful to plan for this by preselecting the atoms in the Draw Atoms list and to
     3851have atoms displayed as &quot;Sticks&quot; or &quot;Ball-and-Sticks.&quot; The
     3852rigid body will be displayed as &quot;Ball-and-Sticks&quot; but bonds will be
     3853in green. Use of the Alt key causes the above mouse movements to reposition the
     3854rigid body rather than change the view of the crystal structure:</p>
     3855
     3856<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
     3857"Times New Roman"'>Alt+Left drag</span></b><span style='mso-fareast-font-family:
     3858"Times New Roman"'>: <o:p></o:p></span></p>
    39153859
    39163860<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    … …  
    39183862down rotates the rigid body around screen x &amp; y axes <o:p></o:p></span></p>
    39193863
    3920 <p class=MsoNormal style='margin-left:1.25in'><span class=SpellE><b><span
    3921 style='mso-fareast-font-family:"Times New Roman"'>Alt+Middle</span></b></span><b><span
    3922 style='mso-fareast-font-family:"Times New Roman"'> drag</span></b><span
    3923 style='mso-fareast-font-family:"Times New Roman"'>: <o:p></o:p></span></p>
     3864<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
     3865"Times New Roman"'>Alt+Middle drag</span></b><span style='mso-fareast-font-family:
     3866"Times New Roman"'>: <o:p></o:p></span></p>
    39243867
    39253868<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    … …  
    39273870down rotates the rigid body around screen z axis (out of screen) <o:p></o:p></span></p>
    39283871
    3929 <p class=MsoNormal style='margin-left:1.25in'><span class=SpellE><b><span
    3930 style='mso-fareast-font-family:"Times New Roman"'>Alt+Right</span></b></span><b><span
    3931 style='mso-fareast-font-family:"Times New Roman"'> drag</span></b><span
    3932 style='mso-fareast-font-family:"Times New Roman"'>: <o:p></o:p></span></p>
     3872<p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family:
     3873"Times New Roman"'>Alt+Right drag</span></b><span style='mso-fareast-font-family:
     3874"Times New Roman"'>: <o:p></o:p></span></p>
    39333875
    39343876<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    3935 "Times New Roman"'>Holding Alt while dragging the mouse with the right button
    3936 down translates the rigid body in the screen x &amp; y directions (rotate the
    3937 plot to see and move in the rigid body in the third direction.) Pressing the
     3877"Times New Roman"'>Holding Alt while dragging the mouse with the right button down
     3878translates the rigid body in the screen x &amp; y directions (rotate the plot
     3879to see and move in the rigid body in the third direction.) Pressing the
    39383880&quot;Lock&quot; checkbox next to the origin location prevents the origin from
    39393881being changed in this way. <o:p></o:p></span></p>
    … …  
    39523894the <a href="#Data">&quot;Data&quot; tab</a>) in a structural study. The sample
    39533895orientation relative to the detector axes is specified here and the detector
    3954 orientation is specified for each histogram as goniometer omega, chi, <span
    3955 class=GramE>phi</span> and azimuth values (details below). These values must be
    3956 specified. </p>
     3896orientation is specified for each histogram as goniometer omega, chi, phi and
     3897azimuth values (details below). These values must be specified. </p>
    39573898
    39583899<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'><o:p>&nbsp;</o:p></p>
    … …  
    39603901<p class=MsoNormal style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    39613902margin-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'>Texture
    3962 analysis using GSAS-II employs spherical harmonics modeling, as described by
    3963 Bunge, &quot;Texture Analysis in Materials Science&quot; (1982), and
    3964 implemented by Von Dreele, J. Appl. <span class=SpellE>Cryst</span>., <b
    3965 style='mso-bidi-font-weight:normal'>30</b>, 517-525 (1997) in GSAS. The even
    3966 part of the orientation distribution function (ODF) via the general axis
    3967 equation</p>
     3903analysis using GSAS-II employs spherical harmonics modeling, as described by Bunge,
     3904&quot;Texture Analysis in Materials Science&quot; (1982), and implemented by
     3905Von Dreele, J. Appl. Cryst., <b style='mso-bidi-font-weight:normal'>30</b>,
     3906517-525 (1997) in GSAS. The even part of the orientation distribution function
     3907(ODF) via the general axis equation</p>
    39683908
    39693909<p class=MsoNormal style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    … …  
    39983938        mso-ascii-font-family:"Cambria Math";mso-hansi-font-family:"Cambria Math";
    39993939        font-style:italic;mso-bidi-font-style:normal'><m:ctrlPr></m:ctrlPr></span></m:naryPr><m:sub><i
    4000         style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>n</m:r><m:r>=-</m:r><m:r>L</m:r></span></i></m:sub><m:sup><i
     3940        style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>n</m:r><m:r>=</m:r><m:r>-</m:r><m:r>L</m:r></span></i></m:sub><m:sup><i
    40013941        style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>L</m:r></span></i></m:sup><m:e><m:sSubSup><m:sSubSupPr><span
    40023942          style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    … …  
    40263966 <v:imagedata src="gsasII-phase_files/image003.png" o:title="" chromakey="white"/>
    40273967</v:shape><![endif]--><![if !vml]><img width=357 height=56
    4028 src="gsasII-phase_files/image050.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
     3968src="gsasII-phase_files/image004.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
    40293969
    40303970<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    … …  
    40483988 <v:imagedata src="gsasII-phase_files/image005.png" o:title="" chromakey="white"/>
    40493989</v:shape><![endif]--><![if !vml]><img width=44 height=35
    4050 src="gsasII-phase_files/image051.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     3990src="gsasII-phase_files/image006.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    40513991style='mso-spacerun:yes'> </span>and <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
    40523992   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    … …  
    40644004 <v:imagedata src="gsasII-phase_files/image007.png" o:title="" chromakey="white"/>
    40654005</v:shape><![endif]--><![if !vml]><img width=40 height=35
    4066 src="gsasII-phase_files/image052.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
     4006src="gsasII-phase_files/image008.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
    40674007take on values according to the sample and crystal symmetries, respectively,
    40684008and thus the two inner summations are over only the resulting unique, nonzero
    … …  
    40904030 <v:imagedata src="gsasII-phase_files/image007.png" o:title="" chromakey="white"/>
    40914031</v:shape><![endif]--><![if !vml]><img width=40 height=35
    4092 src="gsasII-phase_files/image052.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
     4032src="gsasII-phase_files/image008.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
    40934033is defined for each reflection, h, <i>via</i> polar and azimuthal coordinates (<span
    40944034style='font-family:Symbol'>f</span>, <span style='font-family:Symbol'>b</span>)
    40954035of a unit vector coincident with h relative to the reciprocal lattice. For most
    40964036crystal symmetries, <span style='font-family:Symbol'>f</span> is the angle
    4097 between h and the n-<span class=SpellE>th</span> order major rotation axis of
    4098 the space group (usually the c-axis) and <span style='font-family:Symbol'>b</span>
    4099 is the angle between the projections of h and any secondary axis (usually the
    4100 a-axis) onto the normal plane.<span style='mso-spacerun:yes'>  </span>In a
    4101 similar way the sample harmonic factor, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
     4037between h and the n-th order major rotation axis of the space group (usually
     4038the c-axis) and <span style='font-family:Symbol'>b</span> is the angle between
     4039the projections of h and any secondary axis (usually the a-axis) onto the
     4040normal plane.<span style='mso-spacerun:yes'>  </span>In a similar way the
     4041sample harmonic factor, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
    41024042   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    41034043   mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    … …  
    41144054 <v:imagedata src="gsasII-phase_files/image009.png" o:title="" chromakey="white"/>
    41154055</v:shape><![endif]--><![if !vml]><img width=44 height=35
    4116 src="gsasII-phase_files/image053.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
     4056src="gsasII-phase_files/image010.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
    41174057is defined according to polar and azimuthal coordinates (<span
    41184058style='font-family:Symbol'>y</span>, <span style='font-family:Symbol'>g</span>)
    … …  
    41884128 <v:imagedata src="gsasII-phase_files/image011.png" o:title="" chromakey="white"/>
    41894129</v:shape><![endif]--><![if !vml]><img width=428 height=56
    4190 src="gsasII-phase_files/image054.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><br>
     4130src="gsasII-phase_files/image012.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><br>
    41914131Note that this version of the general axis equation differs from that shown in
    41924132Von Dreele (1997) in that the assignment of m and n are reversed. </p>
    … …  
    41964136a diffraction experiment the crystal reflection coordinates (<span
    41974137style='font-family:Symbol'>f</span>, <span style='font-family:Symbol'>b</span>)
    4198 are determined by the choice of reflection index (<span class=SpellE>hkl</span>)
    4199 while the sample coordinates (<span style='font-family:Symbol'>y</span>, <span
    4200 style='font-family:Symbol'>g</span>) are determined by the sample orientation
    4201 on the diffractometer. To define the sample coordinates (<span
    4202 style='font-family:Symbol'>y</span>, <span style='font-family:Symbol'>g</span>),
    4203 we have defined an instrument coordinate system (I, J, K) such that K is normal
    4204 to the diffraction plane and J is coincident with the direction of the incident
     4138are determined by the choice of reflection index (hkl) while the sample
     4139coordinates (<span style='font-family:Symbol'>y</span>, <span style='font-family:
     4140Symbol'>g</span>) are determined by the sample orientation on the
     4141diffractometer. To define the sample coordinates (<span style='font-family:
     4142Symbol'>y</span>, <span style='font-family:Symbol'>g</span>), we have defined
     4143an instrument coordinate system (I, J, K) such that K is normal to the
     4144diffraction plane and J is coincident with the direction of the incident
    42054145radiation beam toward the source. We further define a standard set of
    42064146right-handed eulerian goniometer angles (<span style='font-family:Symbol'>W</span>,
    … …  
    42364176normal'><span style='font-family:Symbol'>F</span>+</b><b style='mso-bidi-font-weight:
    42374177normal'><span style='font-family:Symbol'>F</span><sub>s</sub>)</b><b
    4238 style='mso-bidi-font-weight:normal'><span style='font-family:Symbol'>C</span><span
    4239 class=SpellE><sub>s</sub><span style='font-family:Symbol'>W</span><sub>s</sub></span><o:p></o:p></b></p>
     4178style='mso-bidi-font-weight:normal'><span style='font-family:Symbol'>C</span><sub>s</sub></b><b
     4179style='mso-bidi-font-weight:normal'><span style='font-family:Symbol'>W</span><sub>s</sub><o:p></o:p></b></p>
    42404180
    42414181<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    … …  
    42464186
    42474187<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    4248 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
    4249 class=GramE><i>cos</i>(</span><span style='font-family:Symbol'>y</span>) = <!--[if gte msEquation 12]><m:oMath><i
     4188margin-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'><i>cos</i>(<span
     4189style='font-family:Symbol'>y</span>) = <!--[if gte msEquation 12]><m:oMath><i
    42504190 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>M</m:r></span></i><m:d><m:dPr><span
    42514191   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    … …  
    42634203top:15.0pt;mso-text-raise:-15.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    42644204EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    4265  type="#_x0000_t75" style='width:33.75pt;height:50.25pt'>
     4205 type="#_x0000_t75" style='width:33.95pt;height:50.2pt'>
    42664206 <v:imagedata src="gsasII-phase_files/image013.png" o:title="" chromakey="white"/>
    42674207</v:shape><![endif]--><![if !vml]><img width=45 height=67
    4268 src="gsasII-phase_files/image055.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     4208src="gsasII-phase_files/image014.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    42694209style='mso-spacerun:yes'> </span>and<span style='mso-spacerun:yes'>   </span><i>tan</i>(<span
    42704210style='font-family:Symbol'>g</span>) = <!--[if gte msEquation 12]><m:oMath><m:f><m:fPr><m:type
    … …  
    42984238top:15.0pt;mso-text-raise:-15.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    42994239EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    4300  type="#_x0000_t75" style='width:80.25pt;height:50.25pt'>
     4240 type="#_x0000_t75" style='width:80.1pt;height:50.2pt'>
    43014241 <v:imagedata src="gsasII-phase_files/image015.png" o:title="" chromakey="white"/>
    43024242</v:shape><![endif]--><![if !vml]><img width=107 height=67
    4303 src="gsasII-phase_files/image056.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
     4243src="gsasII-phase_files/image016.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
    43044244
    43054245<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    … …  
    43204260 <v:imagedata src="gsasII-phase_files/image017.png" o:title="" chromakey="white"/>
    43214261</v:shape><![endif]--><![if !vml]><img width=61 height=35
    4322 src="gsasII-phase_files/image057.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     4262src="gsasII-phase_files/image018.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    43234263style='mso-spacerun:yes'> </span>and <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
    43244264   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    … …  
    43364276 <v:imagedata src="gsasII-phase_files/image019.png" o:title="" chromakey="white"/>
    43374277</v:shape><![endif]--><![if !vml]><img width=58 height=35
    4338 src="gsasII-phase_files/image058.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
     4278src="gsasII-phase_files/image020.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
    43394279are developed from (those for <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
    43404280   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    … …  
    43494289top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    43504290EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    4351  type="#_x0000_t75" style='width:45.65pt;height:26.35pt'>
     4291 type="#_x0000_t75" style='width:45.75pt;height:26.25pt'>
    43524292 <v:imagedata src="gsasII-phase_files/image017.png" o:title="" chromakey="white"/>
    43534293</v:shape><![endif]--><![if !vml]><img width=61 height=35
    4354 src="gsasII-phase_files/image057.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     4294src="gsasII-phase_files/image018.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    43554295style='mso-spacerun:yes'> </span>are similar)</p>
    43564296
    … …  
    44034343"Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US;
    44044344mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
    4405  id="_x0000_i1025" type="#_x0000_t75" style='width:158.2pt;height:42.1pt'>
     4345 id="_x0000_i1025" type="#_x0000_t75" style='width:158.25pt;height:42pt'>
    44064346 <v:imagedata src="gsasII-phase_files/image021.png" o:title="" chromakey="white"/>
    44074347</v:shape><![endif]--><![if !vml]><img width=211 height=56
    4408 src="gsasII-phase_files/image059.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
     4348src="gsasII-phase_files/image022.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
    44094349
    44104350<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    … …  
    44254365top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    44264366EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    4427  type="#_x0000_t75" style='width:30.95pt;height:26.35pt'>
     4367 type="#_x0000_t75" style='width:30.75pt;height:26.25pt'>
    44284368 <v:imagedata src="gsasII-phase_files/image023.png" o:title="" chromakey="white"/>
    44294369</v:shape><![endif]--><![if !vml]><img width=41 height=35
    4430 src="gsasII-phase_files/image060.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
     4370src="gsasII-phase_files/image024.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
    44314371are defined via a Fourier expansion as</p>
    44324372
    … …  
    44784418 <v:imagedata src="gsasII-phase_files/image025.png" o:title="" chromakey="white"/>
    44794419</v:shape><![endif]--><![if !vml]><img width=199 height=70
    4480 src="gsasII-phase_files/image061.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
     4420src="gsasII-phase_files/image026.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
    44814421
    44824422<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    … …  
    45314471 <v:imagedata src="gsasII-phase_files/image027.png" o:title="" chromakey="white"/>
    45324472</v:shape><![endif]--><![if !vml]><img width=205 height=70
    4533 src="gsasII-phase_files/image062.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
     4473src="gsasII-phase_files/image028.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
    45344474
    45354475<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    45364476margin-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'>for
    4537 <span class=SpellE>n</span> odd.<span style='mso-spacerun:yes'>  </span>Each sum
    4538 is only over either the even or odd values of s, respectively, because of the
    4539 properties of the Fourier coefficients, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
     4477n odd.<span style='mso-spacerun:yes'>  </span>Each sum is only over either the
     4478even or odd values of s, respectively, because of the properties of the Fourier
     4479coefficients, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
    45404480   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    45414481   mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
    … …  
    45524492 <v:imagedata src="gsasII-phase_files/image029.png" o:title="" chromakey="white"/>
    45534493</v:shape><![endif]--><![if !vml]><img width=29 height=35
    4554 src="gsasII-phase_files/image063.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>.<span
     4494src="gsasII-phase_files/image030.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>.<span
    45554495style='mso-spacerun:yes'>  </span>These Fourier coefficients are determined so
    45564496that the definition </p>
    … …  
    46744614"Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US;
    46754615mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
    4676  id="_x0000_i1025" type="#_x0000_t75" style='width:408.7pt;height:55.25pt'>
     4616 id="_x0000_i1025" type="#_x0000_t75" style='width:408.7pt;height:55.5pt'>
    46774617 <v:imagedata src="gsasII-phase_files/image031.png" o:title="" chromakey="white"/>
    46784618</v:shape><![endif]--><![if !vml]><img width=545 height=74
    4679 src="gsasII-phase_files/image064.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
     4619src="gsasII-phase_files/image032.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
    46804620
    46814621<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    … …  
    47104650top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    47114651EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    4712  type="#_x0000_t75" style='width:101.9pt;height:26.35pt'>
     4652 type="#_x0000_t75" style='width:102pt;height:26.25pt'>
    47134653 <v:imagedata src="gsasII-phase_files/image033.png" o:title="" chromakey="white"/>
    47144654</v:shape><![endif]--><![if !vml]><img width=136 height=35
    4715 src="gsasII-phase_files/image065.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     4655src="gsasII-phase_files/image034.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    47164656style='mso-spacerun:yes'> </span>and <!--[if gte msEquation 12]><m:oMath><m:func><m:funcPr><span
    47174657   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    … …  
    47434683top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    47444684EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    4745  type="#_x0000_t75" style='width:94.3pt;height:26.35pt'>
     4685 type="#_x0000_t75" style='width:94.5pt;height:26.25pt'>
    47464686 <v:imagedata src="gsasII-phase_files/image035.png" o:title="" chromakey="white"/>
    47474687</v:shape><![endif]--><![if !vml]><img width=126 height=35
    4748 src="gsasII-phase_files/image066.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     4688src="gsasII-phase_files/image036.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    47494689style='mso-spacerun:yes'> </span>are combined depending on the symmetry and the
    47504690value of n (or m) along with appropriate normalization coefficients to give the
    … …  
    47624702top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    47634703EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    4764  type="#_x0000_t75" style='width:45.65pt;height:26.35pt'>
     4704 type="#_x0000_t75" style='width:45.75pt;height:26.25pt'>
    47654705 <v:imagedata src="gsasII-phase_files/image037.png" o:title="" chromakey="white"/>
    47664706</v:shape><![endif]--><![if !vml]><img width=61 height=35
    4767 src="gsasII-phase_files/image067.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     4707src="gsasII-phase_files/image038.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    47684708style='mso-spacerun:yes'> </span>and <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
    47694709   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    … …  
    47824722 <v:imagedata src="gsasII-phase_files/image039.png" o:title="" chromakey="white"/>
    47834723</v:shape><![endif]--><![if !vml]><img width=63 height=35
    4784 src="gsasII-phase_files/image068.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>.<span
     4724src="gsasII-phase_files/image040.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>.<span
    47854725style='mso-spacerun:yes'>  </span>For cubic crystal symmetry, the term <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
    47864726   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    … …  
    47994739 <v:imagedata src="gsasII-phase_files/image037.png" o:title="" chromakey="white"/>
    48004740</v:shape><![endif]--><![if !vml]><img width=61 height=35
    4801 src="gsasII-phase_files/image067.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     4741src="gsasII-phase_files/image038.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    48024742style='mso-spacerun:yes'> </span>is obtained directly from the Fourier
    48034743expansion</p>
    … …  
    48584798 <v:imagedata src="gsasII-phase_files/image041.png" o:title="" chromakey="white"/>
    48594799</v:shape><![endif]--><![if !vml]><img width=248 height=72
    4860 src="gsasII-phase_files/image069.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
     4800src="gsasII-phase_files/image042.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
    48614801
    48624802<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    … …  
    48764816 <v:imagedata src="gsasII-phase_files/image043.png" o:title="" chromakey="white"/>
    48774817</v:shape><![endif]--><![if !vml]><img width=25 height=39
    4878 src="gsasII-phase_files/image070.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
     4818src="gsasII-phase_files/image044.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
    48794819as tabulated by Bunge (1982). </p>
    48804820
    … …  
    48964836 <v:imagedata src="gsasII-phase_files/image045.png" o:title="" chromakey="white"/>
    48974837</v:shape><![endif]--><![if !vml]><img width=29 height=35
    4898 src="gsasII-phase_files/image071.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
     4838src="gsasII-phase_files/image046.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]>,
    48994839and the three sample orientation angles, <span style='font-family:Symbol'>W</span><sub>s</sub>,
    49004840<span style='font-family:Symbol'>C</span><sub>s</sub>, <span style='font-family:
    … …  
    49124852top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    49134853EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    4914  type="#_x0000_t75" style='width:21.8pt;height:26.35pt'>
     4854 type="#_x0000_t75" style='width:21.75pt;height:26.25pt'>
    49154855 <v:imagedata src="gsasII-phase_files/image045.png" o:title="" chromakey="white"/>
    49164856</v:shape><![endif]--><![if !vml]><img width=29 height=35
    4917 src="gsasII-phase_files/image071.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     4857src="gsasII-phase_files/image046.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    49184858style='mso-spacerun:yes'> </span>and the sample orientation angles <span
    49194859style='font-family:Symbol'>W</span><sub>s</sub>, <span style='font-family:Symbol'>C</span><sub>s</sub>,
    … …  
    49684908"Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US;
    49694909mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
    4970  id="_x0000_i1025" type="#_x0000_t75" style='width:180.5pt;height:54.25pt'>
     4910 id="_x0000_i1025" type="#_x0000_t75" style='width:180.75pt;height:54pt'>
    49714911 <v:imagedata src="gsasII-phase_files/image047.png" o:title="" chromakey="white"/>
    49724912</v:shape><![endif]--><![if !vml]><img width=241 height=72
    4973 src="gsasII-phase_files/image072.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
     4913src="gsasII-phase_files/image048.png" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p>
    49744914
    49754915<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    … …  
    50194959
    50204960<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
    5021 usual arrangement here is to have a capillary sample perpendicular to the diffraction
    5022 plane. The capillary may be spun about its cylinder axis for powder averaging
    5023 and to impose cylindrical symmetry on the texture which is perpendicular to the
    5024 diffraction plane. Thus, <span style='font-family:Symbol'>W</span>, <span
    5025 style='font-family:Symbol'>F = 0</span> and <span style='font-family:Symbol'>C
    5026 =90.</span></p>
     4961usual arrangement here is to have a capillary sample perpendicular to the
     4962diffraction plane. The capillary may be spun about its cylinder axis for powder
     4963averaging and to impose cylindrical symmetry on the texture which is
     4964perpendicular to the diffraction plane. Thus, <span style='font-family:Symbol'>W</span>,
     4965<span style='font-family:Symbol'>F = 0</span> and <span style='font-family:
     4966Symbol'>C =90.</span></p>
    50274967
    50284968<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'>3)
    … …  
    50474987<p class=MsoNormal style='margin-left:.75in'>1. Menu ‘<b>Texture/Refine
    50484988texture’ </b>– refines the spherical harmonics texture model using the
    5049 predetermined values of <span class=SpellE>Prfo</span> for all histogram
    5050 reflection sets as demonstrated in <a
     4989predetermined values of Prfo for all histogram reflection sets as demonstrated
     4990in <a
    50514991href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DTexture/Texture%20analysis%20of%202D%20data%20in%20GSAS-II.htm">2DTexture</a>
    50524992tutorial.</p>
    … …  
    50755015style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    50765016</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>as
    5077 an &quot;Axial pole distribution&quot; which simulates the intensity of a reflection
    5078 during a phi scan.<o:p></o:p></span></p>
     5017an &quot;Axial pole distribution&quot; which simulates the intensity of a
     5018reflection during a phi scan.<o:p></o:p></span></p>
    50795019
    50805020<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    50855025</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>as
    50865026a &quot;pole figure,&quot; where a projection of the probability of finding a
    5087 pole (<span class=SpellE>hkl</span>) is plotted as a function of sample
    5088 orientation.<o:p></o:p></span></p>
     5027pole (hkl) is plotted as a function of sample orientation.<o:p></o:p></span></p>
    50895028
    50905029<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    50955034</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>as
    50965035an &quot;inverse pole figure,&quot; where a projection of the probability of
    5097 finding all poles (<span class=SpellE>hkls</span>) is plotted for a selected
    5098 sample orientation.<o:p></o:p></span></p>
     5036finding all poles (hkls) is plotted for a selected sample orientation.<o:p></o:p></span></p>
    50995037
    51005038<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    51055043</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>or
    51065044as a &quot;3D pole distribution&quot; that shows the probability of finding a
    5107 pole (<span class=SpellE>hkl</span>) is plotted as a function of sample
    5108 orientation. <o:p></o:p></span></p>
     5045pole (hkl) is plotted as a function of sample orientation. <o:p></o:p></span></p>
    51095046
    51105047<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    51115048margin-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
    51125049style='mso-fareast-font-family:"Times New Roman"'>For Axial distribution, pole
    5113 figure and 3D pole distribution one must next select the <span class=SpellE>hkl</span>
    5114 of the desired pole, for Inverse pole figure one must select a sample direction
    5115 (typically 0 0 1).<o:p></o:p></span></p>
     5050figure and 3D pole distribution one must next select the hkl of the desired
     5051pole, for Inverse pole figure one must select a sample direction (typically 0 0
     50521).<o:p></o:p></span></p>
    51165053
    51175054<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    51625099
    51635100<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5164 auto;text-indent:-.25in;mso-list:l9 level1 lfo14;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
    5165 name=Phase-Pawley><![if !supportLists]><span style='mso-fareast-font-family:
    5166 "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5167 </span></span></span><![endif]>Select the <b style='mso-bidi-font-weight:normal'>mag</b>
    5168 column – the entries will be sorted with the largest at the top.</a></p>
     5101auto;text-indent:-.25in;mso-list:l9 level1 lfo14;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
     5102style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     5103style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
     5104the <b style='mso-bidi-font-weight:normal'>mag</b> column – the entries will be
     5105sorted with the largest at the top.</p>
    51695106
    51705107<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5171 auto;text-indent:-.25in;mso-list:l9 level1 lfo14;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
    5172 name="Phase-Pawley_reflections"><![if !supportLists]><span style='mso-fareast-font-family:"Times New Roman"'><span
    5173 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5174 </span></span></span><![endif]>Select the </a><span class=SpellE><span
    5175 style='mso-bookmark:Pawley'><b style='mso-bidi-font-weight:normal'>dzero</b></span></span><span
    5176 style='mso-bookmark:Pawley'> column – the entries will be sorted with the
    5177 smallest (distance from origin) at the top.</span></p>
     5108auto;text-indent:-.25in;mso-list:l9 level1 lfo14;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
     5109style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
     5110style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
     5111the <b style='mso-bidi-font-weight:normal'>dzero</b> column – the entries will
     5112be sorted with the smallest (distance from origin) at the top.</p>
    51785113
    51795114<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5180 auto;text-indent:-.25in;mso-list:l9 level1 lfo14;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
    5181 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5182 "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5183 </span></span></span><![endif]>Select the <span class=SpellE><b>dcent</b></span>
    5184 column – the entries will be sorted with the smallest distance from the unit
    5185 cell center at the top.</span></p>
     5115auto;text-indent:-.25in;mso-list:l9 level1 lfo14;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
     5116style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
     5117style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
     5118the <b>dcent</b> column – the entries will be sorted with the smallest distance
     5119from the unit cell center at the top.</p>
    51865120
    51875121<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5188 auto;text-indent:-.25in;mso-list:l9 level1 lfo14;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
    5189 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5190 "Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5191 </span></span></span><![endif]>Menu <b style='mso-bidi-font-weight:normal'>‘Map
    5192 peaks<span class=GramE>’ <span style='font-weight:normal'><span
    5193 style='mso-spacerun:yes'> </span>–</span></span></b></span></p>
    5194 
    5195 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5196 auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5197 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5198 "Times New Roman"'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5199 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Move
    5200 peaks</b> – this copies selected peaks to the </span><a href="#Phase-Atoms"><span
    5201 style='mso-bookmark:Pawley'>Atoms</span><span style='mso-bookmark:Pawley'></span></a><span
    5202 style='mso-bookmark:Pawley'> list and the </span><a href="#_Draw_Atoms"><span
    5203 style='mso-bookmark:Pawley'>Draw Atoms</span><span style='mso-bookmark:Pawley'></span></a><span
    5204 style='mso-bookmark:Pawley'> list. They will be appended to the end of each
    5205 list each with the name ‘UNK’ and the atom type as ‘H’. They will also be drawn
    5206 as small white spheres at their respective positions in the structure drawing.
