Changeset 1440 for trunk/help

Timestamp:

Jul 24, 2014 10:00:59 AM (11 years ago)

Author:

vondreele

Message:

missing stuff in Fit peaks tutorial & add comment about Show hkl positions.

Location:

trunk/help

Files:

• Fit Peaks.htm (modified) (44 diffs)
• Fit Peaks_files/filelist.xml (modified) (1 diff)
• Fit Peaks_files/image029.jpg (added)
• Fit Peaks_files/image030.jpg (added)
• Fit Peaks_files/image031.png (added)

trunk/help/Fit Peaks.htm ¶

@@ -23 +23 @@
   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>2</o:Revision>
-  <o:TotalTime>845</o:TotalTime>
+  <o:Revision>3</o:Revision>
+  <o:TotalTime>857</o:TotalTime>
   <o:Created>2014-07-21T14:48:00Z</o:Created>
-  <o:LastSaved>2014-07-21T14:48:00Z</o:LastSaved>
+  <o:LastSaved>2014-07-24T14:58:00Z</o:LastSaved>
   <o:Pages>12</o:Pages>
-  <o:Words>2763</o:Words>
-  <o:Characters>15750</o:Characters>
+  <o:Words>2797</o:Words>
+  <o:Characters>15949</o:Characters>
   <o:Company>Argonne National Laboratory</o:Company>
-  <o:Lines>131</o:Lines>
-  <o:Paragraphs>36</o:Paragraphs>
-  <o:CharactersWithSpaces>18477</o:CharactersWithSpaces>
+  <o:Lines>132</o:Lines>
+  <o:Paragraphs>37</o:Paragraphs>
+  <o:CharactersWithSpaces>18709</o:CharactersWithSpaces>
   <o:Version>14.00</o:Version>
  </o:DocumentProperties>
@@ -45 +45 @@
  <w:WordDocument>
   <w:Zoom>FullPage</w:Zoom>
+  <w:SpellingState>Clean</w:SpellingState>
+  <w:GrammarState>Clean</w:GrammarState>
   <w:TrackMoves>false</w:TrackMoves>
   <w:TrackFormatting/>
@@ -900 +902 @@
         mso-hansi-font-family:Tahoma;
         mso-bidi-font-family:Tahoma;}
+span.SpellE
+        {mso-style-name:"";
+        mso-spl-e:yes;}
+span.GramE
+        {mso-style-name:"";
+        mso-gram-e:yes;}
 .MsoChpDefault
         {mso-style-type:export-only;
@@ -1106 +1114 @@
 </style>
 <![endif]--><!--[if gte mso 9]><xml>
- <o:shapedefaults v:ext="edit" spidmax="1027"/>
+ <o:shapedefaults v:ext="edit" spidmax="1026"/>
 </xml><![endif]--><!--[if gte mso 9]><xml>
  <o:shapelayout v:ext="edit">
@@ -1117 +1125 @@
 <div class=WordSection1>
 
-<h1>Fit Peaks/Autoindexing in GSAS-II </h1>
+<h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
 
 <p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
@@ -1135 +1143 @@
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
 Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder
-data file</span></b> menu item to read the data file into the current GSAS-II
-project. This read option is set to read any of the powder data formats defined
-for GSAS (angles in centidegrees, TOF in µsec). Other submenu items will read
-the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>cif</span></b> format or the <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b> format (angles in
-degrees) used by Topas, etc.<span style='mso-spacerun:yes'>  </span>Change the
-file directory to <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>Exercises/LaB6</span></b><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'> to find the file; you may need to
-change the file type to <b style='mso-bidi-font-weight:normal'>All files (*.*)</b>
-to find the desired file.</span></p>
+data file</span></b> menu item to read the data file into the current GSAS-II project.
+This read option is set to read any of the powder data formats defined for GSAS
+(angles in <span class=SpellE>centidegrees</span>, TOF in µsec). Other submenu
+items will read the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>cif</span></b></span> format or the <span class=SpellE><b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span> format (angles
+in degrees) used by <span class=SpellE>Topas</span>, etc.<span
+style='mso-spacerun:yes'>  </span>Change the file directory to <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Exercises/LaB6</span></b><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'> to find the file; you may need to change the file type to <b
+style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
+file.</span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
@@ -1166 +1176 @@
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
 Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
-Dialog box asking <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p>
+Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
+proceed.</p>
 
