Changeset 1745 for Tutorials/MCsimanneal/MCSA in GSAS.htm

Timestamp:

Mar 20, 2015 8:49:59 AM (8 years ago)

Author:

vondreele

Message:

changes to various tutorials - mostly getting file references correct & removing hyperlinks

File:

• Tutorials/MCsimanneal/MCSA in GSAS.htm (modified) (37 diffs)

Tutorials/MCsimanneal/MCSA in GSAS.htm

@@ -23 +23 @@
   <o:Author>vondreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>2</o:Revision>
-  <o:TotalTime>581</o:TotalTime>
+  <o:Revision>3</o:Revision>
+  <o:TotalTime>767</o:TotalTime>
   <o:Created>2015-03-16T21:14:00Z</o:Created>
-  <o:LastSaved>2015-03-16T21:14:00Z</o:LastSaved>
+  <o:LastSaved>2015-03-19T20:13:00Z</o:LastSaved>
   <o:Pages>1</o:Pages>
-  <o:Words>2420</o:Words>
-  <o:Characters>13797</o:Characters>
+  <o:Words>2432</o:Words>
+  <o:Characters>13865</o:Characters>
   <o:Company>Argonne National Laboratory</o:Company>
-  <o:Lines>114</o:Lines>
+  <o:Lines>115</o:Lines>
   <o:Paragraphs>32</o:Paragraphs>
-  <o:CharactersWithSpaces>16185</o:CharactersWithSpaces>
+  <o:CharactersWithSpaces>16265</o:CharactersWithSpaces>
   <o:Version>15.00</o:Version>
  </o:DocumentProperties>
@@ -44 +44 @@
 <!--[if gte mso 9]><xml>
  <w:WordDocument>
+  <w:Zoom>116</w:Zoom>
+  <w:SpellingState>Clean</w:SpellingState>
+  <w:GrammarState>Clean</w:GrammarState>
   <w:TrackMoves>false</w:TrackMoves>
   <w:TrackFormatting/>
@@ -644 +647 @@
         {font-family:"Cambria Math";
         panose-1:2 4 5 3 5 4 6 3 2 4;
-        mso-font-charset:1;
+        mso-font-charset:0;
         mso-generic-font-family:roman;
-        mso-font-format:other;
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+        mso-font-signature:-536870145 1107305727 0 0 415 0;}
 @font-face
         {font-family:Calibri;
@@ -1098 +1100 @@
         mso-fareast-theme-font:minor-fareast;
         mso-bidi-font-family:Calibri;}
+span.SpellE
+        {mso-style-name:"";
+        mso-spl-e:yes;}
+span.GramE
+        {mso-style-name:"";
+        mso-gram-e:yes;}
 .MsoChpDefault
         {mso-style-type:export-only;
@@ -1104 +1112 @@
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         mso-bidi-font-size:10.0pt;
-        font-family:"Calibri",sans-serif;
         mso-ascii-font-family:Calibri;
         mso-hansi-font-family:Calibri;
@@ -1259 +1266 @@
 <p class=MsoNormal>In these exercises you will use GSAS-II to solve the
 structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
-diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets were
-kindly provided by Peter Stephens (SUNY StonyBrook) and were originally
-collected on NSLS beam line X3b1. The MC/SA technique is needed in these cases
-because as you will see the data does not extend very far in 2&#920; so one
-cannot use charge flipping to solve them. The steps for each begin with peak
-selection and fitting, then indexing to identify the lattice parameters. A
-Pawley refinement is used to obtain a set of structure factors needed for the
-MC/SA runs. We will use previously developed models for the two molecules; I
-used the freeware program Avogadro (<a href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
+diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
+were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
+and were originally collected on NSLS beam line X3b1. The MC/SA technique is
+needed in these cases because as you will see the data does not extend very far
+in 2&#920; so one cannot use charge flipping to solve them. The steps for each
+begin with peak selection and fitting, then indexing to identify the lattice
+parameters. A Pawley refinement is used to obtain a set of structure factors
+needed for the MC/SA runs. We will use previously developed models for the two
+molecules; I used the freeware program Avogadro (<a
+href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
 to create them.</p>
 