    5207 You should next go to the </span><a href="#Phase-Atoms"><span style='mso-bookmark:
    5208 Pawley'>Atoms</span><span style='mso-bookmark:Pawley'></span></a><span
    5209 style='mso-bookmark:Pawley'> page and change the atom type to whatever element
    5210 you desire; it will be renamed automatically.</span></p>
    5211 
    5212 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5213 auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5214 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5215 "Times New Roman"'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5216 </span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    5217 normal'>View point</b></span><b style='mso-bidi-font-weight:normal'> </b>– this
    5218 positions the viewpoint (large 3D RGB cross) at the 1<sup>st</sup> selected
    5219 peak.</span></p>
    5220 
    5221 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5222 auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5223 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5224 "Times New Roman"'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5225 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>View pt</b>.
    5226 <b style='mso-bidi-font-weight:normal'>dist</b>. – this calculates distance
    5227 from viewpoint to all selected map peaks.</span></p>
    5228 
    5229 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5230 auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5231 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5232 "Times New Roman"'><span style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5233 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Hide/Show
    5234 bonds </b>– toggle display of lines (bonds) between peaks</span></p>
    5235 
    5236 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5237 auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5238 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5239 "Times New Roman"'><span style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5240 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Calc <span
    5241 class=SpellE>dist</span>/ang </b>– if 2 peaks are selected, this calculates the
    5242 distance between them. If 3 peaks are selected this calculates the angle
    5243 between them; NB: selection order matters. If selection is not 2 or 3 peaks
    5244 this is ignored. Output is on the console window.</span></p>
    5245 
    5246 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5247 auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5248 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5249 "Times New Roman"'><span style='mso-list:Ignore'>f.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     5122auto;text-indent:-.25in;mso-list:l9 level1 lfo14;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
     5123style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
     5124style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     5125<b style='mso-bidi-font-weight:normal'>‘Map peaks’ </b><span
     5126style='mso-spacerun:yes'> </span>–</p>
     5127
     5128<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5129auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5130style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
     5131style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5132style='mso-bidi-font-weight:normal'>Move peaks</b> – this copies selected peaks
     5133to the <a href="#Phase-Atoms">Atoms</a> list and the <a href="#_Draw_Atoms">Draw
     5134Atoms</a> list. They will be appended to the end of each list each with the
     5135name ‘UNK’ and the atom type as ‘H’. They will also be drawn as small white
     5136spheres at their respective positions in the structure drawing. You should next
     5137go to the <a href="#Phase-Atoms">Atoms</a> page and change the atom type to
     5138whatever element you desire; it will be renamed automatically.</p>
     5139
     5140<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5141auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5142style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
     5143style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5144style='mso-bidi-font-weight:normal'>View point </b>– this positions the
     5145viewpoint (large 3D RGB cross) at the 1<sup>st</sup> selected peak.</p>
     5146
     5147<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5148auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5149style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
     5150style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5151style='mso-bidi-font-weight:normal'>View pt</b>. <b style='mso-bidi-font-weight:
     5152normal'>dist</b>. – this calculates distance from viewpoint to all selected map
     5153peaks.</p>
     5154
     5155<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5156auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5157style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
     5158style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5159style='mso-bidi-font-weight:normal'>Hide/Show bonds </b>– toggle display of
     5160lines (bonds) between peaks</p>
     5161
     5162<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5163auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5164style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
     5165style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5166style='mso-bidi-font-weight:normal'>Calc dist/ang </b>– if 2 peaks are
     5167selected, this calculates the distance between them. If 3 peaks are selected
     5168this calculates the angle between them; NB: selection order matters. If
     5169selection is not 2 or 3 peaks this is ignored. Output is on the console window.</p>
     5170
     5171<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5172auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5173style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
     5174style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    52505175</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Equivalent
    52515176peaks </b>– this selects all peaks related to selection by space group
    5252 symmetry.</span></p>
    5253 
    5254 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5255 auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5256 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5257 "Times New Roman"'><span style='mso-list:Ignore'>g.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5258 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Invert
    5259 peak positions </b>– inversion through cell center of map and all positions.</span></p>
    5260 
    5261 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5262 auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5263 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5264 "Times New Roman"'><span style='mso-list:Ignore'>h.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5265 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Roll
    5266 charge flip map </b>– popup allows shifting of the map &amp; all peak positions
    5267 by unit cell fractions; can be along combinations of axes.</span></p>
    5268 
    5269 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5270 auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5271 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5272 "Times New Roman"'><span style='mso-list:Ignore'>i.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     5177symmetry.</p>
     5178
     5179<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5180auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5181style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
     5182style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5183style='mso-bidi-font-weight:normal'>Invert peak positions </b>– inversion
     5184through cell center of map and all positions.</p>
     5185
     5186<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5187auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5188style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span
     5189style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5190style='mso-bidi-font-weight:normal'>Roll charge flip map </b>– popup allows
     5191shifting of the map &amp; all peak positions by unit cell fractions; can be
     5192along combinations of axes.</p>
     5193
     5194<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5195auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5196style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span
     5197style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    52735198</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Unique
    52745199peaks </b>– this selects only the unique peak positions amongst those selected;
    52755200a popup allows selection of atom subset closest to x=0, y=0, z=0 origin or
    5276 center.</span></p>
    5277 
    5278 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5279 auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5280 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5281 "Times New Roman"'><span style='mso-list:Ignore'>j.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     5201center.</p>
     5202
     5203<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5204auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5205style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span
     5206style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    52825207</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Save
    5283 peaks </b>– saves the peak list as a csv file.</span></p>
    5284 
    5285 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5286 auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5287 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5288 "Times New Roman"'><span style='mso-list:Ignore'>k.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5289 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Delete
    5290 peaks </b>– this deletes selected peaks. The shading on the remaining peaks is
    5291 changed to reflect any change in the maximum after deletion.</span></p>
     5208peaks </b>– saves the peak list as a csv file.</p>
     5209
     5210<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5211auto;text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5212style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>k.<span
     5213style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5214style='mso-bidi-font-weight:normal'>Delete peaks </b>– this deletes selected
     5215peaks. The shading on the remaining peaks is changed to reflect any change in
     5216the maximum after deletion.</p>
    52925217
    52935218<p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto;
    5294 text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><span
    5295 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5296 "Times New Roman"'><span style='mso-list:Ignore'>l.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     5219text-indent:-.25in;mso-list:l9 level2 lfo14;tab-stops:list 1.0in'><![if !supportLists]><span
     5220style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>l.<span
     5221style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    52975222</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Clear
    52985223peaks </b>– this deletes all the peaks in the map peak list; they are also
    5299 removed from the crystal structure drawing plot.</span></p>
    5300 
    5301 <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'><span
    5302 style='mso-bookmark:Pawley'>Pawley reflections<span class=MsoHyperlink><span
    5303 style='color:#5B9BD5;mso-themecolor:accent1'><o:p></o:p></span></span></span></h4>
    5304 
    5305 <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
    5306 style='mso-bookmark:Pawley'>This gives the list of reflections used in a Pawley
    5307 refinement and they can only be seen if the ‘Do Pawley refinement’ flag is set
    5308 (see </span><a href="#_General_Phase_Parameters"><span style='mso-bookmark:
    5309 Pawley'>General</span><span style='mso-bookmark:Pawley'></span></a><span
    5310 style='mso-bookmark:Pawley'>).</span></p>
    5311 
    5312 <h5 style='margin-left:.5in'><span style='mso-bookmark:Pawley'>What can I do
    5313 here?</span></h5>
     5224removed from the crystal structure drawing plot.</p>
     5225
     5226<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
     5227name="_Pawley_reflections"></a><o:p>&nbsp;</o:p></p>
     5228
     5229<h4>Pawley reflections</h4>
     5230
     5231<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
     5232gives the list of reflections used in a Pawley refinement; for them to be used the
     5233‘Do Pawley refinement’ flag must be set (see <a
     5234href="#_General_Phase_Parameters">General</a>), otherwise they are ignored.</p>
     5235
     5236<h5 style='margin-left:.5in'>What can I do here?</h5>
    53145237
    53155238<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    5316 text-indent:-.25in;mso-list:l3 level1 lfo16;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
    5317 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5318 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5319 </span></span></span><![endif]>Menu <b style='mso-bidi-font-weight:normal'>‘Operations’</b>
    5320 –</span></p>
    5321 
    5322 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5323 auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
    5324 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5325 "Times New Roman"'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5326 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Pawley settings
    5327 </b>– allows setting of Pawley parameters as shown on the </span><a
    5328 href="#_General_Phase_Parameters"><span style='mso-bookmark:Pawley'>General</span><span
    5329 style='mso-bookmark:Pawley'></span></a><span style='mso-bookmark:Pawley'> tab.</span></p>
    5330 
    5331 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5332 auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
    5333 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5334 "Times New Roman"'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5335 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Pawley
    5336 create</b> – this creates a new set of Pawley reflections, over writing any
    5337 preexisting Pawley set. They are generated with d-spacings larger than the
    5338 limit set as ‘Pawley <span class=SpellE>dmin</span>’ in the General tab for
    5339 this phase. By <span class=GramE>default</span> the refine flags are not set
    5340 and the <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>) = 100.0.</span></p>
    5341 
    5342 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5343 auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
    5344 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5345 "Times New Roman"'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5346 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Pawley
    5347 estimate</b> – this attempts an estimate of <span class=SpellE>Fsq</span>(<span
    5348 class=SpellE>hkl</span>) from the peak heights of the reflection as seen in the
    5349 1<sup>st</sup> powder pattern of those selected in the </span><a href="#_Data"><span
    5350 style='mso-bookmark:Pawley'>Data</span><span style='mso-bookmark:Pawley'></span></a><span
    5351 style='mso-bookmark:Pawley'> tab.</span></p>
    5352 
    5353 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5354 auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
    5355 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5356 "Times New Roman"'><span style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5357 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Pawley
    5358 update </b>– process Pawley reflection set for negative intensities. These are
    5359 set to ½ its absolute value for noncentrosymmetric space groups (0.3
    5360 otherwise); the refine flag is turned off. One should repeat Pawley refinement
    5361 and then do </span><span style='mso-bookmark:Pawley'><b><span style='font-family:
     5239text-indent:-.25in;mso-list:l3 level1 lfo16;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
     5240style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     5241style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     5242<b style='mso-bidi-font-weight:normal'>‘Operations’</b> –</p>
     5243
     5244<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5245auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
     5246style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
     5247style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5248style='mso-bidi-font-weight:normal'>Pawley settings </b>– allows setting of
     5249Pawley parameters as shown on the <a href="#_General_Phase_Parameters">General</a>
     5250tab.</p>
     5251
     5252<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5253auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
     5254style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
     5255style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5256style='mso-bidi-font-weight:normal'>Pawley create</b> – this creates a new set
     5257of Pawley reflections, over writing any preexisting Pawley set. They are
     5258generated with d-spacings larger than the limit set as ‘Pawley dmin’ in the
     5259General tab for this phase. By default, the refine flags are not set and the
     5260Fsq(hkl) = 100.0.</p>
     5261
     5262<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5263auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
     5264style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
     5265style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5266style='mso-bidi-font-weight:normal'>Pawley estimate</b> – this attempts an
     5267estimate of Fsq(hkl) from the peak heights of the reflection as seen in the 1<sup>st</sup>
     5268powder pattern of those shown as ‘<b>Use’</b> in the <a href="#_Data">Data</a>
     5269tab for this phase.</p>
     5270
     5271<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5272auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
     5273style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
     5274style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5275style='mso-bidi-font-weight:normal'>Pawley update </b>– process Pawley
     5276reflection set for negative intensities. These are set to ½ its absolute value
     5277for noncentrosymmetric space groups (0.3 otherwise); the refine flag is turned
     5278off. One should repeat Pawley refinement and then do <b><span style='font-family:
    53625279"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    53635280minor-latin;mso-bidi-theme-font:minor-latin'>Refine all</span></b> and an
    5364 additional refinement. Repeat as needed to remove negative intensities. Set </span><span
    5365 style='mso-bookmark:Pawley'><b><span style='font-family:"Calibri",sans-serif;
     5281additional refinement. Repeat as needed to remove negative intensities. Set <b><span
     5282style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     5283mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Pawley neg.
     5284wt.</span></b> (see <b><span style='font-family:"Calibri",sans-serif;
    53665285mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    5367 minor-latin'>Pawley neg. wt.</span></b> (see </span><span style='mso-bookmark:
    5368 Pawley'><b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    5369 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Pawley
    5370 settings</span></b>) to further suppress negatives.</span></p>
    5371 
    5372 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5373 auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
    5374 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5375 "Times New Roman"'><span style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     5286minor-latin'>Pawley settings</span></b>) to further suppress negatives.</p>
     5287
     5288<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5289auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
     5290style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
     5291style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5292style='mso-bidi-font-weight:normal'>Refine all </b>– sets all refine flags</p>
     5293
     5294<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5295auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
     5296style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
     5297style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    53765298</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Refine
    5377 all </b>– sets all refine flags</span></p>
    5378 
    5379 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5380 auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
    5381 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5382 "Times New Roman"'><span style='mso-list:Ignore'>f.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5383 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Refine
    5384 none </b>– clears all refine flags</span></p>
    5385 
    5386 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5387 auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
    5388 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5389 "Times New Roman"'><span style='mso-list:Ignore'>g.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5390 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Toggle
    5391 selection </b>– toggles all refine flags</span></p>
     5299none </b>– clears all refine flags</p>
     5300
     5301<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5302auto;text-indent:-.25in;mso-list:l7 level2 lfo18;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
     5303style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
     5304style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     5305style='mso-bidi-font-weight:normal'>Toggle selection </b>– toggles all refine
     5306flags</p>
    53925307
    53935308<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5394 auto;text-indent:-.25in;mso-list:l3 level1 lfo16;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
    5395 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    5396 "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5397 </span></span></span><![endif]>You can change the refine flags either by
    5398 clicking on the box or by selecting one and then selecting the column (a single
    5399 click on the column heading). Then type ‘y’ to set the refine flags or ‘n’ to
    5400 clear the flags. You should not refine those reflections that fall below the
    5401 lower limit or above the upper limit of the powder pattern otherwise you may
    5402 have a singular matrix error in your Pawley refinement.</span></p>
     5309auto;text-indent:-.25in;mso-list:l3 level1 lfo16;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
     5310style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     5311style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>You
     5312can change the refine flags either by clicking on the box or by selecting one
     5313and then selecting the column (a single click on the column heading). Then type
     5314‘y’ to set the refine flags or ‘n’ to clear the flags. You should not refine
     5315those reflections that are below the lower limit or above the upper limit of
     5316the powder pattern otherwise you will have singular matrix errors in your
     5317Pawley refinement (adds to the refinement time as bad parameters are removed).
     5318Reflections that fall inside excluded regions may also result in refinement
     5319singularities.</p>
    54035320
    54045321<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    54085325can delete an individual reflection from the Pawley set by selecting its row
    54095326(will be highlighted) and then pressing the Delete key (this is not reversable
    5410 &amp; only <span class=GramE>deletes</span> the 1<sup>st</sup> one selected).</p>
     5327&amp; only deletes the 1<sup>st</sup> one selected).</p>
    54115328
    54125329<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    … …  
    54145331style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    54155332style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>You
    5416 can change the individual <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>)
    5417 values by selecting it, typing in the new <span class=GramE>value</span> and
    5418 then pressing enter or selecting somewhere else in the table.</p>
     5333can change the individual Fsq(hkl) values by selecting it, typing in the new
     5334value and then pressing enter or selecting somewhere else in the table.</p>
    54195335
    54205336<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
    … …  
    54255341<a
    54265342href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/StackingFaults-I/Stacking%20Faults-I.htm">Stacking
    5427 Faults-I</a> tutorial. The computations are done by a modified version of <span
    5428 class=SpellE>DIFFaX</span>. See M.M.J. Treacy, J.M. Newsam and M.W. Deem, Proc.
    5429 Roy. Soc. <span class=SpellE>Lond</span>. 433A, 499-520 (1991) for more
    5430 information on <span class=SpellE>DIFFaX</span> and please cite this if you use
    5431 this section of GSAS-II.</p>
     5343Faults-I</a> tutorial. The computations are done by a modified version of
     5344DIFFaX. See M.M.J. Treacy, J.M. Newsam and M.W. Deem, Proc. Roy. Soc. Lond.