 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
@@ -1181 +1195 @@
 Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.prm</span></b> instrument
 parameter file is automatically selected; it was produced by 11BM-B instrument
-processing software when the corresponding <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>fxye</span></b> file was created from the 12 detector raw data. If
-absent or the name doesn’t match the data file name, a file dialog will appear
-for you to select the correct instrument parameter file.</p>
+processing software when the corresponding <span class=SpellE><b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>fxye</span></b></span> file was
+created from the 12 detector raw data. If absent or the name doesn’t match the
+data file name, a file dialog will appear for you to select the correct
+instrument parameter file.</p>
 
 <p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
@@ -1219 +1234 @@
 src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
 
-<p class=MsoNormal>and the plot window will show the powder pattern</p>
+<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
+powder pattern</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1241 +1257 @@
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>changed</span></b> row of entry boxes to set <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>Tmin</span></b> and <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>Tmax</span></b> to <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:
+minor-latin'>changed</span></b> row of entry boxes to set <span class=SpellE><b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span> and <span
+class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
+to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
@@ -1261 +1277 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_29" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:226.5pt;
- height:123.75pt;visibility:visible;mso-wrap-style:square'>
+ id="_x0000_i1050" type="#_x0000_t75" style='width:226.5pt;height:123.75pt;
+ visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=302 height=165
-src="Fit%20Peaks_files/image003.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
+src="Fit%20Peaks_files/image003.png" v:shapes="_x0000_i1050"><![endif]></span></p>
 
 <h2>Step 3: Determine Peak Positions</h2>
@@ -1282 +1298 @@
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this
-point it is wise to zoom in on the data that will be used for indexing. </p>
+mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this point
+it is wise to zoom in on the data that will be used for indexing. </p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
@@ -1295 +1311 @@
   cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=29 height=25
-src="Fit%20Peaks_files/image005.jpg" v:shapes="Picture_x0020_4"><![endif]></span>,
+src="Fit%20Peaks_files/image029.jpg" v:shapes="Picture_x0020_4"><![endif]></span>,
 then press the left mouse in one corner of the region to be used; holding the
 mouse button down, drag over the region to the opposite corner; a box will be
@@ -1311 +1327 @@
   cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=31 height=27
-src="Fit%20Peaks_files/image006.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span
+src="Fit%20Peaks_files/image030.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span
 style='mso-spacerun:yes'> </span>button again to turn off the zoom mode. </p>
 
@@ -1336 +1352 @@
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
-auto'>and peaks are shown in the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>Peak List</span></b> window in order of increasing 2<span
-style='font-family:Symbol'>Q</span>.</p>
+auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Peak List</span></b> window in order of
+increasing 2<span style='font-family:Symbol'>Q</span>.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
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-</v:shape><span style='mso-element:field-end'></span><![endif]--></p>
+auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_29"
+ o:spid="_x0000_i1046" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
+ visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Fit%20Peaks_files/image031.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
+src="Fit%20Peaks_files/image031.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
 
 <p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
@@ -1420 +1392 @@
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ PeakFit </span></b>on the<b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'> Peak List </span></b>window. Do <b
-style='mso-bidi-font-weight:normal'>NOT</b> use the <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu item in the <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span>
+</span></b>on the<b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> Peak
+List </span></b>window. Do <b style='mso-bidi-font-weight:normal'>NOT</b> use
+the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu item
+in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
 Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window;
-that it to be used for Rietveld/Pawley refinements. You will be asked to save the
-current project before the fit will proceed; change directory if desired and
-provide a suitable name (we assume <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>LaB6</span></b>). A window will show the progress of the
-refinement and will close when the least-squares fit is complete (usually very
-fast). The plot is updated with the fit, the peak list window is updated with
-the new peak values and a summary of the refinement is shown on the console
-window as well.</p>
+that it to be used for <span class=SpellE>Rietveld</span>/Pawley refinements.
+You will be asked to save the current project before the fit will proceed;
+change directory if desired and provide a suitable name (we assume <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>LaB6</span></b>). A window will show
+the progress of the refinement and will close when the least-squares fit <span
+class=GramE>is</span> complete (usually very fast). The plot is updated with
+the fit, the peak list window is updated with the new peak values and a summary
+of the refinement is shown on the console window as well.</p>
 