-<p class=MsoNormal>If you have not done so already, <a
-href="../../../GSASII/help/Starting%20GSAS.htm">start GSAS-II</a>.</p>
+<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
 
 <h2>Step 1. Import powder data for 3-aminoquinoline</h2>
@@ -1285 +1292 @@
 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/MCSA</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>
+minor-latin'>exercises/<span class=SpellE>MCsimanneal</span></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=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
-the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
+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'>Quinoli.gda</span></b></span><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'>Quinoli.gda</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'> data</span> file in the first dialog and press <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
+Calibri;mso-bidi-theme-font:minor-latin'> data</span> file in the first dialog
+and 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'>Open</span></b>. There will be a
-Dialog box asking <b style='mso-bidi-font-weight:normal'><span
+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 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>
+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=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
@@ -1316 +1328 @@
 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'>BNL-I.instprm</span></b> instrument
-parameter file in the second dialog and press <b style='mso-bidi-font-weight:
+Calibri;mso-bidi-theme-font:minor-latin'>BNL-<span class=SpellE>I.instprm</span></span></b>
+instrument parameter file in the second dialog and 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;
@@ -1323 +1335 @@
 file type 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'>*.instprm</span></b> (GSAS-II instrument parameter file). The
-powder pattern will immediately appear.</p>
+minor-latin'>*.<span class=SpellE>instprm</span></span></b> (GSAS-II instrument
+parameter file). The powder pattern will immediately appear.</p>
 
 <p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
@@ -1346 +1358 @@
  <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
  <o:lock v:ext="edit" aspectratio="t"/>
-</v:shapetype><v:shape id="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
- height:450pt;visibility:visible;mso-wrap-style:square'>
+</v:shapetype><v:shape id="Picture_x0020_28" o:spid="_x0000_i1051" type="#_x0000_t75"
+ style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image001.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="_x0000_i1051"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
 
 <p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
@@ -1375 +1387 @@
 picked 21 peaks, skipping a few very weak ones. Then 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'>Peak fitting/LSQ PeakFit </span></b>to
-fit them. You will need to vary at least <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'>X</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'>Y</span></b> in <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
+minor-latin;mso-hansi-theme-font:minor-latin'>Peak fitting/LSQ <span
+class=SpellE>PeakFit</span> </span></b>to fit them. You will need to vary at
+least <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'>X</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'>Y</span></b>
+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'>Instrument
-Parameters</span></b> along with <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'>pos</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'>int</span></b> 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'>Peak List</span></b>
-to get a reasonable fit suitable for indexing.</p>
+Parameters</span></b> along with <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'>pos</span></b></span> &amp; <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'>int</span></b></span> 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'>Peak List</span></b> to get a reasonable fit
+suitable for indexing.</p>
 
 <h2>Step 3. Indexing</h2>
@@ -1402 +1415 @@
 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin'>Unit Cells List</span></b> for
-indexing. The most likely Bravais lattice for these small organic molecules is
-either Orthorhombic-P or Monoclinic-P; you can try both and see what comes out
-(Hint: it’s <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'>Orthorhombic-P</span></b>). The correct unit cell should almost
-immediately appear with an M20 ~330 with a=7.748, b=7.651, c=12.736,
-Vol=755.01. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:
+indexing. The most likely <span class=SpellE>Bravais</span> lattice for these
+small organic molecules is either Orthorhombic-P or Monoclinic-P; you can try
+both and see what comes out (Hint: it’s <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'>Orthorhombic-P</span></b>). The correct unit
+cell should almost immediately appear with an M20 ~200 with a=7.748, b=7.651,
+c=12.736, Vol=755.01. NB: your solution may have <span class=GramE>a &amp;</span>
+b switched. Do <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'>Cell Index/Refine/Copy Cell</span></b>; you can then try various
@@ -1487 +1501 @@
 box and enter the d-spacing (1.8133) into 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'>Pawley dmin</span></b> box.</p>
+minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
+box.</p>
 
