Changeset 872

Timestamp:

Mar 22, 2013 10:24:31 AM (10 years ago)

Author:

vondreele

Message:

cleanup tutorial

File:

• trunk/help/Charge Flipping - sucrose.htm (modified) (34 diffs)

trunk/help/Charge Flipping - sucrose.htm

@@ -24 +24 @@
   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>13</o:Revision>
-  <o:TotalTime>1342</o:TotalTime>
+  <o:Revision>14</o:Revision>
+  <o:TotalTime>1423</o:TotalTime>
   <o:Created>2013-03-15T18:32:00Z</o:Created>
-  <o:LastSaved>2013-03-21T16:12:00Z</o:LastSaved>
+  <o:LastSaved>2013-03-22T15:24:00Z</o:LastSaved>
   <o:Pages>17</o:Pages>
-  <o:Words>3395</o:Words>
-  <o:Characters>19358</o:Characters>
+  <o:Words>3367</o:Words>
+  <o:Characters>19197</o:Characters>
   <o:Company>Argonne National Laboratory</o:Company>
-  <o:Lines>161</o:Lines>
+  <o:Lines>159</o:Lines>
   <o:Paragraphs>45</o:Paragraphs>
-  <o:CharactersWithSpaces>22708</o:CharactersWithSpaces>
+  <o:CharactersWithSpaces>22519</o:CharactersWithSpaces>
   <o:Version>14.00</o:Version>
  </o:DocumentProperties>
@@ -953 +953 @@
 fitting-indexing exercise</a>. If you didn’t do that exercise, do it now.</p>
 
-<h2><span class=GramE>Step 1.</span> Setup for Pawley refinement</h2>
+<h2>Step 1: Setup for Pawley refinement</h2>
 
 <p class=MsoNormal>There are a number of steps that must be done in preparation
@@ -969 +969 @@
 Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
 mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
-symbol;mso-symbol-font-family:Symbol'>Q</span></span>. It is an area relatively
-clear of peaks and makes a good place to end the calculations with a reflection
-set of ~1Å resolution as needed for charge flipping. Enter <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'>23.55</span></b> for <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'>Tmax</span></b></span> as the upper limit and make a note of the
-exact d-spacing (1.0125Å) using the mouse cursor on the plot.</p>
+symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
+relatively clear of peaks that makes a good place to end the calculations with
+a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution needed
+for charge flipping. Enter <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'>23.55</span></b> for <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'>Tmax</span></b></span>
+as the upper limit and make a note of the exact d-spacing (1.0125Å) using the
+mouse cursor on the plot.</p>
 
 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
@@ -1021 +1022 @@
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
-box and enter the d-spacing (1.0125) 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 <span class=SpellE>dmin</span></span></b>
-box.</p>
+box and enter the d-spacing (<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'>1.0125</span></b>) 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 <span
+class=SpellE>dmin</span></span></b> box.</p>
 
 <p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
@@ -1093 +1096 @@
 surfaces</p>
 
-<p class=MsoNormal><span class=GramE>and</span> preferred orientation
+<p class=MsoNormal><span class=GramE>as</span> well as preferred orientation
 correction curves.</p>
 
@@ -1119 +1122 @@
 you didn’t skip a step as it might not work correctly if you did.</p>
 
-<h2>Step 2 Pawley refinement</h2>
+<h2>Step 2: Pawley refinement</h2>
 
 <p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
@@ -1197 +1200 @@
 
 <p class=MsoNormal>What you see is that the background has a substantial
-diffuse scattering feature at ~5deg as well as some peak shape issues (which
-may be a consequence of the poor background fit). Also notice the negative <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>
-value 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>; the problem is that the default <span class=SpellE>mustrain</span>
-value (1000.0) is much too high for this material and we’d like the fit to be
+diffuse scattering feature at ~5deg and there are some peak shape issues (which
+may be a consequence of the poor background fit). We’d like the fit to be
 better before trying charge flipping. First select <span class=GramE><b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
@@ -1263 +1260 @@
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until
-the refinement converges. After a set of refinement cycles go to the Pawley reflections
+the refinement converges. After a set of refinement cycles go 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'>Pawley reflections</span></b>
 tab and check the intensities. If there are many negatives amongst the highest
 angle reflections 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'>Pawley update</span></b>, this replaces all
-the values with those in the extracted from the profile and listed in the <b
+the values with those in the extracted from the profile as listed 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'>Reflection
-list</span></b> for the PWDR data set. Next 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> tab set the <b
+list</span></b> for the PWDR data set. This makes all the negative intensities
+positive. Next 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> tab 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'>Pawley neg.
@@ -1293 +1293 @@
 <p class=MsoNormal>Let’s see if this is good enough for charge flipping.</p>
 