 <p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1460 +1432 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
 add refinement of the peak positions. This can be done by clicking on all the
-refinement flags for the individual peaks or it is possible to set them all at the
-same time using this recipe: </p>
+refinement flags for the individual peaks or it is possible to set them all at
+the same time using this recipe: </p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
 auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
-on any value in the table to select it, for example the first peak position. A
-black box appears around the value. </p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE>single-click</span> on any value in the table to select it, for
+example the first peak position. A black box appears around the value. </p>
 
 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
 text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
-on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
-label above the peak position check-boxes. The entire column of checkboxes is
-highlighted in blue. Press the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>y</span></b> key to turn on all refinement flags (<b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>n</span></b> would turn them off).</p>
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
+class=GramE>single-click</span> on the <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>refine</span></b> label above the peak
+position check-boxes. The entire column of checkboxes is highlighted in blue.
+Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>y</span></b> key to turn on all
+refinement flags (<b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>n</span></b> would turn them off).</p>
 
 <p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ PeakFit</span></b>
+Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
 menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
@@ -1497 +1470 @@
 refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
 performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
-width) and/or gamma (Lorentzian width) for individual peaks. &nbsp;To do this,
-click the refinement flags for sigma and/or gamma in the Peak List window.
-&nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
-widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening
-equation as described below.&nbsp;Note - one cannot refine ALL peak widths
-using both individual&nbsp;sigma &amp; gamma&nbsp;values AND&nbsp;instrumental
-broadening terms at the same time.<b style='mso-bidi-font-weight:normal'>&nbsp;</b><o:p></o:p></span></p>
+width) and/or gamma (<span class=SpellE>Lorentzian</span> width) for individual
+peaks. &nbsp;To do this, click the refinement flags for sigma and/or gamma in
+the Peak List window. &nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the
+LS&nbsp;refinement of&nbsp;peak widths can be&nbsp;constrained to&nbsp;follow
+an instrumental broadening equation as described below.&nbsp;Note - one cannot
+refine ALL peak widths using both individual&nbsp;sigma &amp; gamma&nbsp;values
+AND&nbsp;instrumental broadening terms at the same time.<b style='mso-bidi-font-weight:
+normal'>&nbsp;</b><o:p></o:p></span></p>
 
 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
@@ -1523 +1497 @@
 
 <p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
-corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
-coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
-values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
+corresponding to the values of the Gaussian U, V, W, <span class=SpellE>Lorentzian</span>
+X &amp; Y coefficients; ‘+’ marks show the individual values based on the sig
+&amp; gam values for the peaks in Peak List. Select the refine flag checkbox
+for Gaussian <b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>,
 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>W</span></b>, and Lorentzian <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+Calibri;mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>W</span></b>, and <span class=SpellE>Lorentzian</span>
+<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
 Calibri;mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
@@ -1551 +1525 @@
 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ PeakFit</span></b>
+Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
 menu item. At this point a good fit should be seen by zooming in on individual
 peaks. For example see </p>
@@ -1562 +1536 @@
 src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
 
-<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to
-the right of the peak top. This is a consequence of the peak asymmetry arising
-from axial divergence in the diffractometer. The Rwp is ~6% as shown on the
-console window. Again the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>Peak List</span></b> entries are all updated with new values and
-those in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b> are
-also updated.</p>
-
-<h2>Step 5. Prepare Indexing Peak List</h2>
-
-<p class=MsoNormal>A separate list of peaks is kept for use in autoindexing. It
-is found in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
-"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Index
-Peak List</span></b> item in the data tree. In the initially empty window
-created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>Index Peaks Operations/Load/Reload</span></b> to copy the fitted
-peaks from the <b style='mso-bidi-font-weight:normal'><span style='font-family:
-"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Peak
-List</span></b>.</p>
+<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to the
+right of the peak top. This is a consequence of the peak asymmetry arising from
+axial divergence in the <span class=SpellE>diffractometer</span>. The <span
+class=SpellE>Rwp</span> is ~6% as shown on the console window. Again the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Peak List</span></b> entries are all
+updated with new values and those in <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Instrument Parameters</span></b> are also updated.</p>
+
+<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
+
+<p class=MsoNormal>A separate list of peaks is kept for use in <span
+class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> item in the data
+tree. In the initially empty window created by this action, use menu item <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Index Peaks Operations/Load/Reload</span></b>
+to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>Peak List</span></b>.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1601 +1575 @@
 contaminant).</p>
 