 <p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
@@ -1494 +1509 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_2" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:465.75pt;
- height:375pt;visibility:visible;mso-wrap-style:square'>
+ id="_x0000_i1050" type="#_x0000_t75" style='width:487.5pt;height:375pt;
+ visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/>
-</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=500
-src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
+</v:shape><![endif]--><![if !vml]><img border=0 width=650 height=500
+src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="_x0000_i1050"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1520 +1535 @@
 
 <p class=MsoNormal>Select either choice; the desired data set will be added to
-this phase for analysis. The data tab now shows the new data set; check 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></b>
-button to see the full information</p>
-
-<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_28" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:359.25pt;
+this phase for analysis. The data tab now shows the new data set.</p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_30" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:359.25pt;
  height:375pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500
-src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
 <p class=MsoNormal>This is the location for all the phase dependent parameters
-for this histogram. Notice that it includes phase fraction, size &amp; mustrain
-as well as preferred orientation, elastic strain and extinction corrections.
-The Babinet correction is intended for protein work where a significant region
-of the structure is disordered solvent. There are buttons for plotting size and
-mustrain surfaces and preferred orientation correction curves.</p>
+for this histogram. Notice that it includes phase fraction, size &amp; <span
+class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
+and extinction corrections. The <span class=SpellE>Babinet</span> correction is
+intended for protein work where a significant region of the structure is
+disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
+surfaces and preferred orientation correction curves.</p>
 
 <p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
@@ -1549 +1562 @@
 makes the reflection set over the range covered by setting <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'>Pawley dmin</span></b>. The table
-should list reflections 0-91. Select and check 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> column using
-the same technique you used for the peak list. </p>
+minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>.
+The table should list reflections 0-91. Select and check 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>
+column using the same technique you used for the peak list. </p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1577 +1590 @@
 mso-hansi-theme-font:minor-latin'>aminoquinoline.bck0.gpx</span></b>. It can be
 used to recover from a bad refinement. A progress dialog box will appear
-showing the residual as the refinement proceeds. My refinement completed with
-Rwp ~12.9%; a dialog box appears asking if you wish to load the result. 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'>OK</span></b>.
-To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
-the width and height).</p>
-
-<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_6" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
- height:450pt;visibility:visible;mso-wrap-style:square'>
+showing the residual as the refinement proceeds. My refinement completed with <span
+class=SpellE>Rwp</span> ~12.9%; a dialog box appears asking if you wish to load
+the result. 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'>OK</span></b>. To see the plot select the
+PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="_x0000_i1046" type="#_x0000_t75" style='width:525pt;height:450pt;
+ visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="_x0000_i1046"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1603 +1616 @@
 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'>1</span></b>,
-then change <b style='mso-bidi-font-weight:normal'><span style='font-family:
+then change <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'>pos</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'>19</span></b>, <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'>pos</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'>19</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'>int</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'>100000</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'>sig</span></b>
-to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
+minor-latin'>int</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'>100000</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'>sig</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'>100000</span></b>;
 for the peak only refine <b style='mso-bidi-font-weight:normal'><span
@@ -1620 +1634 @@
 mso-hansi-theme-font:minor-latin'>int</span></b>. I also 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'>No. coeff.</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'>No. <span
+class=SpellE>coeff</span>.</span></b> <span class=GramE>to</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'>5</span></b>;
 the window shows</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_7" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:402pt;
+ id="Picture_x0020_33" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:402pt;
  height:197.25pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
-src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1636 +1651 @@
 <p class=MsoNormal>Do a <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'>Calculate/Refine</span></b>; my Rwp fell to
-~8.5%. 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'>Background</span></b>
-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'>pos</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'>sig</span></b>
-for refinement and 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'>Instrument Parameters</span></b> 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'>X</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'>Y</span></b>
-for refinement; then do <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'>Calculate /Refine</span></b> again. I got
-Rwp~7.5% at convergence and the fit looked like</p>
+mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
+class=SpellE>Rwp</span> fell to ~8.5%. 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'>Background</span></b> select <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'>pos</span></b></span> &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'>sig</span></b> for refinement and 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'>Instrument
+Parameters</span></b> 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'>X</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'>Y</span></b> for refinement; then
+do <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'>Calculate</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'> /Refine</span></b>
+again. I got Rwp~7.5% at convergence and the fit looked like</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'>c<!--[if gte vml 1]><v:shape
- id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:525pt;
- height:450pt;visibility:visible;mso-wrap-style:square'>
+ id="_x0000_i1044" type="#_x0000_t75" style='width:525pt;height:450pt;
+ visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="_x0000_i1044"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1695 +1714 @@
 mso-hansi-theme-font:minor-latin'>Residue rigid bodies</span></b> and then do <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'>Edit/Import
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Body/Import
 XYZ</span></b>. Change the file type 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'>XYZ file (*.xyz)</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'>aminoquinoline.xyz</span></b>.
-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'>Rigid bodies</span></b>
+mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and select <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'>aminoquinoline.xyz</span></b></span>. 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'>Rigid <span class=GramE>bodies</span></span></b>
 window will show</p>
 