     5345433A, 499-520 (1991) for more information on DIFFaX and please cite this if you
     5346use this section of GSAS-II.</p>
    54325347
    54335348<h5 style='margin-left:.5in'>What can I do here?</h5>
    … …  
    54435358style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    54445359style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b
    5445 style='mso-bidi-font-weight:normal'>Load from <span class=SpellE>DIFFaX</span> file
    5446 – </b><span style='mso-bidi-font-weight:bold'>load parameters from a <span
    5447 class=SpellE>DIFFaX</span> input file</span></p>
     5360style='mso-bidi-font-weight:normal'>Load from DIFFaX file – </b><span
     5361style='mso-bidi-font-weight:bold'>load parameters from a DIFFaX input file</span></p>
    54485362
    54495363<p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space:
    … …  
    54605374style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b
    54615375style='mso-bidi-font-weight:normal'>Simulate pattern – </b><span
    5462 style='mso-bidi-font-weight:bold'>run <span class=SpellE>DIFFaX</span> to
    5463 simulate selected pattern<o:p></o:p></span></p>
     5376style='mso-bidi-font-weight:bold'>run DIFFaX to simulate selected pattern<o:p></o:p></span></p>
    54645377
    54655378<p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space:
    … …  
    55155428</span></span></span><![endif]><span style='mso-bidi-font-weight:bold'>Next are
    55165429descriptions of the layers to be used in the calculations. They can be created
    5517 atom-by-atom or imported from another GSAS-II <span class=SpellE>gpx</span>
    5518 file. If a layer is already present, then the new layer can be the same; give
    5519 it a different name.<o:p></o:p></span></p>
     5430atom-by-atom or imported from another GSAS-II gpx file. If a layer is already
     5431present, then the new layer can be the same; give it a different name.<o:p></o:p></span></p>
    55205432
    55215433<p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space:
    … …  
    55515463<p class=MsoNormal style='margin-left:.5in'>This tab displays the modulation
    55525464functions used for incommensurate structures; it will not appear if the
    5553 structure is commensurate (<span class=GramE>i.e.</span> 3D). They include
    5554 modulations on atom site fractions, <span class=GramE>positions</span> and
    5555 thermal motion parameters. If the structure is magnetic, atom moment modulation
    5556 parameters are also shown.</p>
     5465structure is commensurate (i.e. 3D). They include modulations on atom site
     5466fractions, positions and thermal motion parameters. If the structure is
     5467magnetic, atom moment modulation parameters are also shown.</p>
    55575468
    55585469<h5 style='margin-left:.5in'>What can I do here?</h5>
    … …  
    55805491<p class=MsoNormal style='margin-left:.5in'>This tab displays Monte
    55815492Carlo/Simulated Annealing model parameters and results. Each rigid body is
    5582 described by a location (fractional <span class=SpellE><span class=GramE>x,y</span>,z</span>)
    5583 and a quaternion description for the orientation (rotation angle &amp; 3D
    5584 vector) along with possible bond torsion angles on side chains. Each parameter
    5585 has a defined range. The MC/SA controls on the General tab further limit the
    5586 MC/SA run. Selection of a result shows a drawing of the structure with unit
    5587 cell contents for visualization.</p>
     5493described by a location (fractional x,y,z) and a quaternion description for the
     5494orientation (rotation angle &amp; 3D vector) along with possible bond torsion
     5495angles on side chains. Each parameter has a defined range. The MC/SA controls
     5496on the General tab further limit the MC/SA run. Selection of a result shows a
     5497drawing of the structure with unit cell contents for visualization.</p>
    55885498
    55895499<h5 style='margin-left:.5in'>What can I do here?</h5>
    … …  
    56005510
    56015511<p class=MsoNormal style='margin-left:49.5pt;text-indent:-49.5pt'><span
    5602 style='mso-tab-count:2'>                        </span><span class=SpellE>b.</span>
    5603 <b>Add rigid body</b> – add a previously defined rigid body, which may have
    5604 adjustable internal torsion angles.</p>
     5512style='mso-tab-count:2'>                        </span>b. <b>Add rigid body</b>
     5513– add a previously defined rigid body, which may have adjustable internal
     5514torsion angles.</p>
    56055515
    56065516<p class=MsoNormal style='margin-left:49.5pt;text-indent:-49.5pt'><span
    … …  
    56165526<p class=MsoNormal style='margin-left:.5in'>This displays 3 different setups
    56175527each for <a href="https://doi.org/10.1088/0953-8984/19/33/335218">RMCProfile</a>,
    5618 <a href="https://doi.org/10.1002/jcc.24304"><span class=SpellE>fullrmc</span></a>
    5619 and <a href="https://doi.org/10.1088/0953-8984/19/33/335219"><span
    5620 class=SpellE>PDFfit</span></a> as selected by a radio button at the top of the
    5621 window. RMCProfile and <span class=SpellE>fullrmc</span> are “big box”
    5622 modelling routines and <span class=SpellE>PDFfit</span> is a “small box”
    5623 modelling routine; all for fitting structural models to pair distribution
    5624 functions (PDF). Tutorials for using RMCProfile and <span class=SpellE>PDFfit</span>
    5625 can be found in the GSAS-II Help; <span class=SpellE>fullrmc</span> is
     5528<a href="https://doi.org/10.1002/jcc.24304">fullrmc</a> and <a
     5529href="https://doi.org/10.1088/0953-8984/19/33/335219">PDFfit</a> as selected by
     5530a radio button at the top of the window. RMCProfile and fullrmc are “big box”
     5531modelling routines and PDFfit is a “small box” modelling routine; all for
     5532fitting structural models to pair distribution functions (PDF). Tutorials for
     5533using RMCProfile and PDFfit can be found in the GSAS-II Help; fullrmc is
    56265534currently under construction. These routines all run as stand-alone
    56275535applications which are initiated by GSAS-II. When finished, GSAS-II processes
    … …  
    56295537The two big box routines can have very long running times; they run as separate
    56305538console programs. GSAS-II is active while they are running and can
    5631 “interrogate” them for intermediate results. <span class=SpellE>PDFfit</span>
    5632 has a short running time and GSAS-II is “locked out” until it finishes; its
    5633 result can be examined after.</p>
     5539“interrogate” them for intermediate results. PDFfit has a short running time
     5540and GSAS-II is “locked out” until it finishes; its result can be examined
     5541after.</p>
    56345542
    56355543<h5 style='margin-left:.5in'>What can I do here?</h5>
    … …  
    56395547
    56405548<p class=MsoNormal style='margin-left:.75in;tab-stops:.75in'><span
    5641 style='mso-tab-count:1'>      </span>1. <b>Setup RMC</b> – this builds the input
    5642 files and python script (if needed) for running the selected RMC program.</p>
     5549style='mso-tab-count:1'>      </span>1. <b>Setup RMC</b> – this builds the
     5550input files and python script (if needed) for running the selected RMC program.</p>
    56435551
    56445552<p class=MsoNormal style='margin-left:1.0in;tab-stops:1.0in'><span
    56455553style='mso-tab-count:1'>            </span>2. <b>Execute</b> – this executes
    56465554the chosen RMC program in a new console which will vanish when finishes (after
    5647 a “press any key” command). When finished, GSAS-II will extract results and
    5648 place them in appropriate places in the project.</p>
     5555a “press any key” command). When finished, GSAS-II will extract results and place
     5556them in appropriate places in the project.</p>
    56495557
    56505558<p class=MsoNormal style='margin-left:1.0in;tab-stops:1.0in'>3. <b>Stop run</b>
    5651 – only valid for <span class=SpellE>fullrmc</span>; stops the RMC run &amp;
    5652 saves progress so it can be continued later.</p>
     5559– only valid for fullrmc; stops the RMC run &amp; saves progress so it can be
     5560continued later.</p>
    56535561
    56545562<p class=MsoNormal style='margin-left:1.0in;tab-stops:1.0in'>4. <b>Plot</b> –
    56555563this displays the resulting graphical output from the RMC run. For RMCProfile
    5656 and <span class=SpellE>fullrmc</span> this can be 5 or more plots, for <span
    5657 class=SpellE>PDFfit</span> it is only the observed and calculated G(r) plot
    5658 with a difference curve.</p>
     5564and fullrmc this can be 5 or more plots, for PDFfit it is only the observed and
     5565calculated G(r) plot with a difference curve.</p>
    56595566
    56605567<p class=MsoNormal style='margin-left:1.0in;tab-stops:1.0in'><o:p>&nbsp;</o:p></p>
    … …  
    56635570similar. There is a block for “metadata” items for your convenience; they have
    56645571no impact on the calculations. Next is timing controls for the big box programs
    5665 (<span class=SpellE>PDFfit</span> has none). Then is structural information and
    5666 finally the data section for the patterns to be fitted. The big box programs
    5667 are for only single runs while <span class=SpellE>PDFfit</span> can be used to
    5668 process a sequence of G(r) data collected as a function of, e.g., temperature
    5669 (giving Sequential PDFfit2 results).</p>
     5572(PDFfit has none). Then is structural information and finally the data section
     5573for the patterns to be fitted. The big box programs are for only single runs
     5574while PDFfit can be used to process a sequence of G(r) data collected as a
     5575function of, e.g., temperature (giving Sequential PDFfit2 results).</p>
    56705576
    56715577<h4 style='margin-left:.25in'><a name=Phase-ISODISTORT>ISODISTORT</a></h4>
    … …  
    56735579<p class=MsoNormal style='margin-left:.5in'>This displays the setup for using
    56745580the web-based application, <a href="https://iso.byu.edu/iso/isodistort.php">ISODISTORT</a>,
    5675 to identify the possible mode distortions of a parent structure. To use it you must
    5676 be connected to the internet. Two ISODISTORT Methods are supported in GSAS-II:
    5677 Method-1 identifies all possible subgroups that result from simple mode
    5678 distortions that are associated with a single irreducible representation.
     5581to identify the possible mode distortions of a parent structure. To use it you
     5582must be connected to the internet. Two ISODISTORT Methods are supported in
     5583GSAS-II: Method-1 identifies all possible subgroups that result from simple
     5584mode distortions that are associated with a single irreducible representation.
    56795585Method-4 is more useful in that it finds the mode decomposition of a parent
    56805586structure to give a specified distorted structure and is set up to find only
    56815587atom displacement modes. See help pages for <a
    56825588href="https://iso.byu.edu/iso/isodistort.php">ISODISTORT</a> for more
    5683 information. The ultimate product of using ISODISTORT is a special <span
    5684 class=SpellE>cif</span> file with constraints describing the mode distortions;
    5685 this is imported into GSAS-II to form a new phase with these constraints.</p>
     5589information. The ultimate product of using ISODISTORT is a special cif file
     5590with constraints describing the mode distortions; this is imported into GSAS-II
     5591to form a new phase with these constraints.</p>
    56865592
    56875593<h5 style='margin-left:.5in'>What can I do here?</h5>
    56885594
    56895595<p class=MsoNormal style='margin-left:.5in'>If this is a freshly created phase
    5690 (not an imported ISODISTORT <span class=SpellE>cif</span>) then you can choose
    5691 the Method (4 is default) and select parent structure and distorted child
    5692 structure (for Method 4).</p>
     5596(not an imported ISODISTORT cif) then you can choose the Method (4 is default)
     5597and select parent structure and distorted child structure (for Method 4).</p>
    56935598
    56945599<p class=MsoNormal style='margin-left:.5in'><o:p>&nbsp;</o:p></p>
    56955600
    56965601<p class=MsoNormal style='margin-left:.5in'>If you chose Method 1 &amp; run
    5697 ISODISTORT, a table of possible substructures is displayed; a <span
    5698 class=SpellE>cif</span> file with mode distortion constraints can be produced
    5699 from your selection. The table can be filtered by crystal class.</p>
     5602ISODISTORT, a table of possible substructures is displayed; a cif file with
     5603mode distortion constraints can be produced from your selection. The table can
     5604be filtered by crystal class.</p>
    57005605
    57015606<p class=MsoNormal style='margin-left:.5in'><o:p>&nbsp;</o:p></p>
    57025607
    57035608<p class=MsoNormal style='margin-left:.5in'>If this is a phase imported from an
    5704 ISODISTORT <span class=SpellE>cif</span> file, the mode displacements are shown
    5705 with sliders to allow visualization of the displacements in a drawing of the
    5706 crystal structure (prepare this first before trying a slider). A structure
    5707 refinement using this phase will employ the mode distortions as constraints on
    5708 the atom coordinates; there should be as many as there are free variable
    5709 coordinates in the structure. The values (in <span style='font-family:"Calibri",sans-serif'>Å</span>)
     5609ISODISTORT cif file, the mode displacements are shown with sliders to allow
     5610visualization of the displacements in a drawing of the crystal structure
     5611(prepare this first before trying a slider). A structure refinement using this
     5612phase will employ the mode distortions as constraints on the atom coordinates;
     5613there should be as many as there are free variable coordinates in the
     5614structure. The values (in <span style='font-family:"Calibri",sans-serif'>Å</span>)
    57105615represent the largest atom shift associated with the mode; shown is a list of
    57115616atom coordinates affected by each mode.</p>
    … …  
    57185623from the web site with the controls as shown.</p>
    57195624
    5720 <p class=MsoNormal style='margin-left:.5in'>2) <b>Make <span class=SpellE>cif</span>
    5721 file</b> – active after table from Method 1 is displayed; generate <span
    5722 class=SpellE>cif</span> file by ISODISTORT web site with mode distortion
    5723 constraints.</p>
    5724 
    5725 <p class=MsoNormal style='margin-left:.5in'>3) <b>Make <span class=SpellE>PDFfit</span>
    5726 phase</b> – active when mode distortions are shown. Makes new phase specific
    5727 for fitting PDF data via PDFfit2.</p>
     5625<p class=MsoNormal style='margin-left:.5in'>2) <b>Make cif file</b> – active
     5626after table from Method 1 is displayed; generate cif file by ISODISTORT web site
     5627with mode distortion constraints.</p>
     5628
     5629<p class=MsoNormal style='margin-left:.5in'>3) <b>Make PDFfit phase</b> –
     5630active when mode distortions are shown. Makes new phase specific for fitting
     5631PDF data via PDFfit2.</p>
    57285632
    57295633<p class=MsoNormal style='margin-left:.5in'>4) <b>Show modes</b> – active when
    … …  
    57365640<h4 style='margin-left:.25in'><a name=Phase-Dysnomia>Dysnomia</a></h4>
    57375641
    5738 <p class=MsoNormal style='margin-left:.5in'>This is displayed if the <b>Use <span
    5739 class=SpellE>Dysnomia</span></b> box in the General tab is checked. <a
    5740 href="https://doi.org/10.1017/S088571561300002X"><span class=SpellE>Dysnomia</span></a>
    5741 is a maximum entropy method for improving Fourier density maps. The <span
    5742 class=SpellE>Dysnomia</span> tab gives controls for its operation.</p>
     5642<p class=MsoNormal style='margin-left:.5in'>This is displayed if the <b>Use
     5643Dysnomia</b> box in the General tab is checked. <a
     5644href="https://doi.org/10.1017/S088571561300002X">Dysnomia</a> is a maximum
     5645entropy method for improving Fourier density maps. The Dysnomia tab gives
     5646controls for its operation.</p>
    57435647
    57445648<h5 style='margin-left:.5in'>What can I do here?</h5>
    … …  
    57465650<p class=MsoNormal style='margin-left:.5in'><b>Operations</b> menu – </p>
    57475651
    5748 <p class=MsoNormal style='margin-left:.5in'>1) <b>Load from <span class=SpellE>Dysnomia</span>
    5749 file</b> – as previously saved set of controls.</p>
    5750 
    5751 <p class=MsoNormal style='margin-left:.5in'>2) <b>Save <span class=SpellE>Dysnomia</span>
    5752 file</b> – saves data needed to run <span class=SpellE>Dysnomia</span></p>
    5753 
    5754 <p class=MsoNormal style='margin-left:.5in'>3) <b>Run <span class=SpellE>Dysnomia</span></b>
    5755 – execute the routine from GSAS-II (not a separate console). Replaces existing
    5756 map with one improved by maximum entropy.</p>
     5652<p class=MsoNormal style='margin-left:.5in'>1) <b>Load from Dysnomia file</b> –
     5653as previously saved set of controls.</p>
     5654
     5655<p class=MsoNormal style='margin-left:.5in'>2) <b>Save Dysnomia file</b> – saves
     5656data needed to run Dysnomia</p>
     5657
     5658<p class=MsoNormal style='margin-left:.5in'>3) <b>Run Dysnomia</b> – execute
     5659the routine from GSAS-II (not a separate console). Replaces existing map with
     5660one improved by maximum entropy.</p>
    57575661
    57585662<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    57655669</span></div>
    57665670
    5767 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><!-- hhmts start -->Last modified: Thu Mar 24 16:28:36 CDT 2022 <!-- hhmts end --><o:p></o:p></span></p>
     5671<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><!-- hhmts start -->Last
     5672modified: Thu Mar 24 16:28:36 CDT 2022 <!-- hhmts end --><o:p></o:p></span></p>
    57685673
    57695674</div>

  • trunk/help/gsasII-phase_files/filelist.xml

    r5252 r5257  
    66 <o:File HRef="colorschememapping.xml"/>
    77 <o:File HRef="image001.png"/>
    8  <o:File HRef="image049.png"/>
     8 <o:File HRef="image002.png"/>
    99 <o:File HRef="image003.png"/>
    10  <o:File HRef="image050.png"/>
     10 <o:File HRef="image004.png"/>
    1111 <o:File HRef="image005.png"/>
    12  <o:File HRef="image051.png"/>
     12 <o:File HRef="image006.png"/>
    1313 <o:File HRef="image007.png"/>
    14  <o:File HRef="image052.png"/>
     14 <o:File HRef="image008.png"/>
    1515 <o:File HRef="image009.png"/>
    16  <o:File HRef="image053.png"/>
     16 <o:File HRef="image010.png"/>
    1717 <o:File HRef="image011.png"/>
    18  <o:File HRef="image054.png"/>
     18 <o:File HRef="image012.png"/>
    1919 <o:File HRef="image013.png"/>
    20  <o:File HRef="image055.png"/>
     20 <o:File HRef="image014.png"/>
    2121 <o:File HRef="image015.png"/>
    22  <o:File HRef="image056.png"/>
     22 <o:File HRef="image016.png"/>
    2323 <o:File HRef="image017.png"/>
    24  <o:File HRef="image057.png"/>
     24 <o:File HRef="image018.png"/>
    2525 <o:File HRef="image019.png"/>
    26  <o:File HRef="image058.png"/>
     26 <o:File HRef="image020.png"/>
    2727 <o:File HRef="image021.png"/>
    28  <o:File HRef="image059.png"/>
     28 <o:File HRef="image022.png"/>
    2929 <o:File HRef="image023.png"/>
    30  <o:File HRef="image060.png"/>
     30 <o:File HRef="image024.png"/>
    3131 <o:File HRef="image025.png"/>
    32  <o:File HRef="image061.png"/>
     32 <o:File HRef="image026.png"/>
    3333 <o:File HRef="image027.png"/>
    34  <o:File HRef="image062.png"/>
     34 <o:File HRef="image028.png"/>
    3535 <o:File HRef="image029.png"/>
    36  <o:File HRef="image063.png"/>
     36 <o:File HRef="image030.png"/>
    3737 <o:File HRef="image031.png"/>
    38  <o:File HRef="image064.png"/>
     38 <o:File HRef="image032.png"/>
    3939 <o:File HRef="image033.png"/>
    40  <o:File HRef="image065.png"/>
     40 <o:File HRef="image034.png"/>
    4141 <o:File HRef="image035.png"/>
    42  <o:File HRef="image066.png"/>
     42 <o:File HRef="image036.png"/>
    4343 <o:File HRef="image037.png"/>
    44  <o:File HRef="image067.png"/>
     44 <o:File HRef="image038.png"/>
    4545 <o:File HRef="image039.png"/>
    46  <o:File HRef="image068.png"/>
     46 <o:File HRef="image040.png"/>
    4747 <o:File HRef="image041.png"/>
    48  <o:File HRef="image069.png"/>
     48 <o:File HRef="image042.png"/>
    4949 <o:File HRef="image043.png"/>
    50  <o:File HRef="image070.png"/>
     50 <o:File HRef="image044.png"/>
    5151 <o:File HRef="image045.png"/>
    52  <o:File HRef="image071.png"/>
     52 <o:File HRef="image046.png"/>
    5353 <o:File HRef="image047.png"/>
    54  <o:File HRef="image072.png"/>
     54 <o:File HRef="image048.png"/>
    5555 <o:File HRef="filelist.xml"/>
    5656</xml>

  • trunk/help/gsasII.html

    r5256 r5257  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele, Robert B.</o:LastAuthor>
    27   <o:Revision>179</o:Revision>
    28   <o:TotalTime>5558</o:TotalTime>
     27  <o:Revision>181</o:Revision>
     28  <o:TotalTime>5681</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2022-03-30T20:11:00Z</o:LastSaved>
     30  <o:LastSaved>2022-03-31T15:52:00Z</o:LastSaved>
    3131  <o:Pages>1</o:Pages>
    32   <o:Words>14193</o:Words>
    33   <o:Characters>80904</o:Characters>
     32  <o:Words>14672</o:Words>
     33  <o:Characters>83636</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    35   <o:Lines>674</o:Lines>
    36   <o:Paragraphs>189</o:Paragraphs>
    37   <o:CharactersWithSpaces>94908</o:CharactersWithSpaces>
     35  <o:Lines>696</o:Lines>
     36  <o:Paragraphs>196</o:Paragraphs>
     37  <o:CharactersWithSpaces>98112</o:CharactersWithSpaces>
    3838  <o:Version>16.00</o:Version>
    3939 </o:DocumentProperties>
    … …  
    4949 <w:WordDocument>
    5050  <w:Zoom>148</w:Zoom>
    51   <w:SpellingState>Clean</w:SpellingState>
    52   <w:GrammarState>Clean</w:GrammarState>
    5351  <w:TrackMoves>false</w:TrackMoves>
    5452  <w:TrackFormatting/>
    … …  
    975973        mso-bidi-font-family:"Times New Roman";}
    976974p
    977         {mso-style-priority:99;
     975        {mso-style-noshow:yes;
     976        mso-style-priority:99;
    978977        mso-margin-top-alt:auto;
    979978        margin-right:0in;
    … …  
    13061305        font-family:"Times New Roman",serif;
    13071306        mso-fareast-font-family:"Times New Roman";}
    1308 span.SpellE
    1309         {mso-style-name:"";
    1310         mso-spl-e:yes;}
    1311 span.GramE
    1312         {mso-style-name:"";
    1313         mso-gram-e:yes;}
    13141307.MsoChpDefault
    13151308        {mso-style-type:export-only;
    … …  
    25162509<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    25172510"Times New Roman"'>The data tree shows contents of a GSAS-II project (which can
    2518 be read or saved as a .<span class=SpellE>gpx</span> file) in a hierarchical
    2519 view. Clicking on any item in the tree opens that information on the right side
    2520 of the window in the &quot;Data Editing&quot; section, where information in