-<h2>Step 6. Run Autoindexing</h2>
+<h2><span class=GramE>Step 6.</span> Run <span class=SpellE>Autoindexing</span></h2>
 
 <p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
@@ -1637 +1611 @@
 src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
 
-<h2>Step 7. Review Cell Choices</h2>
+<h2><span class=GramE>Step 7.</span> Review Cell Choices</h2>
 
 <p class=MsoNormal>Review the list of cells associated with the <b
@@ -1645 +1619 @@
 Note that as one selects a unit cell, the generated reflections for that cell
 are shown in the plot with dashed red lines. Sliding the cursor over these
-lines shows a small popup window with the indexed hkl for them. Note how the
-first cell in the list (M20~2970) with a=5.87864 Å generates very many lines
-with no corresponding peaks (NB: this solution might not always show up!)</p>
+lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
+for them. Note how the first cell in the list (M20~2970) with a=5.87864 Å
+generates very many lines with no corresponding peaks (NB: this solution might
+not always show up!)</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1657 +1632 @@
 style='mso-spacerun:yes'> </span></p>
 
-<p class=MsoNormal>while the (M20~600) cell with a=2.93932 Å generates not
-enough lines to match all the peaks</p>
+<p class=MsoNormal><span class=GramE>while</span> the (M20~600) cell with
+a=2.93932 Å generates not enough lines to match all the peaks</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1667 +1642 @@
 src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_39"><![endif]></span></p>
 
-<h2>Step 8. Select/Refine Cell</h2>
+<h2><span class=GramE>Step 8.</span> Select/Refine Cell</h2>
 
 <p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
-indexes all peaks with almost a perfect fit to the peak positions (compare
-dashed red lines to solid blue ones). Import the cell information using the <b
+indexes all peaks with almost a perfect fit to the peak positions (compare dashed
+red lines to solid blue ones). Import the cell information using the <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
@@ -1683 +1658 @@
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
 Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Refine Cell</span></b>
-menu option. The M20 improves to ~3600 and the a cell parameter value shifts from
-4.15683 to 4.15691 when zero is refined. (NB: The certificate value for NIST
-SRM 660a is 4.15692 Å). Press the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>Show hkl positions </span></b>button to update the plot including
-the refined <b style='mso-bidi-font-weight:normal'><span style='font-family:
-"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Zero
-offset</span></b> (in this case hardly anything happens!) </p>
+menu option. The M20 improves to ~3600 and <span class=GramE>the a</span> cell
+parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The
+certificate value for NIST SRM 660a is 4.15692 Å). Press the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
+positions </span></b>button to update the plot including the refined <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> (in this case
+hardly anything happens!). <span style='mso-spacerun:yes'> </span></p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1711 +1687 @@
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>Zero offset</span></b> is shown.</p>
+mso-bidi-theme-font:minor-latin'>Zero offset</span></b> is shown. NB: the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show <span
+class=SpellE>hkl</span> positions</span></b> button has an additional use; you
+can enter the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>Bravais</span></b></span><b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'> lattice</span></b>, <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Space group</span></b>
+&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Unit cell</span></b>
+for any material. Then pressing <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
+will use that cell to index the lines in <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>Index Peak List</span></b>. This might be
+useful to identify e.g. a second phase in your pattern.</p>
 
 <p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
@@ -1726 +1721 @@
 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
 minor-latin'>Phases</span></b> (if it wasn’t already present). This new phase
-can be used in future analysis (e.g. Rietveld or Pawley refinement).</p>
+can be used in future analysis (e.g. <span class=SpellE>Rietveld</span> or
+Pawley refinement).</p>
 
 <p class=MsoNormal>To continue with the second part of this exercise, select
@@ -1736 +1732 @@
 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
 minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
-the current project saved; if <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>Yes</span></b> then all the peak fitting/indexing &amp; cell
-refinement results will be saved to the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>No</span></b> then the file will remain as it was when created at
-Step 4 above.</p>
-
-<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/Autoindexing in
-GSAS-II</a> </h1>
+the current project saved; if <span class=GramE><b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the peak
+fitting/indexing &amp; cell refinement results will be saved to the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>LaB6.gpx</span></b> file. If <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>No</span></b> then the file will
+remain as it was when created at Step 4 above.</p>
+
+<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
+class=SpellE><span style='mso-bookmark:kryptonite_peak_fit'>Autoindexing</span></span><span
+style='mso-bookmark:kryptonite_peak_fit'> in GSAS-II</span> </h1>
 