@@ -1716 +1736 @@
 <p class=MsoNormal>If you select 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'>Plot?</span></b> box a drawing will appear</p>
-
-<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_1" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:286.5pt;
- height:234pt;visibility:visible;mso-wrap-style:square'>
+mso-hansi-theme-font:minor-latin'>Plot?</span></b> <span class=GramE>box</span>
+a drawing will appear</p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="_x0000_i1041" type="#_x0000_t75" style='width:286.5pt;height:234pt;
+ visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image021.png" o:title="" croptop="13685f"
   cropbottom="15961f" cropleft="36898f" cropright="13504f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312
-src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="_x0000_i1041"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1788 +1809 @@
 <p class=MsoNormal>You see the four equivalent molecules for space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>
 whose centers fall within the unit cell; the reference one is that in the lower
-left corner with C1 at the origin. You can enter values 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'>x,y,z</span></b>
-boxes and see how the structure changes. Similarly, you can enter an angle 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'>Oa</span></b>
-or a vector 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'>Oi,Oj,Ok</span></b><span
+left corner with C1 at the origin. You can enter values in 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'>x<span class=GramE>,y,z</span></span></b></span> boxes and see how
+the structure changes. Similarly, you can enter an angle in <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'>Oa</span></b></span>
+or a vector in 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'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><span
 style='mso-spacerun:yes'>  </span>box to see the effects of rotating the
 molecule. Each of these parameters has a defined range for the MC/SA
@@ -1813 +1835 @@
 boxes 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'>AV</span></b> 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'>Oa</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'>Oi,Oj,Ok Vary?</span></b>
-pulldown. The MC/SA window should look like</p>
-
-<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_39" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:448.5pt;
- height:193.5pt;visibility:visible;mso-wrap-style:square'>
+minor-latin'>AV</span></b> from 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'>Oa</span></b></span>, <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'>Oi<span class=GramE>,Oj,Ok</span></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'> Vary?</span></b>
+<span class=GramE>pulldown</span>. The MC/SA window should look like</p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="_x0000_i1037" type="#_x0000_t75" style='width:448.5pt;height:193.5pt;
+ visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258
-src="MCSA%20in%20GSAS_files/image030.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
+src="MCSA%20in%20GSAS_files/image030.gif" v:shapes="_x0000_i1037"><![endif]></span><span
 style='mso-spacerun:yes'> </span></p>
 