    2521 that item can be viewed or edited. For example, the <a
    2522 href="gsasII-pwdr.html#PWDR_Sample_Parameters">&quot;Sample Parameters&quot;</a>
    2523 item under a ‘PWDR’ entry contains information about how data were collected,
    2524 such as the sample temperature <a href="gsasII-pwdr.html#PWDR_Sample_Parameters">(see
    2525 below)</a>. The arrow keys (up &amp; down) move the selection to successive
    2526 entries in the data tree; both the data window and the associated plot (if any)
    2527 will change.<o:p></o:p></span></p>
     2511be read or saved as a .gpx file) in a hierarchical view. Clicking on any item
     2512in the tree opens that information on the right side of the window in the
     2513&quot;Data Editing&quot; section, where information in that item can be viewed
     2514or edited. For example, the <a href="gsasII-pwdr.html#PWDR_Sample_Parameters">&quot;Sample
     2515Parameters&quot;</a> item under a ‘PWDR’ entry contains information about how
     2516data were collected, such as the sample temperature <a
     2517href="gsasII-pwdr.html#PWDR_Sample_Parameters">(see below)</a>. The arrow keys
     2518(up &amp; down) move the selection to successive entries in the data tree; both
     2519the data window and the associated plot (if any) will change.<o:p></o:p></span></p>
    25282520
    25292521<h4 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    … …  
    25862578
    25872579<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><img
    2588 border=0 width=727 height=55 id="_x0000_i1115" src=graphbar.jpg
     2580border=0 width=727 height=55 id="_x0000_i1128" src=graphbar.jpg
    25892581alt="toolbar on plots"></span></p>
    25902582
    … …  
    26822674
    26832675<p class=MsoNormal style='margin-left:.5in'><b><span style='mso-fareast-font-family:
    2684 "Times New Roman"'>{less <span class=GramE>than}+</span>{greater than}</span></b><span
    2685 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     2676"Times New Roman"'>{less than}+{greater than}</span></b><span style='mso-fareast-font-family:
     2677"Times New Roman"'><o:p></o:p></span></p>
    26862678
    26872679<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    … …  
    26902682
    26912683<p class=MsoNormal style='margin-left:.5in'><b><span style='mso-fareast-font-family:
    2692 "Times New Roman"'>{greater <span class=GramE>than}+</span>{less than}</span></b><span
    2693 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     2684"Times New Roman"'>{greater than}+{less than}</span></b><span style='mso-fareast-font-family:
     2685"Times New Roman"'><o:p></o:p></span></p>
    26942686
    26952687<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    … …  
    26982690
    26992691<p class=MsoNormal style='margin-left:.5in'><b><span style='mso-fareast-font-family:
    2700 "Times New Roman"'>{up arrow}<span class=GramE>/{</span>down arrow}</span></b><span
    2701 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     2692"Times New Roman"'>{up arrow}/{down arrow}</span></b><span style='mso-fareast-font-family:
     2693"Times New Roman"'><o:p></o:p></span></p>
    27022694
    27032695<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    … …  
    27062698
    27072699<p class=MsoNormal style='margin-left:.5in'><b><span style='mso-fareast-font-family:
    2708 "Times New Roman"'>{down arrow}<span class=GramE>/{</span>up arrow}</span></b><span
    2709 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     2700"Times New Roman"'>{down arrow}/{up arrow}</span></b><span style='mso-fareast-font-family:
     2701"Times New Roman"'><o:p></o:p></span></p>
    27102702
    27112703<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    … …  
    27142706
    27152707<p class=MsoNormal style='margin-left:.5in'>Below the toolbar may be a status
    2716 bar that on the left may show either an instruction for a keyed input or a <span
    2717 class=GramE>pull down</span> selection of keyed input; on the right may be
    2718 displayed position dependent information that is updated as the mouse is moved
    2719 over the plot region.</p>
     2708bar that on the left may show either an instruction for a keyed input or a pull
     2709down selection of keyed input; on the right may be displayed position dependent
     2710information that is updated as the mouse is moved over the plot region.</p>
    27202711
    27212712<div class=MsoNormal align=center style='text-align:center'><span
    … …  
    27482739
    27492740<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    2750 "Times New Roman"'>Open a previously saved GSAS-II project file ({project}.<span
    2751 class=SpellE>gpx</span>). If you currently have a project file open, you are
    2752 asked if it is OK to overwrite it; Cancel will cancel the read process. <o:p></o:p></span></p>
     2741"Times New Roman"'>Open a previously saved GSAS-II project file
     2742({project}.gpx). If you currently have a project file open, you are asked if it
     2743is OK to overwrite it; Cancel will cancel the read process. <o:p></o:p></span></p>
    27532744
    27542745<p style='margin-left:.9in'>Note that as files are saved, copies of the
    2755 previous version are saved as backup files, named as {project}.<span
    2756 class=SpellE>bak</span>{<span class=SpellE><i>i</i></span>}.<span class=SpellE>gpx</span>,
    2757 where <span class=SpellE><i>i</i></span> starts as 0 and is increased after
    2758 each save operation. NB: you may open a backup .<span class=SpellE>gpx</span>
    2759 file (<span class=GramE>e.g.</span> name.bak3.gpx) to return to a previous
     2746previous version are saved as backup files, named as {project}.bak{<i>i</i>}.gpx,
     2747where <i>i</i> starts as 0 and is increased after each save operation. NB: you
     2748may open a backup .gpx file (e.g. name.bak3.gpx) to return to a previous
    27602749version of your project, but if you do so, it is best to immediately use the <b'>Save
    2761 As... menu command (you may wish to use <span class=SpellE>name.gpx</span> to
    2762 overwrite the current version or select a new name.) If you forget <span
    2763 class=GramE>specify</span> a project name, then name.bak3 will be considered
    2764 the project name and backups will then be named name.bak3.bak0.gpx, etc.</p>
     2750As... menu command (you may wish to use name.gpx to overwrite the current
     2751version or select a new name.) If you forget specify a project name, then
     2752name.bak3 will be considered the project name and backups will then be named
     2753name.bak3.bak0.gpx, etc.</p>
    27652754
    27662755<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    28332822<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    28342823"Times New Roman"'>Form the sum of previously read powder patterns; each with a
    2835 multiplier. Can be used to accumulate data, subtract <span class=GramE>background</span>
    2836 or empty container patterns, etc. Patterns used to form the sum must be of
    2837 identical range and step size. Result is a new PWDR entry in the GSAS-II data
    2838 tree. <o:p></o:p></span></p>
     2824multiplier. Can be used to accumulate data, subtract background or empty
     2825container patterns, etc. Patterns used to form the sum must be of identical
     2826range and step size. Result is a new PWDR entry in the GSAS-II data tree. <o:p></o:p></span></p>
    28392827
    28402828<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    28442832<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    28452833"Times New Roman"'>Form the sum of previously read 2-D images; each with a
    2846 multiplier. Can be used to accumulate data, subtract <span class=GramE>background</span>
    2847 or empty container patterns, etc. Images used to form the sum must be of
    2848 identical size and source. Result is a new IMG entry in the GSAS-II data tree,
    2849 and a GSAS-II image file is written for future use. <o:p></o:p></span></p>
     2834multiplier. Can be used to accumulate data, subtract background or empty
     2835container patterns, etc. Images used to form the sum must be of identical size
     2836and source. Result is a new IMG entry in the GSAS-II data tree, and a GSAS-II
     2837image file is written for future use. <o:p></o:p></span></p>
    28502838
    28512839<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    28602848enter the space group symbol and then the lattice parameters. <br>
    28612849Note that nonstandard space group symbols are permitted; space group names must
    2862 have spaces between the axial fields (<span class=GramE>e.g.</span> use ‘P n a
    2863 21’ not ‘Pna21’). <o:p></o:p></span></p>
     2850have spaces between the axial fields (e.g. use ‘P n a 21’ not ‘Pna21’). <o:p></o:p></span></p>
    28642851
    28652852<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    28772864<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    28782865"Times New Roman"'>Rename a histogram entry. This should only be done before
    2879 the histogram is used in any phases: <span class=GramE>e.g.</span> only rename
    2880 data immediately after reading. <o:p></o:p></span></p>
     2866the histogram is used in any phases: e.g. only rename data immediately after
     2867reading. <o:p></o:p></span></p>
    28812868
    28822869<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    28852872
    28862873<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    2887 "Times New Roman"'>This will remove an item from the data tree. A dialog box with
    2888 a list of choices for histograms is presented. Be sure to remove a <span
    2889 class=GramE>histograms</span> from all phases before deleting it from the tree.
    2890 <o:p></o:p></span></p>
     2874"Times New Roman"'>This will remove an item from the data tree. A dialog box
     2875with a list of choices for histograms is presented. Be sure to remove a
     2876histograms from all phases before deleting it from the tree. <o:p></o:p></span></p>
    28912877
    28922878<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    29252911
    29262912<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    2927 "Times New Roman"'>View LS <span class=SpellE>parms</span></span></b><span
    2928 style='mso-fareast-font-family:"Times New Roman"'> <o:p></o:p></span></p>
     2913"Times New Roman"'>View LS parms</span></b><span style='mso-fareast-font-family:
     2914"Times New Roman"'> <o:p></o:p></span></p>
    29292915
    29302916<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    … …  
    29332919indicate parameters that are not refinable. The total number of refined
    29342920parameters is also shown at the top of the list. The value of each parameter is
    2935 also given. The parameter names are of the form ‘<span class=SpellE>p:h:name:id</span>’
    2936 where ‘p’ is the phase index, ‘h’ is the histogram index and ‘id’ is the item
    2937 index (if needed). Indexes all begin with ‘0’ (zero). <o:p></o:p></span></p>
     2921also given. The parameter names are of the form ‘p:h:name:id’ where ‘p’ is the
     2922phase index, ‘h’ is the histogram index and ‘id’ is the item index (if needed).
     2923Indexes all begin with ‘0’ (zero). <o:p></o:p></span></p>
    29382924
    29392925<p style='margin-left:.9in'>Note that for atom positions, the coordinate values
    2940 (named as ‘<span class=GramE>p::</span><span class=SpellE>A<i>w</i>:n</span>’,
    2941 where p is the phase number, n is the atom number and <i>w</i> is x, y or z) is
    2942 not a refinable parameter, but the shift in the value is. The refined
    2943 parameters are ‘<span class=GramE>p::</span><span class=SpellE>A<i>w</i>:n</span>’.
    2944 The reason this is done is that by treating an atom position as <span
    2945 class=SpellE>x+<span class=GramE>dx,y</span>+dy,z+dz</span> where the “d” values
    2946 indicate shifts from the starting position and the shifts are refined rather
    2947 than the <span class=SpellE>x,y</span>, or z values is that this simplifies
    2948 symmetry constraints. As an example, suppose we have an atom on a symmetry
    2949 constrained site, x,1/2-<span class=GramE>x,z.</span> The process needed to define
    2950 this constraint, so that if x moves positively y <span class=GramE>has to</span>
    2951 move negatively by the same amount would be messy. With refinement of shifts,
    2952 all we need to do is constrain <span class=SpellE>dy</span> (‘<span
    2953 class=GramE>0::</span><span class=SpellE>dAy:n</span>’) to be equal to -dx
    2954 (-1*‘0::<span class=SpellE>dAx:n</span>’). </p>
     2926(named as ‘p::A<i>w</i>:n’, where p is the phase number, n is the atom number
     2927and <i>w</i> is x, y or z) is not a refinable parameter, but the shift in the
     2928value is. The refined parameters are ‘p::A<i>w</i>:n’. The reason this is done
     2929is that by treating an atom position as x+dx,y+dy,z+dz where the “d” values indicate
     2930shifts from the starting position and the shifts are refined rather than the
     2931x,y, or z values is that this simplifies symmetry constraints. As an example,
     2932suppose we have an atom on a symmetry constrained site, x,1/2-x,z. The process
     2933needed to define this constraint, so that if x moves positively y has to move
     2934negatively by the same amount would be messy. With refinement of shifts, all we
     2935need to do is constrain dy (‘0::dAy:n’) to be equal to -dx (-1*‘0::dAx:n’). </p>
    29552936
    29562937<p style='margin-left:.9in'>Press the window exit button to exit this dialog
    … …  
    29762957<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><span
    29772958style='mso-tab-count:1'>            </span><span style='mso-spacerun:yes'>    
    2978 </span><b>Run <span class=SpellE>Fprime</span><o:p></o:p></b></span></p>
     2959</span><b>Run Fprime<o:p></o:p></b></span></p>
    29792960
    29802961<p class=MsoNormal style='margin-left:67.5pt'><span style='mso-fareast-font-family:
    2981 "Times New Roman"'>This run the utility routine <span class=SpellE>Fprime</span>
    2982 that displays real and imaginary components of the x-ray form factors for user
    2983 selected elements as a function of wavelength/energy. Allows an informed choice
    2984 of wavelength for resonant x-ray scattering experiments<o:p></o:p></span></p>
     2962"Times New Roman"'>This run the utility routine Fprime that displays real and
     2963imaginary components of the x-ray form factors for user selected elements as a
     2964function of wavelength/energy. Allows an informed choice of wavelength for
     2965resonant x-ray scattering experiments<o:p></o:p></span></p>
    29852966
    29862967<p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    … …  
    29932974
    29942975<p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    2995 "Times New Roman"'>Run <span class=SpellE>PlotXNFF</span><o:p></o:p></span></b></p>
     2976"Times New Roman"'>Run PlotXNFF<o:p></o:p></span></b></p>
    29962977
    29972978<p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:
    2998 "Times New Roman"'>This runs the utility routine <span class=SpellE>PlotXNFF</span>
    2999 which displays resonant (if any) neutron scattering lengths for all isotopes of
    3000 a selected element. It also displays the x-ray and magnetic neutron form
    3001 factors for all valences (if any) for this element.<o:p></o:p></span></p>
     2979"Times New Roman"'>This runs the utility routine PlotXNFF which displays
     2980resonant (if any) neutron scattering lengths for all isotopes of a selected
     2981element. It also displays the x-ray and magnetic neutron form factors for all
     2982valences (if any) for this element.<o:p></o:p></span></p>
    30022983
    30032984<ol start=4 type=1>
    … …  
    30112992information from external files that can be created and customized easily. See
    30122993the <a href="https://gsas-ii.readthedocs.io/en/latest/imports.html">GSAS-II
    3013 Import Modules section</a> of the <a href="#Programmers"><span class=GramE><strong>Programmers</strong></span><strong>
     2994Import Modules section</a> of the <a href="#Programmers"><strong>Programmers
    30142995documentation</strong></a> for more information on this. Since it is easy to
    30152996support new formats, the documentation below may not list all supported
    … …  
    30253006when selected with the mouse shows further submenus with specific imports that
    30263007are available. Any of these files can be accessed from a zip file. GSAS-II can
    3027 read many different <span class=GramE>image</span> file formats including
    3028 MAR345 files, Quantum ADSC files, and tiff files from Perkin-Elmer, Pilatus,
    3029 and GE. Although many of these formats have data fields that should contain
    3030 relevant information for the exposure (<span class=GramE>e.g.</span>
    3031 wavelength), these are rarely filled in correctly by the data acquisition
    3032 software. Thus, you should have separately noted this information as it will be
    3033 needed. NB: gain maps can be imported but they must be 1000*the gain value
    3034 (typically ~1) as integers; GSAS-II will rescale the gain map by 1/1000 and
    3035 apply it to the image.<o:p></o:p></span></p>
     3008read many different image file formats including MAR345 files, Quantum ADSC
     3009files, and tiff files from Perkin-Elmer, Pilatus, and GE. Although many of
     3010these formats have data fields that should contain relevant information for the
     3011exposure (e.g. wavelength), these are rarely filled in correctly by the data
     3012acquisition software. Thus, you should have separately noted this information
     3013as it will be needed. NB: gain maps can be imported but they must be 1000*the
     3014gain value (typically ~1) as integers; GSAS-II will rescale the gain map by
     30151/1000 and apply it to the image.<o:p></o:p></span></p>
    30363016
    30373017<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    30413021<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    30423022"Times New Roman"'>Creates a new phase by reading unit cell/symmetry/atom
    3043 coordinate information. GSAS-II can read information from <span class=GramE>a
    3044 number of</span> different format files including: <o:p></o:p></span></p>
    3045 
    3046 <p class=MsoNormal style='margin-left:.9in'><span class=GramE><span
    3047 style='mso-fareast-font-family:"Times New Roman"'>GSAS .EXP</span></span><span
    3048 style='mso-fareast-font-family:"Times New Roman"'> <o:p></o:p></span></p>
     3023coordinate information. GSAS-II can read information from a number of different
     3024format files including: <o:p></o:p></span></p>
     3025
     3026<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
     3027"Times New Roman"'>GSAS .EXP <o:p></o:p></span></p>
    30493028
    30503029<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    3051 "Times New Roman"'>This reads one phase from a (old) GSAS experiment file (<span
    3052 class=SpellE>name.EXP</span>). The file name is found in a directory dialog;
    3053 you can change directories as needed. <span class=GramE>Only .EXP</span> (or
    3054 .exp) file names are shown. If the selected file has more than one phase, a
    3055 dialog is shown with the <span class=GramE>choices;</span> only one can be
    3056 chosen. If you want more than one, redo this command. After selecting a phase,
    3057 a dialog box is shown with the proposed phase name. You can change it if
    3058 desired. <o:p></o:p></span></p>
     3030"Times New Roman"'>This reads one phase from a (old) GSAS experiment file
     3031(name.EXP). The file name is found in a directory dialog; you can change
     3032directories as needed. Only .EXP (or .exp) file names are shown. If the
     3033selected file has more than one phase, a dialog is shown with the choices; only
     3034one can be chosen. If you want more than one, redo this command. After
     3035selecting a phase, a dialog box is shown with the proposed phase name. You can
     3036change it if desired. <o:p></o:p></span></p>
    30593037
    30603038<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    … …  
    30633041<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    30643042"Times New Roman"'>This reads the macromolecular phase information from a
    3065 Protein Data Base file (name.PDB or <span class=SpellE>name.ENT</span>). The
    3066 file name is found in a directory dialog; you can change directories as needed.
    3067 Only .PDB (or .<span class=SpellE>pdb</span>) <span class=GramE>or .ENT</span>
    3068 (or .<span class=SpellE>ent</span>) file names are shown. Be careful that the
    3069 space group symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II
    3070 conventions (<span class=GramE>e.g.</span> with spaces between axial fields). A
    3071 dialog box is shown with the proposed phase name. You can change it if desired.
    3072 <o:p></o:p></span></p>
     3043Protein Data Base file (name.PDB or name.ENT). The file name is found in a
     3044directory dialog; you can change directories as needed. Only .PDB (or .pdb) or
     3045.ENT (or .ent) file names are shown. Be careful that the space group symbol on
     3046the ‘CRYST1’ record in the PDB file follows the GSAS-II conventions (e.g. with
     3047spaces between axial fields). A dialog box is shown with the proposed phase
     3048name. You can change it if desired. <o:p></o:p></span></p>
    30733049
    30743050<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    … …  
    30773053<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    30783054"Times New Roman"'>This reads one phase from a Crystallographic Information
    3079 File ({name<span class=GramE>}.CIF</span> (or .<span class=SpellE>cif</span>).
    3080 The file name is found in a directory dialog; you can change directories as
    3081 needed. If the selected file has more than one phase, a dialog is shown with
    3082 the <span class=GramE>choices;</span> only one can be chosen. If you want more
     3055File ({name}.CIF (or .cif). The file name is found in a directory dialog; you
     3056can change directories as needed. If the selected file has more than one phase,
     3057a dialog is shown with the choices; only one can be chosen. If you want more
    30833058than one, redo this command. After selecting a phase, a dialog box is shown
    30843059with the proposed phase name. You can change it if desired. <o:p></o:p></span></p>
    30853060
    30863061<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    3087 "Times New Roman"'>GSAS-II .<span class=SpellE>gpx</span> file <o:p></o:p></span></p>
     3062"Times New Roman"'>GSAS-II .gpx file <o:p></o:p></span></p>
    30883063
    30893064<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    3090 "Times New Roman"'>This reads one phase from a GSAS-II project file ({name}.<span
    3091 class=SpellE>gpx</span>). The file name is found in a directory dialog; you can
    3092 change directories as needed. If the selected file has more than one phase, a
    3093 dialog is shown with the choices; If you want more than one, redo this command.