 <p class=MsoNormal>In this exercise we will fit peaks and index them for the
-new mineral <a href="http://en.wikipedia.org/wiki/Jadarite">jadarite</a> (aka “<a
-href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The data were
-also collected on 11BM-B at APS. The unit cell is monoclinic so it is a more
-substantial test of the indexing capability of GSAS-II.</p>
-
-<h2>Step 1. Read in the data. </h2>
+new mineral <a href="http://en.wikipedia.org/wiki/Jadarite"><span class=SpellE>jadarite</span></a>
+(aka “<a href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The
+data were also collected on 11BM-B at APS. The unit cell is monoclinic so it is
+a more substantial test of the indexing capability of GSAS-II.</p>
+
+<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
 
 <p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
@@ -1764 +1761 @@
 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
 minor-latin'>\Exercises\kryptonite\11bmb_6231.fxye</span></b>; it has a
-corresponding <b style='mso-bidi-font-weight:normal'><span style='font-family:
-"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>prm</span></b>
-file. Load them in &amp; the plot is</p>
+corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>prm</span></b></span> file. Load them in &amp; the plot is</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1811 +1808 @@
 </p>
 
-<h2>Step 4. Refine peaks</h2>
-
-<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example
-above, refine the peaks and the profile shape parameters in <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
-will be asked for a project file name at the first refinement (I used ‘<b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>jadarite’</span></b>). In the end my
-refinement converged at Rwp=11.41% and some peaks do show some discrepancy as
-the sample is more complex than the simple <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away during
-refinement (one weak one at ~6.67 is particularly troublesome). However, this
-is good enough to proceed.</p>
-
-<h2>Step 5. Prepare Indexing Peak List</h2>
+<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
+
+<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example above,
+refine the peaks and the profile shape parameters in <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You will be
+asked for a project file name at the first refinement (I used ‘<span
+class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>’</span></b>). In the end my
+refinement converged at <span class=SpellE>Rwp</span>=11.41% and some peaks do
+show some discrepancy as the sample is more complex than the simple <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
+no peaks drift away during refinement (one weak one at ~6.67 is particularly
+troublesome). However, this is good enough to proceed.</p>
+
+<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
 
 <p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
@@ -1852 +1852 @@
 mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
 
-<h2>Step 6. Index the cell</h2>
+<h2><span class=GramE>Step 6.</span> Index the cell</h2>
 
 <p class=MsoNormal>Let’s assume that we know the cell is primitive monoclinic.
-In a real world case we wouldn’t know this and we would have to try each
-Bravais lattice. These can be done as a group, but it takes time to go through
-all the bad cases.</p>
+In a real world case we wouldn’t know this and we would have to try each <span
+class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
+time to go through all the bad cases.</p>
 
 <p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
@@ -1912 +1912 @@
 space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>Show hkl positions</span></b> each time to
-see which lines vanish. By sliding the cursor over the index lines without any
-visible peak you can see that the missing ones are 010, 100, 001, 110, 030,
-111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are accidental but
-the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the space group P2<sub>1</sub>/n.
-Armed with this information you can <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>kryptonite’</span></b>) and select <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b>
-from the GSAS-II data tree.</p>
+mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
+each time to see which lines vanish. By sliding the cursor over the index lines
+without any visible peak you can see that the missing ones are 010, 100, 001,
+110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
+accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
+space group P2<sub>1</sub>/n. Armed with this information you can <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the
+indexed cell (I called it ‘<b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
+the GSAS-II data tree.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1946 +1947 @@
 src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
 
-<p class=MsoNormal>This concludes this exercise; <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>Save</span></b> the project file as it is
-needed for the <b style='mso-bidi-font-weight:normal'><span style='font-family:
-"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><a
-href="Charge%20Flipping%20in%20GSAS.htm">Charge Flipping</a></span></b>
+<p class=MsoNormal>This concludes this exercise; <span class=GramE><b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Save</span></b></span> the project file
+as it is needed for the <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'><a href="Charge%20Flipping%20in%20GSAS.htm">Charge Flipping</a></span></b>
 exercise. The features of the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
@@ -1959 +1960 @@
 minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
 