@@ -1845 +1870 @@
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> then the
-structure factors will be Pawley model values, Fsq(hkl) in Pawley table, and
-the covariance matrix developed from the refinement will be used for peak
-overlap effects in the MC/SA calculations. Alternatively, if you choose <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'>PWDR
-Quinoli.gda Bank 1 </span></b>then the structure factors will be those, Fosq in
+structure factors will be Pawley model values, <span class=SpellE><span
+class=GramE>Fsq</span></span><span class=GramE>(</span><span class=SpellE>hkl</span>)
+in Pawley table, and the covariance matrix developed from the refinement will
+be used for peak overlap effects in the MC/SA calculations. Alternatively, if
+you choose <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'>PWDR <span class=SpellE>Quinoli.gda</span> Bank 1 </span></b>then
+the structure factors will be those, <span class=SpellE>Fosq</span> in
 Reflection table, extracted during the Pawley refinement and the peak FWHMs
 will be used for peak overlap effects in the MC/SA calculations. Notice that
-the Pawley Fsq(hkl) values are the same as the Fcsq Reflection List values.
-Here I chose <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'>Pawley reflections</span></b> for the <b style='mso-bidi-font-weight:
+the Pawley <span class=SpellE><span class=GramE>Fsq</span></span><span
+class=GramE>(</span><span class=SpellE>hkl</span>) values are the same as the <span
+class=SpellE>Fcsq</span> Reflection List values. Here I chose <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'>PWDR <span
+class=SpellE>Quinoli.gda</span> Bank 1 </span></b>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'>Reflection set</span></b> as it
@@ -1886 +1915 @@
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. trials</span></b>;
 this is the number of random tries at each “temperature” in the annealing
-schedule. When done 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'>General</span></b> window should look like</p>
-
-<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_16" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:7in;
+schedule. I also 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'>4 MC/SA runs</span></b> <span class=GramE>When</span>
+done 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'>General</span></b>
+window should look like</p>
+
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_38" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:7in;
  height:375pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image031.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500
-src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_38"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1913 +1945 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_19" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:560.25pt;
+ id="Picture_x0020_39" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:564pt;
  height:273.75pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image033.png" o:title=""/>
-</v:shape><![endif]--><![if !vml]><img border=0 width=747 height=365
-src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
+</v:shape><![endif]--><![if !vml]><img border=0 width=752 height=365
+src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1925 +1957 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_20" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:279.75pt;
- height:243.75pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title="" croptop="11773f"
-  cropbottom="16530f" cropleft="37715f" cropright="13079f"/>
-</v:shape><![endif]--><![if !vml]><img border=0 width=373 height=325
-src="MCSA%20in%20GSAS_files/image036.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
+ id="Picture_x0020_1" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:364.5pt;
+ height:298.5pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title="" croptop="8643f"
+  cropbottom="21002f" cropleft="39996f" cropright="10456f"/>
+</v:shape><![endif]--><![if !vml]><img border=0 width=486 height=398
+src="MCSA%20in%20GSAS_files/image036.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1936 +1968 @@
 <p class=MsoNormal>If you are lucky (like I was!) then the result is clearly a
 good solution with a very low Residual (~4.8%). This problem typically gives
-suitable solutions with Residuals of 4-5%. If no good solution appears (e.g.
-molecules clashing), then you should just rerun MC/SA perhaps using more runs
-or more trials. Be sure to set 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'>Keep</span></b> box for any solutions you
-want to retain; the others will be cleared before the next MC/SA run starts.
-When you think you have a good one, <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'>Select</span></b> it; the parameters will be
-copied to the appropriate boxes in the upper part of the MC/SA window and the
-structure is drawn again. Next we want to refine this solution so go back 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'>General</span></b>
-tab.</p>
+suitable solutions with Residuals of 4-5%. If your cell indexing resulted in <span
+class=GramE>a &amp;</span> b swapped, you should view the structure along b
+(green). If no good solution appears (e.g. molecules clashing), then you should
+just rerun MC/SA perhaps using more runs or more trials. Be sure to set 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'>Keep</span></b>
+box for any solutions you want to retain; the others will be cleared before the
+next MC/SA run starts. When you think you have a good one, <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'>Select</span></b></span>
+it; the parameters will be copied to the appropriate boxes in the upper part of
+the MC/SA window and the structure is drawn again. Next we want to refine this
+solution so go back 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'>General</span></b> tab.</p>
 