-<h2>Step 3 Charge flipping</h2>
+<h2>Step 3: Charge flipping</h2>
 
 <p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
@@ -1317 +1317 @@
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
-data set; these should match the Pawley reflection set.</p>
+data set; these should match 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 reflection</span></b> set.</p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -1351 +1353 @@
 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
 minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
-ones. <span class=GramE>For sucrose, set this 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'>12.</span></b></span> When ready
-select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+ones. For sucrose set it 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'>12.</span></b> When ready 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'>Compute/Charge
 flipping</span></b>; a progress bar dialog will appear that tracks the residual
 found in each charge flipping cycle. It will quickly drop to some level
-(42-44%) and then perhaps drop again into the 20-25% range after a considerable
-length of time for a successful charge flipping run. You should save the
+(42-44%) and then for a successful charge flipping run perhaps drop again into
+the 20-25% range after a considerable length of time. You should save the
 project if you get an apparently good solution. Many times it will not drop
 below ~40%; just try <b style='mso-bidi-font-weight:normal'><span
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@@ -1500 +1502 @@
 <p class=MsoNormal>The result looks very promising! Charge flipping operates
 without regard to symmetry and GSAS-II attempts to locate the map with respect
-to the symmetry elements from the computed reflection phases. NB: charge
-flipping also will give a solution without regard to handedness. This solution
-may be either the correct one for sucrose or its reverse. Errors in these
+to the symmetry elements from the computed reflection phases. (NB: charge
+flipping also will give a solution without regard to handedness; this solution
+may be either the correct one for sucrose or its inverse.) Errors in these
 phases can disrupt this process so that the map and peak positions are offset
 from their true positions. To discover this and fix it, rotate the drawing
@@ -1538 +1540 @@
 src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
 
-<h2>Step 4 Obtain solution from charge flip result</h2>
+<h2>Step 4: Obtain solution from charge flip result</h2>
 
 <p class=MsoNormal>The next step is to extract the unique peak positions from
-the map and make atoms out of them. The map peak list is sorted with the
-highest peak first; you can change the sorting to be along any of the column
+the map and make atoms out of them. The map peak list is initially sorted by
+peak magnitude; you can change the sorting to be along any of the column
 headings in the table by a single click on the desired heading. The <span
 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
@@ -1652 +1654 @@
 src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
 
-<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out into
-two groups with a clear gap between M79 and M64. The higher ones are likely to
-be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of
-ambiguity in the middle, but just assign the top 11 as O and the rest as C and
-see what happens. You can do this by selecting a block of atoms, go to <b
+<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out
+into two groups with a clear gap between M79 and M64. The higher ones are
+likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit
+of ambiguity in the middle, but just assign the top 11 as O and the rest as C
+and see what happens. You can do this by selecting a block of atoms, go 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'>Edit/Modify
@@ -1678 +1680 @@
 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'>Draw atoms</span></b>
-tab. Pick the appropriate column and make the selection from the dialog
-box.<span style='mso-spacerun:yes'>  </span></p>
+tab. Double click the appropriate column heading and make the selection from
+the dialog box.<span style='mso-spacerun:yes'>  </span></p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1688 +1690 @@
 src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
 
-<p class=MsoNormal>Interestingly the atoms identified exactly matched with the
-magnitudes of the charge flip map peaks with O at the top and C at the bottom.</p>
-
 <p class=MsoNormal>Now one can safely remove the map peaks (do <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
@@ -1748 +1747 @@
 they will probably be outside the unit cell box. Do this on the drawing 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'>Shift</span></b>
-left &amp; right mouse buttons, they will show in green. </p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift left</span></b>
+for the first one &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'>Shift right</span></b> for <span
+class=SpellE>the</span> rest, they will show in green. </p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -1819 +1821 @@
 src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
 
-<p class=MsoNormal>Save the project file; the next step is to <span
-class=GramE>do<span style='mso-spacerun:yes'>  </span>the</span> Rietveld
-refinement on the completed structure.</p>
-
-<h2>Step 5 Complete the structure</h2>
+<p class=MsoNormal>Save the project file; the next step is to complete the
+structure by finding H-atoms and then do the final Rietveld refinements.</p>
+
+<h2>Step 5: Complete the structure</h2>
 