-<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/Autoindexing in
-GSAS-II </h1>
+<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span>
+in GSAS-II </h1>
 
 <p class=MsoNormal>In this exercise we will fit peaks and index them for
@@ -1971 +1972 @@
 is a more substantial test of the indexing capability of GSAS-II.</p>
 
-<h2>Step 1. Read in the data. </h2>
+<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
 
 <p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
@@ -1977 +1978 @@
 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
 minor-latin'>\Exercises\sucrose\11bmb_8716.fxye</span></b>; it has a
-corresponding <b style='mso-bidi-font-weight:normal'><span style='font-family:
+corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
+minor-latin'>prm</span></b></span> file and is for Domino® sugar ground under
+acetone. <span class=GramE>The other <span class=SpellE><b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b></span> file in
+this directory <b style='mso-bidi-font-weight:normal'><span style='font-family:
 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>prm</span></b>
-file and is for Domino® sugar ground under acetone. The other <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b>
-file in this directory <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X
-powdered sugar used “as is” out of the box. Load the <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the
-plot is</p>
+minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X powdered sugar used
+“as is” out of the box.</span> Load the <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the plot is</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1999 +2000 @@
 
 <p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
-lower part of the pattern; I’ve also chosen to plot the square root of the intensity
-(use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>S</span></b>’
-key) as this shows weak peaks better.</p>
+lower part of the pattern; I’ve also chosen to plot the square root of the
+intensity (use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin'>S</span></b>’ key) as this shows weak peaks better.</p>
 
 <h2>Step 2 Set limits</h2>
@@ -2023 +2024 @@
 can be moved by dragging the peak line and peaks can be deleted by
 right-clicking on them. This only works when the zoom and reposition modes
-(below) are not selected. Also note the shoulder at ~6.3 deg that should be
-added to the list. I skipped a couple of very weak peaks; the total list has
-&gt;28 peaks.</p>
+(below) are not selected. Also note the shoulder at ~6.3 <span class=SpellE>deg</span>
+that should be added to the list. I skipped a couple of very weak peaks; the total
+list has &gt;28 peaks.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2036 +2037 @@
 </p>
 
-<h2>Step 4. Refine peaks</h2>
+<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
 
 <p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
@@ -2047 +2048 @@
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
 Calibri;mso-bidi-theme-font:minor-latin'>sucrose’</span></b>). In the end my
-refinement converged at Rwp=7.15% and some peaks do show some discrepancy as
-the sample is more complex than the simple <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away
-during refinement. However, this is good enough to proceed.</p>
-
-<h2>Step 5. Prepare Indexing Peak List</h2>
+refinement converged at <span class=SpellE>Rwp</span>=7.15% and some peaks do
+show some discrepancy as the sample is more complex than the simple <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
+no peaks drift away during refinement. However, this is good enough to proceed.</p>
+
+<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
 
 <p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
@@ -2076 +2077 @@
 mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
 
-<h2>Step 6. Index the cell</h2>
+<h2><span class=GramE>Step 6.</span> Index the cell</h2>
 
 <p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
-In a real world case we wouldn’t know this and we would have to try each
-Bravais lattice. These can be done as a group, but it takes time to go through
-all the bad cases.</p>
+In a real world case we wouldn’t know this and we would have to try each <span
+class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
+time to go through all the bad cases.</p>
 
 <p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
@@ -2131 +2132 @@
 slightly different lattice parameters. Try different space groups, pressing the
 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show hkl
-positions</span></b> each time to see which lines vanish. The correct space
-group is P2<sub>1</sub>. Armed with this information you can <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show <span
+class=SpellE>hkl</span> positions</span></b> each time to see which lines
+vanish. The correct space group is P2<sub>1</sub>. Armed with this information
+you can <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
 Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the

trunk/help/Fit Peaks_files/filelist.xml ¶

@@ -7 +7 @@
  <o:File HRef="image003.png"/>
  <o:File HRef="image004.jpg"/>
- <o:File HRef="image005.jpg"/>
- <o:File HRef="image006.jpg"/>
+ <o:File HRef="image029.jpg"/>
+ <o:File HRef="image030.jpg"/>
  <o:File HRef="image007.png"/>
+ <o:File HRef="image031.png"/>
  <o:File HRef="image008.png"/>
  <o:File HRef="image009.png"/>