    3094 After selecting a phase, a dialog box is shown with the proposed phase name.
    3095 You can change it if desired. <o:p></o:p></span></p>
     3065"Times New Roman"'>This reads one phase from a GSAS-II project file
     3066({name}.gpx). The file name is found in a directory dialog; you can change
     3067directories as needed. If the selected file has more than one phase, a dialog
     3068is shown with the choices; If you want more than one, redo this command. After
     3069selecting a phase, a dialog box is shown with the proposed phase name. You can
     3070change it if desired. <o:p></o:p></span></p>
    30963071
    30973072<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    … …  
    31133088needed for processing a powder diffraction data set, such as data type,
    31143089calibration constants (such as wavelength) and default profile parameters are
    3115 read from a separate file, either a (old) GSAS instrument parameter file (<span
    3116 class=GramE>usually .<span class=SpellE>prm</span></span>, .ins or .<span
    3117 class=SpellE>inst</span> extension) or a new GSAS-II .<span class=SpellE>instparm</span>
    3118 file. <o:p></o:p></span></p>
     3090read from a separate file, either a (old) GSAS instrument parameter file
     3091(usually .prm, .ins or .inst extension) or a new GSAS-II .instparm file. <o:p></o:p></span></p>
    31193092
    31203093<p style='margin-left:.9in'>Note that it is possible to apply corrections to
    31213094the 2-theta, intensity or weight values by adding a Python command(s) to the
    3122 instrument <span class=GramE>(.<span class=SpellE>instprm</span></span>)
    3123 parameter with a variable named <span class=SpellE>CorrectionCode</span>. See
    3124 the <span class=SpellE><tt><span style='font-size:10.0pt'>CorrectionCode.instprm.sample</span></tt></span>
    3125 file provided in the GSAS-II source directory for an example of how this is
    3126 done. </p>
     3095instrument (.instprm) parameter with a variable named CorrectionCode. See the <tt><span
     3096style='font-size:10.0pt'>CorrectionCode.instprm.sample</span></tt> file
     3097provided in the GSAS-II source directory for an example of how this is done. </p>
    31273098
    31283099<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    … …  
    31313102<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    31323103"Times New Roman"'>This reads one powder pattern (histogram) from a
    3133 Crystallographic Information File ({name<span class=GramE>}.CIF</span>). The file
    3134 name is found in a directory dialog; you can change directories as needed. Only
    3135 <span class=GramE>one .<span class=SpellE>cif</span></span> can be chosen. If
    3136 you want more than one, redo this command. <o:p></o:p></span></p>
     3104Crystallographic Information File ({name}.CIF). The file name is found in a
     3105directory dialog; you can change directories as needed. Only one .cif can be
     3106chosen. If you want more than one, redo this command. <o:p></o:p></span></p>
    31373107
    31383108<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    3139 "Times New Roman"'>GSAS-II .<span class=SpellE>gpx</span> file <o:p></o:p></span></p>
     3109"Times New Roman"'>GSAS-II .gpx file <o:p></o:p></span></p>
    31403110
    31413111<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    31423112"Times New Roman"'>This reads powder patterns from a previously created GSAS-II
    3143 <span class=SpellE>gpx</span> project file. If the selected file has more than
    3144 one powder pattern, a dialog is shown with the choices; one or more can be
    3145 selected. It will ask for an appropriate instrument parameter file to go with
    3146 the selected powder data sets. <o:p></o:p></span></p>
     3113gpx project file. If the selected file has more than one powder pattern, a
     3114dialog is shown with the choices; one or more can be selected. It will ask for
     3115an appropriate instrument parameter file to go with the selected powder data
     3116sets. <o:p></o:p></span></p>
    31473117
    31483118<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    3149 "Times New Roman"'>GSAS .<span class=SpellE>fxye</span> files <o:p></o:p></span></p>
     3119"Times New Roman"'>GSAS .fxye files <o:p></o:p></span></p>
    31503120
    31513121<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    31523122"Times New Roman"'>This reads powder patterns (histograms) from the defined
    3153 GSAS format powder data files. GSAS file <span class=GramE>types</span> STD,
    3154 ESD, FXY and FXYE are recognized. Neutron TOF data with a ‘TIME-MAP’ are also
    3155 recognized. The file names are found in a directory dialog; you can change
    3156 directories as needed. If the selected files have more than one powder pattern,
    3157 a dialog is shown with the choice(s). <o:p></o:p></span></p>
     3123GSAS format powder data files. GSAS file types STD, ESD, FXY and FXYE are
     3124recognized. Neutron TOF data with a ‘TIME-MAP’ are also recognized. The file
     3125names are found in a directory dialog; you can change directories as needed. If
     3126the selected files have more than one powder pattern, a dialog is shown with
     3127the choice(s). <o:p></o:p></span></p>
    31583128
    31593129<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    3160 "Times New Roman"'>TOPAS .<span class=SpellE>xye</span> files. <o:p></o:p></span></p>
     3130"Times New Roman"'>TOPAS .xye files. <o:p></o:p></span></p>
    31613131
    31623132<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    … …  
    31713141"Times New Roman"'>This attempts to read one data set from a file trying the
    31723142formats as described above. On occasion, this command may not succeed in
    3173 correctly determining a file format. If it fails, retry by selecting the correct
    3174 format from the list. <o:p></o:p></span></p>
     3143correctly determining a file format. If it fails, retry by selecting the
     3144correct format from the list. <o:p></o:p></span></p>
    31753145
    31763146<p class=MsoNormal style='margin-left:.9in'><i><span style='mso-fareast-font-family:
    31773147"Times New Roman"'>other supported formats</span></i><span style='mso-fareast-font-family:
    3178 "Times New Roman"'>: <span class=GramE>Bruker .RAW</span>; <span class=SpellE>FullProf</span>
    3179 .<span class=SpellE>dat</span>; <span class=SpellE>Panalytical</span> .<span
    3180 class=SpellE>xrdml</span>; Comma-separated .csv; Rigaku .<span class=SpellE>ras</span>
    3181 &amp; .txt <o:p></o:p></span></p>
     3148"Times New Roman"'>: Bruker .RAW; FullProf .dat; Panalytical .xrdml;
     3149Comma-separated .csv; Rigaku .ras &amp; .txt <o:p></o:p></span></p>
    31823150
    31833151<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    … …  
    31893157
    31903158<p class=MsoNormal style='margin-left:.7in'><span style='mso-fareast-font-family:
    3191 "Times New Roman"'>Note that there are also three separate &quot;special&quot; import
    3192 items, as documented below: <o:p></o:p></span></p>
     3159"Times New Roman"'>Note that there are also three separate &quot;special&quot;
     3160import items, as documented below: <o:p></o:p></span></p>
    31933161
    31943162<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    … …  
    31993167it using a set of instrument parameters that are read in from a file or one of
    32003168the default sets provided when Cancel is pressed at the prompt to select a
    3201 file. The user <span class=GramE>is able to</span> specify the data range and
    3202 step size. One or more crystalline phases must also be provided to perform a
    3203 crystallographic simulation. When the &quot;Refine&quot; menu command is
    3204 initially used, the intensities are computed from these phases and the
    3205 &quot;observed&quot; intensity values are set from these computed values, with
    3206 superimposed &quot;random&quot; noise added (increase the scale factor to
    3207 minimize this, if desired). Further refinements can then be used to fit to
    3208 these simulated data. To reset the &quot;observed&quot; intensity values back
    3209 to zero, to recompute them, use the &quot;Edit range&quot; button on the
    3210 &quot;PWDR&quot; tree item that is created by this option. </span></p>
     3169file. The user is able to specify the data range and step size. One or more
     3170crystalline phases must also be provided to perform a crystallographic
     3171simulation. When the &quot;Refine&quot; menu command is initially used, the
     3172intensities are computed from these phases and the &quot;observed&quot;
     3173intensity values are set from these computed values, with superimposed
     3174&quot;random&quot; noise added (increase the scale factor to minimize this, if
     3175desired). Further refinements can then be used to fit to these simulated data.
     3176To reset the &quot;observed&quot; intensity values back to zero, to recompute
     3177them, use the &quot;Edit range&quot; button on the &quot;PWDR&quot; tree item
     3178that is created by this option. </span></p>
    32113179
    32123180<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    … …  
    32173185files as they are added to a directory. The file extension must determine the
    32183186importer that will be used and a filter pattern is specified to determine which
    3219 files will be read (e.g. use &quot;</span><tt><span style='font-size:10.0pt'>*June23<span
    3220 class=GramE>*.<span class=SpellE>fxye</span></span></span></tt><span
     3187files will be read (e.g. use &quot;</span><tt><span style='font-size:10.0pt'>*June23*.fxye</span></tt><span
    32213188style='mso-fareast-font-family:"Times New Roman"'>&quot; so that only files
    32223189that contain the string &quot;June23&quot; will be read. </span></p>
    32233190
    32243191<p class=MsoNormal style='margin-left:.9in'><a name=FPA><span style='mso-fareast-font-family:
    3225 "Times New Roman"'>Fit Instr. profile from fundamental </span></a><span
    3226 class=SpellE><span style='mso-bookmark:FPA'><span style='mso-fareast-font-family:
    3227 "Times New Roman"'>parms</span></span></span><span style='mso-bookmark:FPA'><span
    3228 style='mso-fareast-font-family:"Times New Roman"'>... </span></span></p>
     3192"Times New Roman"'>Fit Instr. profile from fundamental parms... </span></a></p>
    32293193
    32303194<span style='mso-bookmark:FPA'></span>
    … …  
    32343198set of fundamental parameters that describe a constant wavelength (most likely
    32353199Bragg-Brentano) powder diffraction instrument. The user must first specify the
    3236 data range to be used and then a set of <span class=GramE>FP</span>
    3237 (fundamental parameter) values. The FP values and a source spectrum can be
    3238 supplied using a nomenclature <span class=GramE>similar to</span> <span
    3239 class=SpellE>Topas</span> (described further below). They will then be
    3240 converted to the SI units and parameter names used in the NIST FPA code.
    3241 Alternately a file can be supplied with the parameter values used directly in
    3242 that program. With this input, a series of peaks are computed across the
    3243 specified data range and the <a
     3200data range to be used and then a set of FP (fundamental parameter) values. The
     3201FP values and a source spectrum can be supplied using a nomenclature similar to
     3202Topas (described further below). They will then be converted to the SI units
     3203and parameter names used in the NIST FPA code. Alternately a file can be
     3204supplied with the parameter values used directly in that program. With this
     3205input, a series of peaks are computed across the specified data range and the <a
    32443206href="gsasII-pwdr.html#PWDR_Instrument_Parameters">Instrumental Parameters</a>
    32453207that determine the instrumental profile (U, V, W, X, Y and SH/L) are determined
    … …  
    32483210
    32493211<p class=MsoNormal align=center style='text-align:center'><a name=FPAinput><b><span
    3250 style='mso-fareast-font-family:"Times New Roman"'>Description of the </span></b></a><span
    3251 class=SpellE><span style='mso-bookmark:FPAinput'><b><span style='mso-fareast-font-family:
    3252 "Times New Roman"'>Topas</span></b></span></span><span style='mso-bookmark:
    3253 FPAinput'><b><span style='mso-fareast-font-family:"Times New Roman"'>-style
    3254 fundamental parameters used as FPA input for GSAS-II</span></b></span><span
     3212style='mso-fareast-font-family:"Times New Roman"'>Description of the
     3213Topas-style fundamental parameters used as FPA input for GSAS-II</span></b></a><span
    32553214style='mso-bookmark:FPAinput'></span><span style='mso-fareast-font-family:"Times New Roman"'>
    32563215<o:p></o:p></span></p>
    … …  
    33163275  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    33173276  padding:0in 5.4pt 0in 5.4pt'>
    3318   <p class=MsoNormal><span class=SpellE><span style='mso-bidi-font-family:Calibri;
    3319   mso-bidi-theme-font:minor-latin'>soller_angle</span></span><span
    3320   style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3277  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3278  minor-latin'>soller_angle<o:p></o:p></span></p>
    33213279  </td>
    33223280  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    33323290  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    33333291  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    3334   minor-latin'>Angular limit for divergence in equatorial plane as limited by <span
    3335   class=SpellE>Soller</span> collimator(s)<o:p></o:p></span></p>
     3292  minor-latin'>Angular limit for divergence in equatorial plane as limited by
     3293  Soller collimator(s)<o:p></o:p></span></p>
    33363294  </td>
    33373295 </tr>
    … …  
    33633321  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    33643322  padding:0in 5.4pt 0in 5.4pt'>
    3365   <p class=MsoNormal><span class=SpellE><span style='mso-bidi-font-family:Calibri;
    3366   mso-bidi-theme-font:minor-latin'>filament_length</span></span><span
    3367   style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3323  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3324  minor-latin'>filament_length<o:p></o:p></span></p>
    33683325  </td>
    33693326  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    33873344  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    33883345  padding:0in 5.4pt 0in 5.4pt'>
    3389   <p class=MsoNormal><span class=SpellE><span style='mso-bidi-font-family:Calibri;
    3390   mso-bidi-theme-font:minor-latin'>sample_length</span></span><span
    3391   style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3346  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3347  minor-latin'>sample_length<o:p></o:p></span></p>
    33923348  </td>
    33933349  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    34033359  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    34043360  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    3405   minor-latin'>Illuminated sample length in axial direction. <span class=GramE>Typically</span>
    3406   the same as <span class=SpellE>filament_length</span>.<o:p></o:p></span></p>
     3361  minor-latin'>Illuminated sample length in axial direction. Typically the same
     3362  as filament_length.<o:p></o:p></span></p>
    34073363  </td>
    34083364 </tr>
    … …  
    34113367  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    34123368  padding:0in 5.4pt 0in 5.4pt'>
    3413   <p class=MsoNormal><span class=SpellE><span style='mso-bidi-font-family:Calibri;
    3414   mso-bidi-theme-font:minor-latin'>receiving_slit_length</span></span><span
    3415   style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3369  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3370  minor-latin'>receiving_slit_length<o:p></o:p></span></p>
    34163371  </td>
    34173372  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    34273382  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    34283383  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    3429   minor-latin'>Length of the receiving slit in axial direction. <span
    3430   class=GramE>Typically</span> the same as <span class=SpellE>filament_length</span>.<o:p></o:p></span></p>
     3384  minor-latin'>Length of the receiving slit in axial direction. Typically the
     3385  same as filament_length.<o:p></o:p></span></p>
    34313386  </td>
    34323387 </tr>
    … …  
    34353390  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    34363391  padding:0in 5.4pt 0in 5.4pt'>
    3437   <p class=MsoNormal><span class=SpellE><span style='mso-bidi-font-family:Calibri;
    3438   mso-bidi-theme-font:minor-latin'>LAC_cm</span></span><span style='mso-bidi-font-family:
    3439   Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3392  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3393  minor-latin'>LAC_cm<o:p></o:p></span></p>
    34403394  </td>
    34413395  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    34433397  mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
    34443398  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    3445   <p class=MsoNormal><span class=GramE><span style='mso-bidi-font-family:Calibri;
    3446   mso-bidi-theme-font:minor-latin'>cm<sup>-1</sup></span></span><span
    3447   style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3399  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3400  minor-latin'>cm<sup>-1</sup><o:p></o:p></span></p>
    34483401  </td>
    34493402  <td width=354 valign=top style='width:265.6pt;border-top:none;border-left:
    … …  
    34603413  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    34613414  padding:0in 5.4pt 0in 5.4pt'>
    3462   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    3463   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3464   color:black'>sample_thickness</span></span><span style='mso-bidi-font-family:
    3465   Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3415  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     3416  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>sample_thickness</span><span
     3417  style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
    34663418  </td>
    34673419  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    34853437  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    34863438  padding:0in 5.4pt 0in 5.4pt'>
    3487   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    3488   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3489   color:black'>convolution_steps</span></span><span style='mso-bidi-font-family:
    3490   Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3439  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     3440  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>convolution_steps</span><span
     3441  style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
    34913442  </td>
    34923443  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    35113462  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    35123463  padding:0in 5.4pt 0in 5.4pt'>
    3513   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    3514   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3515   color:black'>source_width</span></span><span style='mso-bidi-font-family:
    3516   Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3464  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     3465  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>source_width</span><span
     3466  style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
    35173467  </td>
    35183468  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    35363486  padding:0in 5.4pt 0in 5.4pt'>
    35373487  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    3538   mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>tube-<span
    3539   class=SpellE>tails_L</span>-tail</span><span style='mso-bidi-font-family:
    3540   Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3488  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>tube-tails_L-tail</span><span
     3489  style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
    35413490  </td>
    35423491  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    35523501  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    35533502  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    3554   minor-latin'>Width for x-ray intensity occurring beyond the <span
    3555   class=SpellE>Wehnelt</span> shadow as a projection in the axial direction and
    3556   measured in the positive two-theta direction.<o:p></o:p></span></p>
     3503  minor-latin'>Width for x-ray intensity occurring beyond the Wehnelt shadow as
     3504  a projection in the axial direction and measured in the positive two-theta
     3505  direction.<o:p></o:p></span></p>
    35573506  </td>
    35583507 </tr>
    … …  
    35623511  padding:0in 5.4pt 0in 5.4pt'>
    35633512  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    3564   mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>tube-<span
    3565   class=SpellE>tails_R</span>-tail</span><span style='mso-bidi-font-family:
    3566   Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3513  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>tube-tails_R-tail</span><span
     3514  style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
    35673515  </td>
    35683516  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    35783526  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    35793527  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    3580   minor-latin'>Width for x-ray intensity occurring beyond the <span
    3581   class=SpellE>Wehnelt</span> shadow as a projection in the axial direction and
    3582   measured in the negative two-theta direction. <o:p></o:p></span></p>
     3528  minor-latin'>Width for x-ray intensity occurring beyond the Wehnelt shadow as
     3529  a projection in the axial direction and measured in the negative two-theta
     3530  direction. <o:p></o:p></span></p>
    35833531  </td>
    35843532 </tr>
    … …  
    35883536  padding:0in 5.4pt 0in 5.4pt'>
    35893537  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    3590   mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>tube-<span
    3591   class=SpellE>tails_rel</span>-I</span><span style='mso-bidi-font-family:Calibri;
    3592   mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3538  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>tube-tails_rel-I</span><span
     3539  style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
    35933540  </td>
    35943541  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    36213568  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    36223569  padding:0in 5.4pt 0in 5.4pt'>
    3623   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    3624   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3625   color:black'>receiving_slit_width</span></span><span style='mso-fareast-font-family:
    3626   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3627   color:black'><o:p></o:p></span></p>
     3570  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     3571  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>receiving_slit_width<o:p></o:p></span></p>
    36283572  </td>
    36293573  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    36763620  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>)
    36773621  range in equatorial plane that the entire Si PSD subtends (<i>not implemented
    3678   in <span class=SpellE>Topas</span></i>)</span><span style='mso-bidi-font-family:
    3679   Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3622  in Topas</i>)</span><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3623  minor-latin'><o:p></o:p></span></p>
    36803624  </td>
    36813625 </tr>
    … …  
    36933637  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    36943638  padding:0in 5.4pt 0in 5.4pt'>
    3695   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    3696   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3697   color:black'>src_mono_mm</span></span><span style='mso-fareast-font-family:
    3698   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3699   color:black'><o:p></o:p></span></p>
     3639  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     3640  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>src_mono_mm<o:p></o:p></span></p>
    37003641  </td>
    37013642  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    37193660  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    37203661  padding:0in 5.4pt 0in 5.4pt'>
    3721   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    3722   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3723   color:black'>focus_mono_mm</span></span><span style='mso-fareast-font-family:
    3724   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3725   color:black'><o:p></o:p></span></p>
     3662  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     3663  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>focus_mono_mm<o:p></o:p></span></p>
    37263664  </td>
    37273665  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    37493687  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    37503688  padding:0in 5.4pt 0in 5.4pt'>
    3751   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    3752   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3753   color:black'>passband_mistune</span></span><span style='mso-fareast-font-family:
    3754   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3755   color:black'><o:p></o:p></span></p>
     3689  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     3690  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>passband_mistune<o:p></o:p></span></p>
    37563691  </td>
    37573692  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    37773712  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    37783713  padding:0in 5.4pt 0in 5.4pt'>
    3779   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    3780   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3781   color:black'>mono_src_proj_mn</span></span><span style='mso-fareast-font-family:
    3782   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3783   color:black'><o:p></o:p></span></p>
     3714  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     3715  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>mono_src_proj_mn<o:p></o:p></span></p>
    37843716  </td>
    37853717  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    37873719  mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
    37883720  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    3789   <p class=MsoNormal><span class=SpellE><span style='mso-bidi-font-family:Calibri;
    3790   mso-bidi-theme-font:minor-latin'>μm</span></span><span style='mso-bidi-font-family:
    3791   Calibri;mso-bidi-theme-font:minor-latin'> (micron)<o:p></o:p></span></p>
     3721  <p class=MsoNormal><span style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3722  minor-latin'>μm (micron)<o:p></o:p></span></p>
    37923723  </td>
    37933724  <td width=354 valign=top style='width:265.6pt;border-top:none;border-left:
    … …  
    37973728  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    37983729  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>Bandwidth
    3799   setting for the monochromator as set by the projection width of the <span
    3800   class=SpellE>xray</span> source on the monochromator along beam direction and
    3801   in the equatorial plane</span><span style='mso-bidi-font-family:Calibri;
    3802   mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3730  setting for the monochromator as set by the projection width of the xray
     3731  source on the monochromator along beam direction and in the equatorial plane</span><span
     3732  style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
    38033733  </td>
    38043734 </tr>
    … …  
    38073737  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    38083738  padding:0in 5.4pt 0in 5.4pt'>
    3809   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    3810   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3811   color:black'>passband_shoulder</span></span><span style='mso-bidi-font-family:
    3812   Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     3739  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     3740  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>passband_shoulder</span><span
     3741  style='mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
    38133742  </td>
    38143743  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    38353764  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    38363765  padding:0in 5.4pt 0in 5.4pt'>
    3837   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    3838   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3839   color:black'>two_theta_mono</span></span><span style='mso-fareast-font-family:
    3840   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3841   color:black'><o:p></o:p></span></p>
     3766  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     3767  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>two_theta_mono<o:p></o:p></span></p>
    38423768  </td>
    38433769  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    38623788  border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;
    38633789  padding:0in 5.4pt 0in 5.4pt'>
    3864   <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family:
    3865   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3866   color:black'>mono_slit_attenuation</span></span><span style='mso-fareast-font-family:
    3867   "Times New Roman";mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
    3868   color:black'><o:p></o:p></span></p>
     3790  <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     3791  mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:black'>mono_slit_attenuation<o:p></o:p></span></p>
    38693792  </td>
    38703793  <td width=71 valign=top style='width:53.05pt;border-top:none;border-left:
    … …  
    38943817style='mso-fareast-font-family:"Times New Roman"'>J. Res. of NIST</span></i><span
    38953818style='mso-fareast-font-family:"Times New Roman"'>, <b>120</b>, p223. DOI:
    3896 10.6028/jres.120.014. If the incident beam <span class=SpellE>monochomator</span>
    3897 model is used, please also cite: M.H. Mendenhall, D. Black &amp; J.P. Cline
    3898 (2019), <i>J. Appl. <span class=SpellE>Cryst</span>.</i>, <b>52</b>, p1087.
    3899 DOI: 10.1107/S1600576719010951. </span></p>
     381910.6028/jres.120.014. If the incident beam monochomator model is used, please
     3820also cite: M.H. Mendenhall, D. Black &amp; J.P. Cline (2019), <i>J. Appl.
     3821Cryst.</i>, <b>52</b>, p1087. DOI: 10.1107/S1600576719010951. </span></p>
    39003822
    39013823<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    39123834<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    39133835"Times New Roman"'>This reads squared structure factors (as F**2) and sig(F**2)
    3914 from a SHELX format .<span class=SpellE>hkl</span> file. The file names are
    3915 found in a directory dialog; you can change directories as needed. You must
    3916 know the file contains structure factors (as F**2) as the file itself has no
    3917 internal indication of this. <o:p></o:p></span></p>
     3836from a SHELX format .hkl file. The file names are found in a directory dialog;
     3837you can change directories as needed. You must know the file contains structure
     3838factors (as F**2) as the file itself has no internal indication of this. <o:p></o:p></span></p>
    39183839
    39193840<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    … …  
    39223843<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    39233844"Times New Roman"'>This reads structure factors (as F) and sig(F) from a SHELX
    3924 format .<span class=SpellE>hkl</span> file. The file names are found in a
    3925 directory dialog; you can change directories as needed. You must know the file
    3926 contains structure factors (as F values) as the file itself has no internal
    3927 indication of this. <o:p></o:p></span></p>
     3845format .hkl file. The file names are found in a directory dialog; you can
     3846change directories as needed. You must know the file contains structure factors
     3847(as F values) as the file itself has no internal indication of this. <o:p></o:p></span></p>
    39283848
    39293849<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    … …  
    39313851
    39323852<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    3933 "Times New Roman"'>This reads structure factors (as F**2 or F) and <span
    3934 class=GramE>sig(</span>F**2 or F) from a .CIF (or .<span class=SpellE>cif</span>)
    3935 or .FCF (or .<span class=SpellE>fcf</span>) format file. The file names are
     3853"Times New Roman"'>This reads structure factors (as F**2 or F) and sig(F**2 or
     3854F) from a .CIF (or .cif) or .FCF (or .fcf) format file. The file names are
    39363855found in a directory dialog; you can change directories as needed. The internal
    39373856structure of this file indicates in which form the structure factors are used. <o:p></o:p></span></p>
    … …  
    39423861<p class=MsoNormal style='margin-left:1.2in'><span style='mso-fareast-font-family:
    39433862"Times New Roman"'>This attempts to read one data set from a file trying the
    3944 formats as described above. However, since it cannot be determined if SHELX <span
    3945 class=GramE>format .<span class=SpellE>hkl</span></span> contains F or F**2
    3946 values, do not use this command for those files. On occasion, this command may
    3947 not succeed in correctly determining a file format. If it fails, retry by
    3948 selecting the correct format from the list. <o:p></o:p></span></p>
     3863formats as described above. However, since it cannot be determined if SHELX
     3864format .hkl contains F or F**2 values, do not use this command for those files.