 <p class=MsoNormal>MC/SA refinement is achieved by narrowing the search ranges
@@ -1964 +1997 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_22" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:569.25pt;
- height:285pt;visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_40" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:448.5pt;
+ height:273.75pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image037.png" o:title=""/>
-</v:shape><![endif]--><![if !vml]><img border=0 width=759 height=380
-src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
+</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=365
+src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
-<p class=MsoNormal>This is clearly a good result (R ~ 0.4%!) and the structure</p>
+<p class=MsoNormal>This is clearly a good result (R ~ <span class=GramE>2.6%</span>!)
+and the structure</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1984 +2018 @@
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
-<p class=MsoNormal>is identical to the published one</p>
+<p class=MsoNormal><span class=GramE>is</span> identical to the published one</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1994 +2028 @@
 src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
 
-<p class=MsoNormal>as drawn by the Mercury program </p>
+<p class=MsoNormal><span class=GramE>as</span> drawn by the Mercury program </p>
 
 <p class=MsoNormal>(<a
@@ -2049 +2083 @@
 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
-the main GSAS-II data tree window; my R<sub>wp</sub> was ~9%. Next check 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 unit
-cell</span></b> 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'>General</span></b> window and 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'>Data</span></b>
-window, 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'>uniaxial</span></b> model for mustrain, check
-both <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'>Cryst. size</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'>mustrain</span></b>
+the main GSAS-II data tree window; my <span class=SpellE>R<sub>wp</sub></span>
+was ~9%. Next check 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 unit cell</span></b> 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'>General</span></b>
+window and 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'>Data</span></b> window, 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'>uniaxial</span></b>
+model for <span class=SpellE>mustrain</span>, check both <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'>Cryst</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'>. <span
+class=GramE>size</span></span></b> &amp; <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'>mustrain</span></b></span>
 boxes and do another <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'>Calculate/Refine</span></b>; I got an R<sub>wp</sub>
-~8.5% for this. We’ve not refined atom positions or thermal parameters; to do
-this we need to describe the structure as a rigid body.</p>
+mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I got an <span
+class=SpellE>R<sub>wp</sub></span> ~8.5% for this. We’ve not refined atom
+positions or thermal parameters; to do this we need to describe the structure
+as a rigid body.</p>
 
 <h2>Step 9. Rigid body model</h2>
@@ -2115 +2154 @@
 corresponding atoms in the structure (C(2), C(3) &amp; C(6)). Do these in
 order; the drawing will show the shift of molecular origin and then its
-reorientation as the three atoms are selected. 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'>Ready</span></b> when done; the
-structure will be drawn with yellow bonds indicating that it is now a rigid
-body and not independent atoms. 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'>RB Models</span></b> window shows the new
-rigid body</p>
+reorientation as the three atoms are selected. 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'>Ready</span></b></span>
+when done; the structure will be drawn with yellow bonds indicating that it is
+now a rigid body and not independent atoms. 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'>RB Models</span></b> window shows
+the new rigid body</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2134 +2173 @@
 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>
-box, select <b style='mso-bidi-font-weight:normal'><span style='font-family:
+<span class=GramE>box</span>, 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'>AV</span></b> from the pull down, choose <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'>AV</span></b> from the pull down, choose <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'>Uiso</span></b> from the thermal
-parameter model and check its <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> box. Then do <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'>Calculate/Refine</span></b>;
-after a couple of refinement runs I got an R<sub>wp</sub> ~7.9% and 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'>RBModels</span></b>
-window shows the new parameters</p>
+minor-latin'>Uiso</span></b></span> from the thermal parameter model and check
+its <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>
+<span class=GramE>box</span>. Then do <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'>Calculate/Refine</span></b>; after a couple
+of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span> ~7.9% and
+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'>RBModels</span></b></span> window shows the
+new parameters</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2156 +2197 @@
 src="MCSA%20in%20GSAS_files/image052.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
 
-<p class=MsoNormal>and the profile shows the fit</p>
+<p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2167 +2208 @@
 <p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.
 Next is a more complex case involving some internal degrees of freedom in the
-molecule of a-d-lactose.</p>
+molecule of a-d-<span class=GramE>lactose.</span></p>
 
 </div>