 <p class=MsoNormal>To complete the structure you will need to perform a
@@ -1873 +1874 @@
 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 menu; all that was refined is scale and background. I got <span
+GSAS-II data tree menu; only scale and background are refined. I got <span
 class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear
 intensity differences; the atom positions obviously need refinement.</p>
@@ -1892 +1893 @@
 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'>Atoms</span></b>
-tab. Note the warning at the bottom of the window; the origin in space group P
-2<sub>1</sub> has an arbitrary location along the y-axis. Then double click the
-<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub>
+has an arbitrary location along the y-axis. Then double click 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 heading, a dialog box will appear, select the <b style='mso-bidi-font-weight:
@@ -2004 +2005 @@
 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 from</span></b> item (the only choice). The Fourier calculation will use the
-structure factors shown in the <b style='mso-bidi-font-weight:normal'><span
+set from</span></b> item (the only choice). The Fourier calculation will use
+the structure factors 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'>Reflection list</span></b> item for this PWDR
@@ -2049 +2050 @@
 position. Recall that the refinement was just done without any H-atoms; it will
 make the best fit compensating for the missing H-atoms by displacing the C
-&amp;O atoms in the direction of the missing H-atoms. </p>
+&amp; O atoms in the direction of the missing H-atoms. </p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -2062 +2063 @@
 mso-list:l4 level1 lfo14'><![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 a C or O atoms with possible H-atom
+</span></span></span><![endif]>Select a C or O atom with possible H-atom
 density nearby. It will appear green. Do <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
@@ -2102 +2103 @@
 recognizable H-atom positions you can find; the goal is to find all 22 of them
 (you probably will find less than that, but you could guess many of the rest).
-I found all but 5 of them.</p>
+I easily found all but 5 of them.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2130 +2131 @@
 mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust 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'>Contour level</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'>Map radius</span></b>
-as desired. Look for the remaining H-atoms; you may have to guess positions for
-some of them using known stereochemistry rules. My model looked like</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
+level</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'>Map radius</span></b> as desired. Look for
+the remaining H-atoms; you may have to guess positions for some of them using
+known stereochemistry rules. My model looked like</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2203 +2205 @@
 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
 class=SpellE>Rwp</span> will start out high but should converge to where it was
-before this change. I got 8.08% and the Data tab looked like</p>
+before this change. I got 8.08% 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'>Data tab</span></b> looked like</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2212 +2216 @@
 src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
 
-<p class=MsoNormal>This no change in model yet but next 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'>Generalized</span></b>
-for 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'>Mustrain</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'> model</span></b>;
-this is the Stephens phenomenological model for <span class=SpellE>microstrain</span>
-which has 9 terms for monoclinic structures. Check all the boxes for it.</p>
+<p class=MsoNormal>Next 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'>Generalized</span></b> for 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'>Mustrain</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'> model</span></b>; this is the Stephens
+phenomenological model for <span class=SpellE>microstrain</span> which has 9
+terms for monoclinic structures. Check all the boxes for it.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2234 +2238 @@
 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
 class=SpellE>Rwp</span> will start out high but should converge lower than
-where it was before this change. I got 7.65% and the Data tab looked like. If
-you check the <span class=SpellE>Mustrain</span> button in the Select plot type
-box, you will see the interesting <span class=SpellE>mustrain</span> surface
-plot for ground sucrose.</p>
+where it was before this change. I got 7.65% 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'>Data tab</span></b> looked like.
+If you check 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'>Mustrain</span></b></span> button 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'>Select plot
+type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span>
+surface plot for ground sucrose.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2341 +2351 @@
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin'>109.54</span></b>. This is the
-tetrahedral angle so just press OK. 36 restraints will be listed; they are
-listed in order of the B atom. O-atoms should have one angle apiece; C-atoms
-will have more. </p>
+tetrahedral angle so just 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>. 36 restraints will be listed;
+they are listed in order of the B atom. O-atoms should have one angle apiece;
+C-atoms will have more. </p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2367 +2379 @@
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>X-coordinates</span></b>; this will set those
-for all H-atoms. Now do <span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span>,
-the console will list progress on the “Penalty function” (i.e. the restraints)
-and the <span class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase
-the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+for all H-atoms. Now 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>, the console will
+list progress on the “Penalty function” (i.e. the restraints) and the <span
+class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase 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'>Restraint
 weight factors</span></b> to tighten them up at some expense in <span