     3865On occasion, this command may not succeed in correctly determining a file
     3866format. If it fails, retry by selecting the correct format from the list. <o:p></o:p></span></p>
    39493867
    39503868<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    39893907or d-spacing from .txt files. Results are placed in the GSAS-II data tree as
    39903908‘PKS file name’. The data format consists of optional comments (each line
    3991 starts with ‘#’) followed by positions in a single column. If 1<sup>st</sup> position
    3992 is larger than last, they are interpreted as d-spacings, otherwise as 2</span><span
    3993 style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
    3994 "Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
    3995 mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
    3996 Symbol'>Q</span></span><span style='mso-fareast-font-family:"Times New Roman"'>.
    3997 A second column of intensities is optional.<o:p></o:p></span></p>
     3909starts with ‘#’) followed by positions in a single column. If 1<sup>st</sup>
     3910position is larger than last, they are interpreted as d-spacings, otherwise as
     39112</span><span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
     3912mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
     3913mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
     3914symbol;mso-symbol-font-family:Symbol'>Q</span></span><span style='mso-fareast-font-family:
     3915"Times New Roman"'>. A second column of intensities is optional.<o:p></o:p></span></p>
    39983916
    39993917<ol start=5 type=1>
    … …  
    40073925with information inside GSAS-II. These routines can be created and customized
    40083926easily. See the <a href="https://gsas-ii.readthedocs.io/en/latest/exports.html">GSAS-II
    4009 Export Modules section</a> of the <a href="#Programmers"><span class=GramE><strong>Programmers</strong></span><strong>
     3927Export Modules section</a> of the <a href="#Programmers"><strong>Programmers
    40103928documentation</strong></a> for more information on this. Since it is easy to
    40113929support new formats, the documentation below may not list all supported
    … …  
    40273945<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    40283946"Times New Roman"'>Phases can be exported in a variety of formats including a
    4029 simplified CIF file that contains only the unit cell, <span class=GramE>symmetry</span>
    4030 and coordinates. <o:p></o:p></span></p>
     3947simplified CIF file that contains only the unit cell, symmetry and coordinates.
     3948<o:p></o:p></span></p>
    40313949
    40323950<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    40443962
    40453963<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    4046 "Times New Roman"'>Single crystal reflection lists can be exported as text
    4047 files or as a simplified CIF file that contains only structure factors. <o:p></o:p></span></p>
     3964"Times New Roman"'>Single crystal reflection lists can be exported as text files
     3965or as a simplified CIF file that contains only structure factors. <o:p></o:p></span></p>
    40483966
    40493967<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    40513969"Times New Roman"'> <o:p></o:p></span></p>
    40523970
    4053 <p class=MsoNormal style='margin-left:.9in'><span class=GramE><span
    4054 style='mso-fareast-font-family:"Times New Roman"'>This exports</span></span><span
    4055 style='mso-fareast-font-family:"Times New Roman"'> selected images as a
    4056 portable networks graphics format (PNG) file. Alternately, the image controls
    4057 and masks can be written for selected images. If strain analysis has been
    4058 performed on images, the results can also be exported here as a spreadsheet
    4059 (.csv file). <o:p></o:p></span></p>
     3971<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
     3972"Times New Roman"'>This exports selected images as a portable networks graphics
     3973format (PNG) file. Alternately, the image controls and masks can be written for
     3974selected images. If strain analysis has been performed on images, the results
     3975can also be exported here as a spreadsheet (.csv file). <o:p></o:p></span></p>
    40603976
    40613977<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    40733989"Times New Roman"'>This allows peak lists from selected powder histograms to be
    40743990written to a simple text file. There will be a heading for each PWDR GSAS-II
    4075 tree item and columns of values for position, intensity, <span class=GramE>sigma</span>
    4076 and gamma follow. <o:p></o:p></span></p>
     3991tree item and columns of values for position, intensity, sigma and gamma
     3992follow. <o:p></o:p></span></p>
    40773993
    40783994<p class=MsoNormal style='margin-left:.7in'><b><span style='mso-fareast-font-family:
    … …  
    40904006<p class=MsoNormal style='margin-left:.9in'><span style='mso-fareast-font-family:
    40914007"Times New Roman"'>This allows computed PDFs peak lists from selected
    4092 histograms to be written as two simple text files, {name}.gr and {name<span
    4093 class=GramE>}.sq</span>, containing g(r) and s(q), respectively as 2 columns of
    4094 data; a header on each indicated the source file name and the column headings.
    4095 The file name comes from the PDF entry in the GSAS-II data tree. <o:p></o:p></span></p>
     4008histograms to be written as two simple text files, {name}.gr and {name}.sq,
     4009containing g(r) and s(q), respectively as 2 columns of data; a header on each
     4010indicated the source file name and the column headings. The file name comes
     4011from the PDF entry in the GSAS-II data tree. <o:p></o:p></span></p>
    40964012
    40974013<div class=MsoNormal align=center style='text-align:center'><span
    … …  
    41174033"Times New Roman"'>This window provides a place for you to enter whatever text
    41184034commentary you wish. Each time you enter this window, a date/time entry is
    4119 provided for you. A possibly useful technique is to select a portion of the <span
    4120 class=SpellE>project.lst</span> file after a refinement completes (it will
    4121 contain refinement results with residuals, new values &amp; <span class=SpellE>esds</span>)
    4122 and paste it into this Notebook window so it becomes a part of your project
    4123 file.</span> </p>
     4035provided for you. A possibly useful technique is to select a portion of the
     4036project.lst file after a refinement completes (it will contain refinement
     4037results with residuals, new values &amp; esds) and paste it into this Notebook
     4038window so it becomes a part of your project file.</span> </p>
    41244039
    41254040<h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    … …  
    41604075style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    41614076</span></span></span><![endif]><u><span style='mso-fareast-font-family:"Times New Roman"'>analytic
    4162 Hessian</span></u><span style='mso-fareast-font-family:"Times New Roman"'>:
    4163 This is the default option and is usually the most useful. It uses a
     4077Hessian</span></u><span style='mso-fareast-font-family:"Times New Roman"'>: This
     4078is the default option and is usually the most useful. It uses a
    41644079custom-developed least-squares minimizer that uses singular-value decomposition
    41654080(SVD) to reduce the errors caused by correlated variables and the
    … …  
    41734088style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    41744089</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>analytic
    4175 Jacobian: This uses a <span class=SpellE>numpy</span>-provided <span
    4176 class=SpellE><i>leastsq</i></span> minimizer, which not applicable for problem
    4177 with <span class=GramE>a large number of</span> histograms as it requires much
     4090Jacobian: This uses a numpy-provided <i>leastsq</i> minimizer, which not
     4091applicable for problem with a large number of histograms as it requires much
    41784092more memory than the Hessian routines. This because it creates a Jacobian
    41794093matrix that is shaped N x M (N parameters x M observations) while the Hessian
    … …  
    41864100style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    41874101</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>numeric:
    4188 This also uses the <span class=SpellE>numpy</span> <span class=SpellE><i>leastsq</i></span>
    4189 <span class=GramE>minimizer, and</span> is also not applicable for larger
    4190 problems. Unlike, the &quot;analytic Jacobian&quot;, numerical derivatives are
    4191 computed rather than use the analytical derivatives that are coded directly
    4192 into GSAS-II. This will be slower than the analytical derivatives and will is
    4193 often less accurate which results in slower convergence. <i>It is typically
    4194 used for code development to check the accuracy of the analytical derivative
    4195 formulations. </i><o:p></o:p></span></p>
     4102This also uses the numpy <i>leastsq</i> minimizer, and is also not applicable
     4103for larger problems. Unlike, the &quot;analytic Jacobian&quot;, numerical
     4104derivatives are computed rather than use the analytical derivatives that are
     4105coded directly into GSAS-II. This will be slower than the analytical
     4106derivatives and will is often less accurate which results in slower
     4107convergence. <i>It is typically used for code development to check the accuracy
     4108of the analytical derivative formulations. </i><o:p></o:p></span></p>
    41964109
    41974110<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    42084121<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    42094122"Times New Roman"'>Note that the Jacobian refinement tools are the Fortran
    4210 MINPACK <span class=SpellE><i>lmdif</i></span> and <span class=SpellE><i>lmder</i></span>
    4211 algorithms wrapped in python as provided in the <span class=SpellE>Scipy</span>
    4212 package. The Hessian routines were developed for GSAS-II based on routines in <span
    4213 class=SpellE>numpy</span> and <span class=SpellE>scipy</span> and using the
    4214 material in Numerical Recipes (Press, Flannery, <span class=SpellE>Teulosky</span>
    4215 &amp; <span class=SpellE>Vetterling</span>) for the Levenberg-Marquardt. The
    4216 purpose is to minimize the sum of the squares of M nonlinear functions in N
    4217 variables by a modification of the Levenberg-Marquardt algorithm. The <span
    4218 class=SpellE>lmdif</span> and <span class=SpellE>lmder</span> routines were
    4219 written by Burton S. <span class=SpellE>Garbow</span>, Kenneth E. <span
    4220 class=SpellE>Hillstrom</span>, Jorge J. More (Argonne National Laboratory,
    4221 1980). <o:p></o:p></span></p>
     4123MINPACK <i>lmdif</i> and <i>lmder</i> algorithms wrapped in python as provided
     4124in the Scipy package. The Hessian routines were developed for GSAS-II based on
     4125routines in numpy and scipy and using the material in Numerical Recipes (Press,
     4126Flannery, Teulosky &amp; Vetterling) for the Levenberg-Marquardt. The purpose
     4127is to minimize the sum of the squares of M nonlinear functions in N variables
     4128by a modification of the Levenberg-Marquardt algorithm. The lmdif and lmder
     4129routines were written by Burton S. Garbow, Kenneth E. Hillstrom, Jorge J. More
     4130(Argonne National Laboratory, 1980). <o:p></o:p></span></p>
    42224131
    42234132<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
    4224 "Times New Roman"'>Min <span class=GramE>delta-M</span>/M</span></b><span
    4225 style='mso-fareast-font-family:"Times New Roman"'> <o:p></o:p></span></p>
     4133"Times New Roman"'>Min delta-M/M</span></b><span style='mso-fareast-font-family:
     4134"Times New Roman"'> <o:p></o:p></span></p>
    42264135
    42274136<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    42284137"Times New Roman"'>A refinement will stop when the change in the minimization
    4229 function (M=Σ[w(Io-<span class=SpellE>Ic</span>)<sup>2</sup>]) is less than
    4230 this value. The allowed range is 10<sup>-9</sup> to 1.0, with a default of
    4231 0.001. A value of 1.0 stops the refinement after a single cycle. Values less
    4232 than 10<sup>-4</sup> cause refinements to continue even if there is no
    4233 meaningful improvement. <o:p></o:p></span></p>
     4138function (M=Σ[w(Io-Ic)<sup>2</sup>]) is less than this value. The allowed range
     4139is 10<sup>-9</sup> to 1.0, with a default of 0.001. A value of 1.0 stops the
     4140refinement after a single cycle. Values less than 10<sup>-4</sup> cause
     4141refinements to continue even if there is no meaningful improvement. <o:p></o:p></span></p>
    42344142
    42354143<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
    … …  
    42504158weight of 1+λ is applied to the diagonal elements of the Hessian. When λ is
    42514159large, this down-weights the significance of the off-diagonal terms in the
    4252 Hessian. Thus, when λ is large, the refinement is effectively one of <span
    4253 class=GramE>steepest-descents</span>, where correlation between variables is
    4254 ignored. Note that steepest-descents minimization is typically slow and may not
    4255 always find the local minimum. This is only used when with the &quot;analytical
    4256 Hessian&quot; minimizer is selected. <o:p></o:p></span></p>
     4160Hessian. Thus, when λ is large, the refinement is effectively one of
     4161steepest-descents, where correlation between variables is ignored. Note that
     4162steepest-descents minimization is typically slow and may not always find the
     4163local minimum. This is only used when with the &quot;analytical Hessian&quot;
     4164minimizer is selected. <o:p></o:p></span></p>
    42574165
    42584166<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
    … …  
    42804188
    42814189<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
    4282 "Times New Roman"'>Min <span class=SpellE>obs</span>/sig</span></b><span
    4283 style='mso-fareast-font-family:"Times New Roman"'> <o:p></o:p></span></p>
     4190"Times New Roman"'>Min obs/sig</span></b><span style='mso-fareast-font-family:
     4191"Times New Roman"'> <o:p></o:p></span></p>
    42844192
    42854193<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    … …  
    43014209<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    43024210"Times New Roman"'>Removes reflections that are very poorly fit. Should be used
    4303 only with extreme care, since <span class=GramE>poorly-fit</span> reflections
    4304 could be an indication that the structure is wrong. <o:p></o:p></span></p>
     4211only with extreme care, since poorly-fit reflections could be an indication
     4212that the structure is wrong. <o:p></o:p></span></p>
    43054213
    43064214<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
    … …  
    43474255
    43484256<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4349 "Times New Roman"'>Normally, in <span class=GramE>a sequential histograms</span>
    4350 are fit in the order they are in the data tree (which can be reordered by
    4351 dragging tree items), but when this option is selected, the sequential fit is
    4352 performed with the last tree entry first. <o:p></o:p></span></p>
     4257"Times New Roman"'>Normally, in a sequential histograms are fit in the order
     4258they are in the data tree (which can be reordered by dragging tree items), but
     4259when this option is selected, the sequential fit is performed with the last
     4260tree entry first. <o:p></o:p></span></p>
    43534261
    43544262<p class=MsoNormal style='margin-left:1.0in'><b><span style='mso-fareast-font-family:
    … …  
    44094317
    44104318<p style='margin-left:1.0in'>Move the mouse cursor across the plot. If on a
    4411 diagonal cell, the parameter name, value and <span class=SpellE>esd</span> is
    4412 shown both as a tool tip and in the right-hand portion of the status bar. If
    4413 the cursor is off the diagonal, the two parameter names and their covariance
    4414 are shown in the tool tip and the status bar. </p>
     4319diagonal cell, the parameter name, value and esd is shown both as a tool tip
     4320and in the right-hand portion of the status bar. If the cursor is off the
     4321diagonal, the two parameter names and their covariance are shown in the tool
     4322tip and the status bar. </p>
    44154323
    44164324<p style='margin-left:1.0in'>Use the Zoom and Pan buttons to focus on some
    … …  
    44194327<p style='margin-left:1.0in'>Press ‘s’ – A color scheme selection dialog is
    44204328shown. Select a color scheme and press OK, the new color scheme will be
    4421 plotted. The default is ‘<span class=SpellE>RdYlGn</span>’. </p>
     4329plotted. The default is ‘RdYlGn’. </p>
    44224330
    44234331<p style='margin-left:1.0in'>Press ‘p’ – Saves the covariance values in a text
    … …  
    44294337<span style='mso-bookmark:Constraints'></span>
    44304338
    4431 <p class=MsoNormal style='margin-left:.5in'>This window shows the constraints to
    4432 be used in a refinement. Constraints are divided with a tab for each type:
    4433 Phase, Histogram/Phase, Histogram, Global and <span class=SpellE>Sym</span>-Generated.
    4434 Note that the standard parameters in GSAS-II are divided into three classes and
    4435 appear respectively on the Phase, Histogram and Histogram/Phase tabs: </p>
     4339<p class=MsoNormal style='margin-left:.5in'>This window shows the constraints
     4340to be used in a refinement. Constraints are divided with a tab for each type:
     4341Phase, Histogram/Phase, Histogram, Global and Sym-Generated. Note that the
     4342standard parameters in GSAS-II are divided into three classes and appear
     4343respectively on the Phase, Histogram and Histogram/Phase tabs: </p>
    44364344
    44374345<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    44414349style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    44424350</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>those
    4443 pertaining to quantities in each phase (naming pattern &quot;</span><span
    4444 class=GramE><tt><i><span style='font-size:10.0pt'>p</span></i></tt><tt><span
    4445 style='font-size:10.0pt'>::</span></tt></span><tt><i><span style='font-size:
    4446 10.0pt'>name</span></i></tt><span style='mso-fareast-font-family:"Times New Roman"'>&quot;);
    4447 examples include atom coordinates, thermal motion and site fraction parameters;
    4448 <o:p></o:p></span></p>
     4351pertaining to quantities in each phase (naming pattern &quot;</span><tt><i><span
     4352style='font-size:10.0pt'>p</span></i></tt><tt><span style='font-size:10.0pt'>::<i>name</i></span></tt><span
     4353style='mso-fareast-font-family:"Times New Roman"'>&quot;); examples include
     4354atom coordinates, thermal motion and site fraction parameters; <o:p></o:p></span></p>
    44494355
    44504356<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    44544360style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    44554361</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>those
    4456 pertaining to quantities in each histogram (naming pattern &quot;:</span><span
    4457 class=SpellE><tt><i><span style='font-size:10.0pt'>h</span></i></tt><tt><span
    4458 style='font-size:10.0pt'>:<i>name</i></span></tt></span><span style='mso-fareast-font-family:
    4459 "Times New Roman"'>&quot;); such parameters are those that depend only on the
    4460 data set the scale factor and profile coefficients (<span class=GramE>e.g.</span>
    4461 U, V, W, X and Y); <o:p></o:p></span></p>
     4362pertaining to quantities in each histogram (naming pattern &quot;:</span><tt><i><span
     4363style='font-size:10.0pt'>h</span></i></tt><tt><span style='font-size:10.0pt'>:<i>name</i></span></tt><span
     4364style='mso-fareast-font-family:"Times New Roman"'>&quot;); such parameters are
     4365those that depend only on the data set the scale factor and profile
     4366coefficients (e.g. U, V, W, X and Y); <o:p></o:p></span></p>
    44624367
    44634368<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    44674372style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    44684373</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>and
    4469 those pertaining to <span class=SpellE>quanitities</span> defined for each
    4470 histogram in each phase (naming pattern &quot;</span><tt><i><span
    4471 style='font-size:10.0pt'>p</span></i></tt><tt><span style='font-size:10.0pt'>:<i>h</i>:<i>name</i></span></tt><span
     4374those pertaining to quanitities defined for each histogram in each phase
     4375(naming pattern &quot;</span><tt><i><span style='font-size:10.0pt'>p</span></i></tt><tt><span
     4376style='font-size:10.0pt'>:<i>h</i>:<i>name</i></span></tt><span
    44724377style='mso-fareast-font-family:"Times New Roman"'>&quot;); these parameters are
    44734378quantities that can be dependent on both the phase properties and the sample or
    44744379dataset used for the measurement. Examples include phase fractions and
    4475 sample-broadening coefficients such as <span class=SpellE>microstrain</span>
    4476 and crystallite size. <o:p></o:p></span></p>
     4380sample-broadening coefficients such as microstrain and crystallite size. <o:p></o:p></span></p>
    44774381
    44784382<p class=MsoNormal style='margin-left:.5in'>The following types of constraints
    … …  
    44864390"Times New Roman"'>Use this to prevent a parameter from being refined. Most
    44874391valuable when refinement of a parameter is selected in a group for refinement
    4488 (such as x, y &amp; z for an atom or unit cell parameters). For <span
    4489 class=GramE>example</span> of the use of this, if the space group for a phase
    4490 has a polar axis (e.g. the <i>b</i>-axis in P2<sub>1</sub>), then origin with
    4491 respect to <i>b</i> is arbitrary and it is not possible to refine the y
    4492 coordinates for all atoms. Place a Hold on any one y coordinate to keep the
    4493 structure from drifting up or down the y-axis during refinement. <o:p></o:p></span></p>
     4392(such as x, y &amp; z for an atom or unit cell parameters). For example of the
     4393use of this, if the space group for a phase has a polar axis (e.g. the <i>b</i>-axis
     4394in P2<sub>1</sub>), then origin with respect to <i>b</i> is arbitrary and it is
     4395not possible to refine the y coordinates for all atoms. Place a Hold on any one
     4396y coordinate to keep the structure from drifting up or down the y-axis during
     4397refinement. <o:p></o:p></span></p>
    44944398
    44954399<p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    … …  
    45014405a specified ratio (except for atom coordinates, where the ratios are specified
    45024406for the applied shifts, not the actual coordinate values) Examples for typical
    4503 use are sets of atoms that should be constrained to have the same displacement <span
    4504 class=SpellE>paramaters</span> (aka thermal <span class=SpellE><span
    4505 class=GramE>motion,Uiso</span></span>, etc.) or sets of profile coefficients
     4407use are sets of atoms that should be constrained to have the same displacement
     4408paramaters (aka thermal motion,Uiso, etc.) or sets of profile coefficients
    45064409U,V,W across multiple data sets. Note that the first selected parameter is
    4507 treated as <span class=GramE>independent</span> and the remainder are
    4508 &quot;slaved&quot; to that parameter as &quot;dependent parameters.&quot; All
    4509 parameters in an equivalence must be varied. If any parameter is not varied or
    4510 is given a &quot;hold,&quot; a warning is displayed and none of the parameters
    4511 are refined. <o:p></o:p></span></p>
     4410treated as independent and the remainder are &quot;slaved&quot; to that
     4411parameter as &quot;dependent parameters.&quot; All parameters in an equivalence
     4412must be varied. If any parameter is not varied or is given a &quot;hold,&quot;
     4413a warning is displayed and none of the parameters are refined. <o:p></o:p></span></p>
    45124414
    45134415<p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    … …  
    45184420"Times New Roman"'>Defines a set of parameters whose sum (with possible
    45194421non-unitary multipliers) will be equal to a constant. For example, a common use
    4520 for this is to specify the sum of occupancies for atoms sharing a site have a
    4521 sum fixed to unity or so that the sum of occupancies for an atom type that is
    4522 occurs on several sites is fixed to match a <span class=SpellE>compsition</span>-determined
    4523 value. Note that all parameters in the equation are considered as
    4524 &quot;dependent parameters.&quot; If a parameter in a constraint equation is
    4525 held or is not varied, that parameter is removed from the equation (the sum
    4526 value is modified accordingly). If no parameters remain the equation is
    4527 ignored. <o:p></o:p></span></p>
     4422for this is to specify the sum of occupancies for atoms sharing a site have a sum
     4423fixed to unity or so that the sum of occupancies for an atom type that is
     4424occurs on several sites is fixed to match a compsition-determined value. Note
     4425that all parameters in the equation are considered as &quot;dependent
     4426parameters.&quot; If a parameter in a constraint equation is held or is not
     4427varied, that parameter is removed from the equation (the sum value is modified
     4428accordingly). If no parameters remain the equation is ignored. <o:p></o:p></span></p>
    45284429
    45294430<p class=MsoNormal style='margin-left:.75in'><b><span style='mso-fareast-font-family:
    … …  
    45324433
    45334434<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
    4534 "Times New Roman"'>appear <span class=GramE>similar to</span> constraint
    4535 equations in that they define a set of parameters and multipliers, but rather
    4536 than specifying a value for the expression, a new parameter is assigned to that
    4537 sum and these constraints have a very different function. This replaces a
    4538 degree of freedom from the original variables with a new one that modifies the
    4539 parameters where the shift is applied according to the ratio specified in the
    4540 expression. This can be used to create new parameters that redefine the
    4541 relationships between items such as coordinates or magnetic moments. The new
    4542 parameter may optionally be named by the user. The new var expression creates a
    4543 new global parameter, where that new parameter is independent, while all the
    4544 parameters in the expression are considered as dependent. The settings of the
    4545 refine flags for the dependent parameters is not used. Only if the new var
    4546 parameter is marked as refine then it will be refined. However, if any
    4547 dependent variable is set as &quot;hold,&quot; the new var parameter will not
    4548 be refined. <o:p></o:p></span></p>
     4435"Times New Roman"'>appear similar to constraint equations in that they define a
     4436set of parameters and multipliers, but rather than specifying a value for the
     4437expression, a new parameter is assigned to that sum and these constraints have
     4438a very different function. This replaces a degree of freedom from the original
     4439variables with a new one that modifies the parameters where the shift is
     4440applied according to the ratio specified in the expression. This can be used to
     4441create new parameters that redefine the relationships between items such as
     4442coordinates or magnetic moments. The new parameter may optionally be named by
     4443the user. The new var expression creates a new global parameter, where that new
     4444parameter is independent, while all the parameters in the expression are
     4445considered as dependent. The settings of the refine flags for the dependent
     4446parameters is not used. Only if the new var parameter is marked as refine then
     4447it will be refined. However, if any dependent variable is set as
     4448&quot;hold,&quot; the new var parameter will not be refined. <o:p></o:p></span></p>
    45494449
    45504450<p class=MsoNormal style='margin-left:.5in'>Note that when new var and
    45514451constraint equation constraints are defined, they create new global parameters.
    4552 Constraints on these will be rare, but can be managed on the <span
    4553 class=SpellE>Globals</span> tab. Finally, some constraints are defined
    4554 automatically based on restrictions determined by space group symmetry. These
    4555 constraints can be seen, but not changed, using the <span class=SpellE>Sym</span>-Generated
    4556 tab. Other constraints (holds) will be created when rigid bodies are specified.
    4557 </p>
     4452Constraints on these will be rare, but can be managed on the Globals tab.
     4453Finally, some constraints are defined automatically based on restrictions
     4454determined by space group symmetry. These constraints can be seen, but not
     4455changed, using the Sym-Generated tab. Other constraints (holds) will be created
     4456when rigid bodies are specified. </p>
    45584457
    45594458<h5 style='margin-left:.5in'>What can I do here?</h5>
    … …  
    45964495OK. Cancel in either dialog will cancel the operation. The equivalenced
    45974496parameters 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;
    4598 usually M1=1.0 and M2=-<span class=GramE>1.0, but</span> can be changed via the
    4599 ‘Edit’ button. The equation(s) are shown in the window tagged by ‘EQUIV’ to
    4600 mark it as an equivalence assignment. <o:p></o:p></span></p>
     4497usually M1=1.0 and M2=-1.0, but can be changed via the ‘Edit’ button. The
     4498equation(s) are shown in the window tagged by ‘EQUIV’ to mark it as an
     4499equivalence assignment. <o:p></o:p></span></p>
    46014500
    46024501<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    46084507style='mso-fareast-font-family:"Times New Roman"'>: If selected, a dialog box
    46094508will appear with a list of the available parameters. Select one and press OK; a
    4610 second dialog box will appear with only those parameters that can be used in a
    4611 constraint with the first one. Choose those and press OK. Cancel in either
    4612 dialog will cancel the operation. The equivalenced parameters will show as an
    4613 equation of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+…=C;
    4614 the multipliers M1, M2, … and C can be changed via the ‘Edit’ button. The
    4615 equation is shown in the window tagged by ‘CONSTR’ to mark it as a constraint
    4616 equation assignment. <o:p></o:p></span></p>
     4509second dialog box will appear with only those parameters that can be used in a constraint
     4510with the first one. Choose those and press OK. Cancel in either dialog will
     4511cancel the operation. The equivalenced parameters will show as an equation of
     4512the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+…=C; the
     4513multipliers M1, M2, … and C can be changed via the ‘Edit’ button. The equation
     4514is shown in the window tagged by ‘CONSTR’ to mark it as a constraint equation
     4515assignment. <o:p></o:p></span></p>
    46174516
    46184517<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    46364535style='mso-fareast-font-family:"Times New Roman"'>Make atoms equivalent</span></b><span
    46374536style='mso-fareast-font-family:"Times New Roman"'>: This provides a shortcut
    4638 for establishing constraints when two share a single site. Coordinates and <span
    4639 class=SpellE>Uiso</span> values are constrained to be the same and site
    4640 fractions are constrained to add to 1. <o:p></o:p></span></p>
     4537for establishing constraints when two share a single site. Coordinates and Uiso
     4538values are constrained to be the same and site fractions are constrained to add
     4539to 1. <o:p></o:p></span></p>
    46414540
    46424541<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    46594558style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    46604559</span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Show
    4661 <span class=GramE>Errors <span style='font-weight:normal'>:</span></span></span></b><span
    4662 style='mso-fareast-font-family:"Times New Roman"'> this button will be active
    4663 if serious errors -- that would prevent a refinement from being performed --
    4664 are encountered processing the constraints. <o:p></o:p></span></p>
     4560Errors </span></b><span style='mso-fareast-font-family:"Times New Roman"'>:
     4561this button will be active if serious errors -- that would prevent a refinement
     4562from being performed -- are encountered processing the constraints. <o:p></o:p></span></p>
    46654563
    46664564<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    46704568style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    46714569</span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Show
    4672 <span class=GramE>Warnings <span style='font-weight:normal'>:</span></span></span></b><span
    4673 style='mso-fareast-font-family:"Times New Roman"'> this button will be active
    4674 if correctable problems are encountered in processing the constraints, such as
    4675 a constraint being rejected because a parameter is not varied. These warning
    4676 may indicate that the choice of which parameters will be refined is not what
    4677 was planned. <o:p></o:p></span></p>
     4570Warnings </span></b><span style='mso-fareast-font-family:"Times New Roman"'>:
     4571this button will be active if correctable problems are encountered in
     4572processing the constraints, such as a constraint being rejected because a
     4573parameter is not varied. These warning may indicate that the choice of which
     4574parameters will be refined is not what was planned. <o:p></o:p></span></p>
    46784575
    46794576<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    46834580style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    46844581</span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Show
    4685 Generated <span class=GramE>Constraints <span style='font-weight:normal'>:</span></span></span></b><span
    4686 style='mso-fareast-font-family:"Times New Roman"'> After constraints have been
    4687 processed, a series of relationships are developed to determine new variables
    4688 from the current parameters and &quot;inverse&quot; equations that determine
    4689 dependent parameters from the new variables and independent parameters. This
    4690 shows the resulting relationships, as well as any &quot;Hold&quot; variables. <o:p></o:p></span></p>
     4582Generated Constraints </span></b><span style='mso-fareast-font-family:"Times New Roman"'>:
     4583After constraints have been processed, a series of relationships are developed
     4584to determine new variables from the current parameters and &quot;inverse&quot;
     4585equations that determine dependent parameters from the new variables and
     4586independent parameters. This shows the resulting relationships, as well as any
     4587&quot;Hold&quot; variables. <o:p></o:p></span></p>
    46914588
    46924589<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    46964593style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    46974594</span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Delete
    4698 <span class=GramE>Selected <span style='font-weight:normal'>:</span></span></span></b><span
    4699 style='mso-fareast-font-family:"Times New Roman"'> This button will cause all
    4700 the selected constraints on the current tab to be deleted. <o:p></o:p></span></p>
     4595Selected </span></b><span style='mso-fareast-font-family:"Times New Roman"'>:
     4596This button will cause all the selected constraints on the current tab to be
     4597deleted. <o:p></o:p></span></p>
    47014598
    47024599<h5 style='margin-left:.5in'><a name=Constraints-SeqRef>Sequential Refinement
    … …  
    47094606parameters keyed to a particular constraint number. When sequential refinement
    47104607is selected (via the <a href="#Controls">Controls tree item</a>), it becomes
    4711 possible to define constraints of form &quot;<span class=GramE><tt><i><span
    4712 style='font-size:10.0pt'>p</span></i></tt>:*</span>:<tt><i><span
    4713 style='font-size:10.0pt'>name</span></i></tt>&quot; and &quot;:*:<tt><i><span
    4714 style='font-size:10.0pt'>name</span></i></tt>&quot; (where &quot;<tt><i><span
    4715 style='font-size:10.0pt'>p</span></i></tt>&quot; is a phase number and <tt><i><span
    4716 style='font-size:10.0pt'>name</span></i></tt> is a parameter name). The
    4717 &quot;*&quot; here is called a wildcard <span class=GramE>and in a constraint</span>
     4608possible to define constraints of form &quot;<tt><i><span style='font-size:
     460910.0pt'>p</span></i></tt>:*:<tt><i><span style='font-size:10.0pt'>name</span></i></tt>&quot;
     4610and &quot;:*:<tt><i><span style='font-size:10.0pt'>name</span></i></tt>&quot;
     4611(where &quot;<tt><i><span style='font-size:10.0pt'>p</span></i></tt>&quot; is a
     4612phase number and <tt><i><span style='font-size:10.0pt'>name</span></i></tt> is
     4613a parameter name). The &quot;*&quot; here is called a wildcard and in a constraint
    47184614or equivalence will cause that to be used for every histogram in turn. </p>
    47194615
    … …  
    47454641histogram number will be ignored and constraints with a &quot;*&quot; where for
    47464642a histogram number will be used. Note that constraints on phase parameters (of
    4747 form &quot;</span><span class=GramE><tt><i><span style='font-size:10.0pt'>p</span></i></tt><span
    4748 style='mso-fareast-font-family:"Times New Roman"'>::</span></span><tt><i><span
     4643form &quot;</span><tt><i><span style='font-size:10.0pt'>p</span></i></tt><span
     4644style='mso-fareast-font-family:"Times New Roman"'>::</span><tt><i><span
    47494645style='font-size:10.0pt'>name</span></i></tt><span style='mso-fareast-font-family:
    47504646"Times New Roman"'>&quot; -- without a histogram number specified) will be used
    … …  
    47664662unsatisfiable conflict. <o:p></o:p></span></p>
    47674663
    4768 <p class=MsoNormal style='margin-left:.75in'>Also included when a <span
    4769 class=GramE>sequential refinements</span> is selected is a menu button labeled <b>&quot;Selected
     4664<p class=MsoNormal style='margin-left:.75in'>Also included when a sequential
     4665refinements is selected is a menu button labeled <b>&quot;Selected
    47704666histogram.&quot;</b> With this it is possible to look at constraint problems
    47714667when processing a specific histogram. </p>
    … …  
    47974693style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    47984694style='mso-fareast-font-family:"Times New Roman"'>You can change the <b
    4799 style='mso-bidi-font-weight:normal'>Restraint weight factor</b> – this is used
    4800 to scale the weights for the entire set of restraints of this type. Default
    4801 value for the weight factor is 1.0.<o:p></o:p></span></p>
     4695style='mso-bidi-font-weight:normal'>Restraint weight factor</b> – this is used to
     4696scale the weights for the entire set of restraints of this type. Default value
     4697for the weight factor is 1.0.<o:p></o:p></span></p>
    48024698
    48034699<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    48214717style='mso-fareast-font-family:"Times New Roman"'>You can examine the table of
    48224718restraints and change individual values; grayed out regions cannot be changed.
    4823 The ‘calc’ values are determined from the atom positions in your structure, ‘<span
    4824 class=SpellE>obs</span>’ values are the target values for the restraint and ‘<span
    4825 class=SpellE>esd</span>’ is the uncertainty used to weight the restraint in the
    4826 refinement (multiplied by the weight factor).<o:p></o:p></span></p>
     4719The ‘calc’ values are determined from the atom positions in your structure,
     4720‘obs’ values are the target values for the restraint and ‘esd’ is the
     4721uncertainty used to weight the restraint in the refinement (multiplied by the
     4722weight factor).<o:p></o:p></span></p>
    48274723
    48284724<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    48524748this takes you through a sequence of dialog boxes which ask for the identities
    48534749of the atoms involved in the restraint and the value to be assigned to the
    4854 restraint. The <span class=SpellE>esd</span> is given a default value which can
    4855 be changed after the restraints are created.<o:p></o:p></span></p>
     4750restraint. The esd is given a default value which can be changed after the
     4751restraints are created.<o:p></o:p></span></p>
    48564752
    48574753<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    48634759– if the phase is a ‘macromolecule’ then develop the restraints from a selected
    48644760‘macro’ file based on those used in GSAS for this purpose. A file dialog box is
    4865 shown directed to /<span class=SpellE>GSASIImacros</span>; be sure to select
    4866 the correct file.<o:p></o:p></span></p>
     4761shown directed to /GSASIImacros; be sure to select the correct file.<o:p></o:p></span></p>
    48674762
    48684763<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    48794774case a dialog box will appear asking for the residue types or specific torsion
    48804775angles to plot. Each plot will show the observed distribution (blue) obtained
    4881 from a wide variety of <span class=GramE>high resolution</span> protein
    4882 structures and those found (red dots) for your structure. The restraints are
    4883 based on a pseudopotential (red curve or contours – favorable values at the
    4884 peaks) which has been developed from the observed distributions for each
    4885 residue type.<o:p></o:p></span></p>
     4776from a wide variety of high resolution protein structures and those found (red
     4777dots) for your structure. The restraints are based on a pseudopotential (red
     4778curve or contours – favorable values at the peaks) which has been developed
     4779from the observed distributions for each residue type.<o:p></o:p></span></p>
    48864780
    48874781<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    48914785style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Change
    48924786value</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – this
    4893 changes the ‘<span class=SpellE>obsd</span>’ value for selected restraints; a dialog
    4894 box will appear asking for the new value. <o:p></o:p></span></p>
     4787changes the ‘obsd’ value for selected restraints; a dialog box will appear
     4788asking for the new value. <o:p></o:p></span></p>
    48954789
    48964790<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    48994793style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    49004794</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    4901 style='mso-fareast-font-family:"Times New Roman"'>Change <span class=SpellE>esd</span></span></b><span
    4902 style='mso-fareast-font-family:"Times New Roman"'> – this changes the ‘<span
    4903 class=SpellE>esd</span>’ value for selected restraints; a dialog box will
    4904 appear asking for the new value.<o:p></o:p></span></p>
     4795style='mso-fareast-font-family:"Times New Roman"'>Change esd</span></b><span
     4796style='mso-fareast-font-family:"Times New Roman"'> – this changes the ‘esd’
     4797value for selected restraints; a dialog box will appear asking for the new
     4798value.<o:p></o:p></span></p>
    49054799
    49064800<p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto;
    … …  
    49644858XYZ</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    49654859(Residue rigid bodies) this reads a text file containing a set of Cartesian
    4966 coordinates describing a rigid body model. Each line has atom type (<span
    4967 class=GramE>e.g.</span> C, Na, etc.) and Cartesian X, Y and Z.<o:p></o:p></span></p>
     4860coordinates describing a rigid body model. Each line has atom type (e.g. C, Na,
     4861etc.) and Cartesian X, Y and Z.<o:p></o:p></span></p>
    49684862
    49694863<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    … …  
    49864880residues</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    49874881(Residue rigid bodies) this reads a predetermined macro file that contains
    4988 standard (<span class=SpellE>Engh</span> &amp; Huber) coordinates for the amino
    4989 acids found in natural proteins along with predetermined variable torsion angle
    4990 definitions.<o:p></o:p></span></p>
     4882standard (Engh &amp; Huber) coordinates for the amino acids found in natural
     4883proteins along with predetermined variable torsion angle definitions.<o:p></o:p></span></p>
    49914884
    49924885<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    … …  
    49954888style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    49964889style='mso-fareast-font-family:"Times New Roman"'>Once a rigid body is defined
    4997 you can plot it, change its <span class=GramE>name</span> or manipulate any
    4998 torsion angle to see the effect on the plot.<o:p></o:p></span></p>
     4890you can plot it, change its name or manipulate any torsion angle to see the
     4891effect on the plot.<o:p></o:p></span></p>
    49994892
    50004893<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    … …  
    50134906use the Calculate/Sequential refine menu command to run the refinement.) When
    50144907this is selected, the window tabulates the sequential refinement results. The
    5015 columns are the parameter names; the naming convention is ‘<span class=SpellE>p:h:<span
    5016 class=GramE>name:n</span></span>’ where ‘p’ is the phase number,’ h’ is the
    5017 histogram number, ‘name’ is the parameter name, and ‘n’ (if needed) is the item
    5018 number (e.g. atom number). The rows are the data sets used in the sequential
    5019 refinement.</p>
     4908columns are the parameter names; the naming convention is ‘p:h:name:n’ where
     4909‘p’ is the phase number,’ h’ is the histogram number, ‘name’ is the parameter
     4910name, and ‘n’ (if needed) is the item number (e.g. atom number). The rows are
     4911the data sets used in the sequential refinement.</p>
    50204912
    50214913<h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    … …  
    50584950style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    50594951normal;mso-bidi-font-weight:bold'> – this will create a text file of selected
    5060 columns with values and corresponding <span class=SpellE>esds</span>. A file
    5061 dialog box will appear; give a suitable file name; you may change directory if
    5062 desired.<o:p></o:p></span></h5>
     4952columns with values and corresponding esds. A file dialog box will appear; give
     4953a suitable file name; you may change directory if desired.<o:p></o:p></span></h5>
    50634954
    50644955<div class=MsoNormal align=center style='text-align:center'><span
    … …  
    51195010<p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:PDF'><span
    51205011style='mso-fareast-font-family:"Times New Roman"'>By default, the plot will
    5121 show a l=0 layer of reflections on a square grid as rings proportional to <span
    5122 class=SpellE>F<sub>o</sub></span> (blue), F<sub>c</sub> (green) and a central
    5123 dot (green or red) proportional to <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>.<o:p></o:p></span></span></p>
     5012show a l=0 layer of reflections on a square grid as rings proportional to F<sub>o</sub>
     5013(blue), F<sub>c</sub> (green) and a central dot (green or red) proportional to
     5014F<sub>o</sub>-F<sub>c</sub>.<o:p></o:p></span></span></p>
    51245015
    51255016<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
    … …  
    51275018can I do with the plot?</span></span></h5>
    51285019
    5129 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:PDF'>The
    5130 “K” box in the plot controls shows the 14 keystroke controls for the plot –
    5131 they are generally self-explanatory.</span></p>
     5020<p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:PDF'>The “K”
     5021box in the plot controls shows the 14 keystroke controls for the plot – they
     5022are generally self-explanatory.</span></p>
    51325023
    51335024<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'><span
    … …  
    51565047
    51575048<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
    5158 Optimize PDF button can be used to refine the values of the &quot;Flat <span
    5159 class=SpellE>Bkg</span>&quot;, &quot;Background ratio&quot; and &quot;Ruland
    5160 width&quot; parameters to best agree with the -4*pi*r line that is plotted for
    5161 r &lt; <span class=SpellE>Rmin</span>. <span class=SpellE>Rmin</span> should be
    5162 set to a distance below the shortest expected interatomic distance for the
    5163 material. </p>
     5049Optimize PDF button can be used to refine the values of the &quot;Flat
     5050Bkg&quot;, &quot;Background ratio&quot; and &quot;Ruland width&quot; parameters
     5051to best agree with the -4*pi*r line that is plotted for r &lt; Rmin. Rmin
     5052should be set to a distance below the shortest expected interatomic distance
     5053for the material. </p>
    51645054
    51655055<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
    … …  
    51675057
    51685058<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
    5169 PDF parameters can be changed, triggering <span class=SpellE>recomputation</span>
    5170 of the <a href="#PDF_I_Q">I(Q)</a>, <a href="#PDF_S_Q">S(Q)</a>, <a
    5171 href="#PDF_F_Q">F(Q)</a> and <a href="#PDF_G_R">G(R) functions</a>. Available
    5172 menu commands are: </p>
     5059PDF parameters can be changed, triggering recomputation of the <a
     5060href="#PDF_I_Q">I(Q)</a>, <a href="#PDF_S_Q">S(Q)</a>, <a href="#PDF_F_Q">F(Q)</a>
     5061and <a href="#PDF_G_R">G(R) functions</a>. Available menu commands are: </p>
    51735062
    51745063<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
    … …  
    51765065
    51775066<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
    5178 style='mso-fareast-font-family:"Times New Roman"'>Adds a new element to the
    5179 chemical formula by clicking on a periodic table. Note that the number of atoms
    5180 of this type in the empirical formula must still be entered. <o:p></o:p></span></p>
     5067style='mso-fareast-font-family:"Times New Roman"'>Adds a new element to the chemical
     5068formula by clicking on a periodic table. Note that the number of atoms of this
     5069type in the empirical formula must still be entered. <o:p></o:p></span></p>
    51815070
    51825071<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
    … …  
    51845073
    51855074<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
    5186 style='mso-fareast-font-family:"Times New Roman"'>Removes a <span class=GramE>previously-entered</span>
     5075style='mso-fareast-font-family:"Times New Roman"'>Removes a previously-entered
    51875076element from the chemical formula. <o:p></o:p></span></p>
    51885077
    … …  
    51915080
    51925081<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
    5193 style='mso-fareast-font-family:"Times New Roman"'>Copies the current PDF control
    5194 values to other PDF data entries <o:p></o:p></span></p>
     5082style='mso-fareast-font-family:"Times New Roman"'>Copies the current PDF
     5083control values to other PDF data entries <o:p></o:p></span></p>
    51955084
    51965085<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
    … …  
    52145103style='mso-fareast-font-family:"Times New Roman"'>Recomputes the PDF for the
    52155104current entry. This is usually done automatically when values are changed, but
    5216 if <span class=GramE>not</span> this can be forced with this menu item. <o:p></o:p></span></p>
     5105if not this can be forced with this menu item. <o:p></o:p></span></p>
    52175106
    52185107<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
    … …  
    52215110<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
    52225111style='mso-fareast-font-family:"Times New Roman"'>Recomputes the PDFs for all
    5223 selected PDF entries. This is usually done after Copy Controls is used. By <span
    5224 class=GramE>default</span> PDFs are optimized to reduce the low G(r) region,
    5225 but this can be turned off. <o:p></o:p></span></p>
     5112selected PDF entries. This is usually done after Copy Controls is used. By
     5113default PDFs are optimized to reduce the low G(r) region, but this can be
     5114turned off. <o:p></o:p></span></p>
    52265115
    52275116<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
    … …  
    52765165
    52775166<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
    5278 style='mso-fareast-font-family:"Times New Roman"'>Allows only some PDFs to be plotted,
    5279 rather than all. <o:p></o:p></span></p>
     5167style='mso-fareast-font-family:"Times New Roman"'>Allows only some PDFs to be
     5168plotted, rather than all. <o:p></o:p></span></p>
    52805169
    52815170<p class=MsoNormal style='margin-left:.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><span
    … …  
    53455234
    53465235<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
    5347 shows the I(Q) function. See the <a href="#PDF_Controls">PDF Controls</a> for information
    5348 on menu commands and plot options, </p>
     5236shows the I(Q) function. See the <a href="#PDF_Controls">PDF Controls</a> for
     5237information on menu commands and plot options, </p>
    53495238
    53505239<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
    … …  
    53735262– type IMG </span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
    53745263
     5264<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     5265"Times New Roman"'>When a 2D diffraction image (prefix ‘IMG’) is selected from
     5266the data tree, the image is displayed as a color contoured picture. At a
     5267minimum, a small ‘X’ shows the currently defined location of the incident beam on
     5268the image plane (NB: it could off to one side or the other depending on
     5269detector location). Optionally, the integration limits are shown as an interior
     5270arc, an outer arc and green (beginning 2</span><span style='font-family:Symbol;
     5271mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:"Times New Roman";
     5272mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
     5273Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span><span
     5274style='mso-fareast-font-family:"Times New Roman"'> limit) and red (ending 2</span><span
     5275style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
     5276"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
     5277mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
     5278Symbol'>Q</span></span><span style='mso-fareast-font-family:"Times New Roman"'>
     5279limit) as well as “cake” section limits (dashed lines) connecting the two.
     5280These are set in <b>Image Controls</b>. There may be a frame mask (green) that encloses
     5281the area used for subsequent integration or other analysis. Red outlines and
     5282pixels indicated selected areas/pixels that are excluded (masked) from further
     5283use; the settings for these are found in <b>Masks</b>. The data window for IMG
     5284shows some controls, most of which are rarely modified (e.g., pixel dimensions)
     5285and are usually obtained via the image importer from either the image header or
     5286a metadata file associated with the image. It is the user’s/instrument
     5287scientist’s responsibility to ensure the accuracy of these values.<o:p></o:p></span></p>
     5288
     5289<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
     5290can I do here?<o:p></o:p></h5>
     5291
     5292<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     5293"Times New Roman"'>Apart from changing one of the listed values (caution: you
     5294do need to know what their true value is), you can determine the x-ray bean
     5295polarization and create a gain map for your detector. Both require this image
     5296to from a purely isotropic amorphous sample (a glass slide mounted
     5297perpendicular to the incident beam is recommended) with the detector close to
     5298the sample so that the scattering angle at the edge of the detector is at least
     529935° 2</span><span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
     5300mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
     5301mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
     5302symbol;mso-symbol-font-family:Symbol'>Q</span></span><span style='mso-fareast-font-family:
     5303"Times New Roman"'>; better is &gt; 40° 2</span><span style='font-family:Symbol;
     5304mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:"Times New Roman";
     5305mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
     5306Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span><span
     5307style='mso-fareast-font-family:"Times New Roman"'>. A frame mask is recommended
     5308to remove detector edge effects. The image should be as free as possible
     5309(except for beam stop) from shadows and obstructions and normal to the incident
     5310beam. The detector orientation should have been previously calibrated with a
     5311known reference material (e.g., LaB<sub>6</sub> or Si).<o:p></o:p></span></p>
     5312
     5313<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     5314"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
     5315
     5316<p class=MsoNormal style='margin-left:.25in'><b><span style='mso-fareast-font-family:
     5317"Times New Roman"'>Polarization</span></b><span style='mso-fareast-font-family:
     5318"Times New Roman"'> – <b>Calibrate</b>? <o:p></o:p></span></p>
     5319
     5320<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     5321"Times New Roman"'>This begins the calibration procedure (<a
     5322href="https://doi.org/10.1107/S1600576720014132">Von Dreele &amp; Xi, 2021</a>)
     5323for the x-ray beam polarization which integrates a 4° 2</span><span
     5324style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
     5325"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
     5326mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
     5327Symbol'>Q</span></span><span style='mso-fareast-font-family:"Times New Roman"'>
     5328wide ring sampling area with and without an arc mask positioned about 90°
     5329azimuth (top of image) with selected polarization values. The integrations
     5330match with the correct polarization. You will be asked for a 2</span><span
     5331style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
     5332"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
     5333mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
     5334Symbol'>Q</span></span><span style='mso-fareast-font-family:"Times New Roman"'>
     5335position for the sampling mask; choose a value at least 2° 2</span><span
     5336style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-fareast-font-family:
     5337"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
     5338mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
     5339Symbol'>Q</span></span><span style='mso-fareast-font-family:"Times New Roman"'>
     5340less than the maximum 2</span><span style='font-family:Symbol;mso-ascii-font-family:
     5341"Times New Roman";mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:
     5342"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
     5343style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span><span
     5344style='mso-fareast-font-family:"Times New Roman"'> seen for all edges inside
     5345the frame mask. The process takes about 5min, so be patient.<o:p></o:p></span></p>
     5346
     5347<p class=MsoNormal style='margin-left:.25in'><b><span style='mso-fareast-font-family:
     5348"Times New Roman"'>Make gain map …<o:p></o:p></span></b></p>
     5349
     5350<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
     5351"Times New Roman"'>This uses the same image (from a glass slide) used for
     5352polarization analysis to determine a gain map for the detector. The process
     5353uses the result of an integration of the glass pattern to normalize the entire detector
     5354pixel array. The result (~1.0 for all pixels) is the scaled by 1000, converted
     5355to integers and stored as a GSAS-II image file (NB: this is a python pickle
     5356file and thus not usable by other programs) and entered in the GSAS-II data
     5357tree. You can view it to see what the map looks like (select its IMG entry). The
     5358gain map file can be imported into other projects using the same detector. If
     5359selected in Image Controls, the image is immediately corrected for the gain
     5360map.<o:p></o:p></span></p>
     5361
    53755362<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
    53765363name="IMG_Comments"><u>Comments</u></a></h4>
    … …  
    53795366window shows whatever comment lines found in a “metadata” file when the image
    53805367data file was read by GSAS-II. If you are lucky, there will be useful
    5381 information here (<span class=GramE>e.g.</span> sample name, date collected,
    5382 wavelength used, etc.). If not, this window will be blank. The text is
    5383 read-only.</p>
     5368information here (e.g., sample name, date collected, wavelength used, etc.). If
     5369not, this window will be blank. The text is read-only.</p>
    53845370
    53855371<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
    … …  
    53925378
    53935379<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
    5394 command for this window <span class=GramE>are</span> used to perform
    5395 calibration (fitting the calibration values from a diffraction pattern image
    5396 taken with a calibrant) and for integration. Other menu commands allow the
    5397 values on the window to be saved to a file, read from a <span class=GramE>file</span>
    5398 or copied to other images. The &quot;Xfer Angles&quot; menu command scales the
    5399 current integration range for other images located at different detector
    5400 distances. <span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    5401 none;text-underline:none'><o:p></o:p></span></span></p>
     5380commands for this window are used to perform calibration (fitting the
     5381calibration values from a diffraction pattern image taken with a calibrant) and
     5382for integration. Other menu commands allow the values on the window to be saved
     5383to a file, read from a file or copied to other images. The &quot;Xfer
     5384Angles&quot; menu command scales the current integration range for other images
     5385located at different detector distances. <span class=MsoHyperlink><span
     5386style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></p>
    54025387
    54035388<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
    … …  
    54065391<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
    54075392style='mso-fareast-font-family:"Times New Roman"'>Image masks are used
    5408 designate areas of an image that should not be included in the integration, typically
    5409 used due to detector irregularities, shadows of the <span class=SpellE>beamstop</span>,
     5393designate areas of an image that should not be included in the integration,
     5394typically used due to detector irregularities, shadows of the beam stop,
    54105395single-crystal peaks from a mounting, etc. Masks can be created with a menu
    54115396command or with keyboard/mouse shortcuts. There are five types of masks:<o:p></o:p></span></p>
    … …  
    54225407style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    54235408style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5424 style='mso-fareast-font-family:"Times New Roman"'>Ring masks: occludes a
    5425 specific Bragg reflection (a ring placed relative to the image center). The
    5426 location and thickness of the ring are specified in degrees 2-theta. <o:p></o:p></span></p>
     5409style='mso-fareast-font-family:"Times New Roman"'>Ring masks: occludes a specific
     5410Bragg reflection (a ring placed relative to the image center). The location and
     5411thickness of the ring are specified in degrees 2-theta. <o:p></o:p></span></p>
    54275412
    54285413<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    54315416style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    54325417style='mso-fareast-font-family:"Times New Roman"'>Arc masks: occlude a section
    5433 of a Bragg reflection, <span class=GramE>similar to</span> a ring mask, except
    5434 that in addition to the location and thickness of the ring, the mask has a
    5435 starting and ending azimuthal angle. <o:p></o:p></span></p>
     5418of a Bragg reflection, similar to a ring mask, except that in addition to the
     5419location and thickness of the ring, the mask has a starting and ending
     5420azimuthal angle. <o:p></o:p></span></p>
    54365421
    54375422<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    54395424style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    54405425style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5441 style='mso-fareast-font-family:"Times New Roman"'>Polygon masks: occlude an <span
    5442 class=SpellE>arbitary</span> region created by line segments joining a series
    5443 of points specified in image coordinates (mm). Pixels inside the polygon mask
    5444 are not used for integration. <o:p></o:p></span></p>
     5426style='mso-fareast-font-family:"Times New Roman"'>Polygon masks: occlude an arbitrary
     5427region created by line segments joining a series of points specified in image
     5428coordinates (mm). Pixels inside the polygon mask are not used for integration. <o:p></o:p></span></p>
    54455429
    54465430<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    54485432style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    54495433style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5450 style='mso-fareast-font-family:"Times New Roman"'>The Frame mask: occludes an <span
    5451 class=SpellE>arbitary</span> region created by line segments joining a series
    5452 of points specified in image coordinates (mm). <span class=GramE>Typically</span>
    5453 a point is placed near each corner of the image. Only pixels inside the frame
    5454 mask are used for integration. Only one frame mask can be defined. <o:p></o:p></span></p>
     5434style='mso-fareast-font-family:"Times New Roman"'>The Frame mask: occludes an arbitrary
     5435region created by line segments joining a series of points specified in image
     5436coordinates (mm). Typically, a point is placed near each corner of the image.
     5437Only pixels inside the frame mask are used for integration. Only one frame mask
     5438can be defined. <o:p></o:p></span></p>
    54555439
    54565440<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
    … …  
    54835467
    54845468<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
    5485 Spot masks</b> after a menu command by clicking on the location on the image that
    5486 should be masked. There are also two ways to create spot masks with the
     5469Spot masks</b> after a menu command by clicking on the location on the image
     5470that should be masked. There are also two ways to create spot masks with the
    54875471keyboard: </p>
    54885472
    … …  
    54925476mso-fareast-font-family:"Courier New"'><span style='mso-list:Ignore'>o<span
    54935477style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5494 style='mso-fareast-font-family:"Times New Roman"'>Press the 's' key and then <span
    5495 class=GramE>left-click</span> successively on multiple locations for spot
    5496 masks. Press the 's' key again or <a href="#Mac_rightclick">right-click*</a> to
    5497 stop adding spot masks. <o:p></o:p></span></p>
     5478style='mso-fareast-font-family:"Times New Roman"'>Press the 's' key and then
     5479left-click successively on multiple locations for spot masks. Press the 's' key
     5480again or <a href="#Mac_rightclick">right-click*</a> to stop adding spot masks. <o:p></o:p></span></p>
    54985481
    54995482<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    55075490
    55085491<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
    5509 default size for <span class=GramE>newly-created</span> spot masks is
    5510 determined by the <span class=SpellE><tt><span style='font-size:10.0pt'>Spot_mask_diameter</span></tt></span>
    5511 <a href="#Preferences">configuration variable</a> or 1.0 mm, if not specified. </p>
     5492default size for newly-created spot masks is determined by the <tt><span
     5493style='font-size:10.0pt'>Spot_mask_diameter</span></tt> <a href="#Preferences">configuration
     5494variable</a> or 1.0 mm, if not specified. </p>
    55125495
    55135496<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
    5514 Spot mask location</b> by <span class=GramE>left-clicking</span> inside or on
    5515 the edge the of the mask and then drag the spot mask to a new location. </p>
     5497Spot mask location</b> by left-clicking inside or on the edge the of the mask
     5498and then drag the spot mask to a new location. </p>
    55165499
    55175500<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
    … …  
    55265509
    55275510<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
    5528 Ring masks</b> with a menu command and then by left-clicking on the mask center;
    5529 Or, by pressing the 'r' key and then left-clicking. (<a href="#Mac_rightclick">Right-click*</a>
    5530 to cancel.) </p>
     5511Ring masks</b> with a menu command and then by left-clicking on the mask
     5512center; Or, by pressing the 'r' key and then left-clicking. (<a
     5513href="#Mac_rightclick">Right-click*</a> to cancel.) </p>
    55315514
    55325515<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
    5533 default thickness for <span class=GramE>newly-created</span> ring masks is
    5534 determined by the <span class=SpellE><tt><span style='font-size:10.0pt'>Ring_mask_thickness</span></tt></span>
    5535 <a href="#Preferences">configuration variable</a> or 0.1 degrees (2theta) if
    5536 not specified. </p>
     5516default thickness for newly-created ring masks is determined by the <tt><span
     5517style='font-size:10.0pt'>Ring_mask_thickness</span></tt> <a href="#Preferences">configuration
     5518variable</a> or 0.1 degrees (2theta) if not specified. </p>
    55375519
    55385520<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
    5539 Ring mask location</b> by <span class=GramE>left-clicking</span> on either the
    5540 inner or outer circle and drag the circle to the new radius. </p>
     5521Ring mask location</b> by left-clicking on either the inner or outer circle and
     5522drag the circle to the new radius. </p>
    55415523
    55425524<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
    55435525Ring mask thickness</b> by <a href="#Mac_rightclick">right-clicking*</a> either
    5544 on the inner or outer circle and drag the <span class=SpellE>the</span> circle
    5545 change spacing between the inner and outer circle. </p>
     5526on the inner or outer circle and drag the the circle change spacing between the
     5527inner and outer circle. </p>
    55465528
    55475529<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    55505532style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    55515533style='mso-fareast-font-family:"Times New Roman"'>Arc masks: occludes a section
    5552 of a Bragg reflection, <span class=GramE>similar to</span> a ring mask, except that
    5553 in addition to the location and thickness of the ring, the mask has a starting
    5554 and ending azimuthal angle. <o:p></o:p></span></p>
     5534of a Bragg reflection, similar to a ring mask, except that in addition to the
     5535location and thickness of the ring, the mask has a starting and ending
     5536azimuthal angle. <o:p></o:p></span></p>
    55555537
    55565538<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
    … …  
    55605542
    55615543<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
    5562 default size for <span class=GramE>newly-created</span> ring masks is
    5563 determined by <a href="#Preferences">configuration variables</a><br>
    5564 thickness: <span class=SpellE><tt><span style='font-size:10.0pt'>Ring_mask_thickness</span></tt></span>
     5544default size for newly-created ring masks is determined by <a
     5545href="#Preferences">configuration variables</a><br>
     5546thickness: <tt><span style='font-size:10.0pt'>Ring_mask_thickness</span></tt>
    55655547(0.1 degrees 2theta if not specified) and <br>
    5566 azimuthal range: <span class=SpellE><tt><span style='font-size:10.0pt'>Arc_mask_azimuth</span></tt></span>
     5548azimuthal range: <tt><span style='font-size:10.0pt'>Arc_mask_azimuth</span></tt>
    55675549(10.0 degrees if not specified.) </p>
    55685550
    55695551<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
    5570 Arc mask location</b> by <span class=GramE>left-clicking</span> on either the
    5571 inner or outer circle and drag the circle to the new radius. Alternately, <span
    5572 class=GramE>left-click</span> on the upper or lower arc limit (the straight
    5573 lines) and drag them to rotate the center of the arc azimuthal range to a new
    5574 position. </p>
     5552Arc mask location</b> by left-clicking on either the inner or outer circle and
     5553drag the circle to the new radius. Alternately, left-click on the upper or
     5554lower arc limit (the straight lines) and drag them to rotate the center of the
     5555arc azimuthal range to a new position. </p>
    55755556
    55765557<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
    55775558Arc mask thickness or range</b> by <a href="#Mac_rightclick">right-clicking*</a>
    5578 either on the inner or outer circle and drag the <span class=SpellE>the</span>
    5579 circle change spacing between the inner and outer circle. Alternately, <a
    5580 href="#Mac_rightclick">right-click*</a> on the upper or lower arc limit (the
    5581 straight lines) and drag them to change the arc azimuthal range. </p>
     5559either on the inner or outer circle and drag the the circle change spacing
     5560between the inner and outer circle. Alternately, <a href="#Mac_rightclick">right-click*</a>
     5561on the upper or lower arc limit (the straight lines) and drag them to change
     5562the arc azimuthal range. </p>
    55825563
    55835564<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    … …  
    55855566style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    55865567style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    5587 style='mso-fareast-font-family:"Times New Roman"'>Polygon masks: occludes an <span
    5588 class=SpellE>arbitary</span> region created by line segments joining a series
    5589 of points specified in image coordinates (mm). Pixels inside the polygon mask
    5590 are not used for integration. <o:p></o:p></span></p>
     5568style='mso-fareast-font-family:"Times New Roman"'>Polygon masks: occludes an arbitrary
     5569region created by line segments joining a series of points specified in image
     5570coordinates (mm). Pixels inside the polygon mask are not used for integration. <o:p></o:p></span></p>
    55915571
    55925572<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
    5593 Polygon masks</b> with a menu command and then by <span class=GramE>left-clicking</span>
    5594 successively on the vertices of the polygon shape surrounding pixels to be
    5595 excluded. After the last point is defined, <a href="#Mac_rightclick">right-click*</a>
    5596 anywhere to close the mask. Alternately, press the 'p' key and then left-click,
    5597 as before, to define the mask and <a href="#Mac_rightclick">right-click*</a>
    5598 anywhere to close the mask. </p>
     5573Polygon masks</b> with a menu command and then by left-clicking successively on
     5574the vertices of the polygon shape surrounding pixels to be excluded. After the
     5575last point is defined, <a href="#Mac_rightclick">right-click*</a> anywhere to
     5576close the mask. Alternately, press the 'p' key and then left-click, as before,
     5577to define the mask and <a href="#Mac_rightclick">right-click*</a> anywhere to
     5578close the mask. </p>
    55995579
    56005580<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
    5601 Polygon mask</b> by <span class=GramE>left-clicking</span> on any point at a
    5602 vertex in the polygon mask and drag that point to a new position. If the vertex
    5603 is dragged to the same position as any other vertex in the mask the dragged
    5604 point is deleted. </p>
     5581Polygon mask</b> by left-clicking on any point at a vertex in the polygon mask
     5582and drag that point to a new position. If the vertex is dragged to the same
     5583position as any other vertex in the mask the dragged point is deleted. </p>
    56055584
    56065585<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
    … …  
    56155594style='mso-fareast-font-family:"Times New Roman"'>The Frame mask: occludes an
    56165595arbitrary region created by line segments joining a series of points specified
    5617 in image coordinates (mm). <span class=GramE>Typically</span> a point is placed
    5618 near each corner of the image. Only pixels inside the frame mask are used for
    5619 integration. Only one frame mask can be defined. <o:p></o:p></span></p>
     5596in image coordinates (mm). Typically a point is placed near each corner of the
     5597image. Only pixels inside the frame mask are used for integration. Only one
     5598frame mask can be defined. <o:p></o:p></span></p>
    56205599
    56215600<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
    5622 a Frame mask</b> with a menu command and then by <span class=GramE>left-clicking</span>
    5623 successively on the vertices of a polygon. After the last point is defined, <a
    5624 href="#Mac_rightclick">right-click*</a> anywhere to close the frame mask. Alternately,
    5625 press the 'f' key and then left-click, as before, to define the mask and <a
    5626 href="#Mac_rightclick">right-click*</a> anywhere to close the mask. Note that
    5627 if a Frame mask already exists, using the 'f' key or the &quot;Create
     5601a Frame mask</b> with a menu command and then by left-clicking successively on
     5602the vertices of a polygon. After the last point is defined, <a
     5603href="#Mac_rightclick">right-click*</a> anywhere to close the frame mask.
     5604Alternately, press the 'f' key and then left-click, as before, to define the
     5605mask and <a href="#Mac_rightclick">right-click*</a> anywhere to close the mask.
     5606Note that if a Frame mask already exists, using the 'f' key or the &quot;Create
    56285607Frame&quot; menu item causes the existing frame mask to be deleted. </p>
    56295608
    56305609<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
    5631 the Frame mask</b> by <span class=GramE>left-clicking</span> on any point at a
    5632 vertex in the frame mask and drag that point to a new position. If the vertex
    5633 is dragged to the same position as any other vertex in the mask the dragged
    5634 point is deleted. </p>
     5610the Frame mask</b> by left-clicking on any point at a vertex in the frame mask
     5611and drag that point to a new position. If the vertex is dragged to the same
     5612position as any other vertex in the mask the dragged point is deleted. </p>
    56355613
    56365614<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
    5637 a point to the Frame mask</b> by <a href="#Mac_rightclick">right-clicking*</a>
    5638 on any vertex and dragging. A new point is added to the mask immediately after
    5639 the selected point at the position where the mouse is released. </p>
     5615a point to the Frame mask</b> by <a href="#Mac_rightclick">right-clicking*</a> on
     5616any vertex and dragging. A new point is added to the mask immediately after the
     5617selected point at the position where the mouse is released. </p>
    56405618
    56415619<p style='margin-left:.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'><a
    … …  
    56775655<p class=MsoNormal style='margin-left:.25in'>This window shows whatever comment
    56785656lines (preceded by “#”) found when the peaks data file was read by GSAS-II. If
    5679 you are lucky, there will be useful information here (<span class=GramE>e.g.</span>
    5680 sample name, date collected, wavelength used, etc.). If not, this window will
    5681 be blank. The text is read-only.</p>
     5657you are lucky, there will be useful information here (e.g. sample name, date
     5658collected, wavelength used, etc.). If not, this window will be blank. The text
     5659is read-only.</p>
    56825660
    56835661<h4><a name="PKS_Limits">Limits</a></h4>
    … …  
    56945672can I do here?<o:p></o:p></span></h5>
    56955673