Changeset 1435 for trunk

Timestamp:

Jul 23, 2014 12:46:23 PM (11 years ago)

Author:

vondreele

Message:

modify comments about use of Alt key

Location:

trunk/help

Files:

• Charge Flipping - sucrose.htm (modified) (49 diffs)
• Charge Flipping - sucrose_files/filelist.xml (modified) (2 diffs)
• Charge Flipping in GSAS.htm (modified) (22 diffs)
• Charge Flipping in GSAS_files/props053.xml (modified) (1 diff)

trunk/help/Charge Flipping - sucrose.htm ¶

@@ -11 +11 @@
 <meta name=Originator content="Microsoft Word 14">
 <link rel=File-List href="Charge%20Flipping%20-%20sucrose_files/filelist.xml">
-<link rel=Edit-Time-Data href="Charge%20Flipping%20-%20sucrose_files/editdata.mso">
+<link rel=Edit-Time-Data
+href="Charge%20Flipping%20-%20sucrose_files/editdata.mso">
 <!--[if !mso]>
 <style>
@@ -23 +24 @@
   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>2</o:Revision>
+  <o:Revision>3</o:Revision>
   <o:TotalTime>1434</o:TotalTime>
   <o:Created>2014-07-21T14:45:00Z</o:Created>
-  <o:LastSaved>2014-07-21T14:45:00Z</o:LastSaved>
+  <o:LastSaved>2014-07-23T17:43:00Z</o:LastSaved>
   <o:Pages>17</o:Pages>
-  <o:Words>3453</o:Words>
-  <o:Characters>19684</o:Characters>
+  <o:Words>3469</o:Words>
+  <o:Characters>19775</o:Characters>
   <o:Company>Argonne National Laboratory</o:Company>
   <o:Lines>164</o:Lines>
   <o:Paragraphs>46</o:Paragraphs>
-  <o:CharactersWithSpaces>23091</o:CharactersWithSpaces>
+  <o:CharactersWithSpaces>23198</o:CharactersWithSpaces>
   <o:Version>14.00</o:Version>
  </o:DocumentProperties>
@@ -46 +47 @@
  <w:WordDocument>
   <w:Zoom>FullPage</w:Zoom>
+  <w:SpellingState>Clean</w:SpellingState>
+  <w:GrammarState>Clean</w:GrammarState>
   <w:TrackMoves>false</w:TrackMoves>
   <w:TrackFormatting/>
@@ -483 +486 @@
         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;
@@ -938 +947 @@
 <p class=MsoNormal>If you have not done so already, <a
 href="Starting%20GSAS.htm">start GSAS-II</a> and open the GSAS-II project file
-(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'>sucrose.gpx</span></b>) you saved from the third part of the <a
-href="Fit%20Peaks.htm#sucrose_peak_fit">peak fitting-indexing exercise</a>. If
-you didn’t do that exercise, do it now.</p>
+(I called it <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'>sucrose.gpx</span></b></span>) you saved from
+the third part of the <a href="Fit%20Peaks.htm#sucrose_peak_fit">peak
+fitting-indexing exercise</a>. If you didn’t do that exercise, do it now.</p>
 
 <h2>Step 1: Setup for Pawley refinement</h2>
@@ -962 +971 @@
 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 d<sub>min</sub> ~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 <b style='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>
+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>
@@ -1016 +1026 @@
 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 dmin</span></b>
-box.</p>
+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
@@ -1079 +1089 @@
 <p class=MsoNormal>I’ve stretched the window slightly to see the entire
 contents. 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</p>
-
-<p class=MsoNormal>as well as preferred orientation correction curves.</p>
+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</p>
+
+<p class=MsoNormal><span class=GramE>as</span> well as preferred orientation
+correction curves.</p>
 
 <p class=MsoNormal>Next find 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; it will be
-empty except for column headings. 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'>Operations/Pawley create</span></b>; this
-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 0-781. Select and check the refine column using the
-same technique you used for the peak list. </p>
+empty except for column headings. <span class=GramE>Do</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'>Operations/Pawley
+create</span></b>; this 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 <span
+class=SpellE>dmin</span></span></b>. The table should list reflections 0-781.
+Select and check the refine 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
@@ -1128 +1141 @@
 style='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>
-to make sure it has essentially minimized. My refinement completed with Rwp
-~26.3%; 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>
+to make sure it has essentially minimized. My refinement completed with <span
+class=SpellE>Rwp</span> ~26.3%; 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
@@ -1160 +1173 @@
 mso-ascii-theme-font:minor-latin;mso-hansi-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'> 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>.
-The 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'>Sample
-Parameters</span></b> and check <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>Sample X displ</span></b>.; make 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'>Goniometer
-radius</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'>1000</span></b> if you didn’t do this
-earlier. Repeat <b style='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>until converged; I obtained an
-improved residual of ~9.05% with a much better fit at the high angle part of
-the pattern but still not fit well for the lower part.</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
+class=GramE>X</span> </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>. The 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'>Sample Parameters</span></b> and
+check <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
+class=SpellE>displ</span></span></b>.; make 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'>Goniometer radius</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'>1000</span></b>
+if you didn’t do this earlier. Repeat <b style='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>until converged;
+I obtained an improved residual of ~9.05% with a much better fit at the high
+angle part of the pattern but still not fit well for the lower part.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1189 +1202 @@
 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 <b style='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>, set <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+better before trying charge flipping. First select <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'>Background</span></b>,</span>
+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'>Peaks in
 background: No. peaks</span></b> to <b style='mso-bidi-font-weight:normal'><span
@@ -1200 +1213 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_27" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:366pt;
+ id="Picture_x0020_27" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:366.75pt;
  height:197.25pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image007.png" o:title=""/>
-</v:shape><![endif]--><![if !vml]><img border=0 width=488 height=263
+</v:shape><![endif]--><![if !vml]><img border=0 width=489 height=263
 src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span><span
 style='mso-spacerun:yes'> </span></p>
@@ -1209 +1222 @@
 <p class=MsoNormal>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'>5.0</span></b> for <b style='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>, <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-hansi-theme-font:minor-latin'>5.0</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'>pos</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'>100000</span></b>
-for <b style='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>
-and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+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'>int</span></b></span> 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'>1000</span></b>
 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
@@ -1222 +1236 @@
 (as appropriate for broad diffuse peaks) and then check all three refine boxes.
 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>
-pulldown 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'>5</span></b> for the chebyschev part of the background. The window
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
+class=SpellE>coeff</span>.</span></b> <span class=SpellE><span class=GramE>pulldown</span></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'>5</span></b>
+for the <span class=SpellE>chebyschev</span> part of the background. The window
 should look like</p>
 
@@ -1264 +1279 @@
 new negatives that may appear. Then set all the Pawley refinement flags back on
 (excluding any that lead to a singular matrix) and repeat the refinement. After
-refinement, mine converged to ~5.7% with very few negatives and and the plot
-looked like</p>
+refinement, mine converged to ~5.7% with very few negatives and <span
+class=SpellE>and</span> the plot looked like</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1474 +1489 @@
 position:absolute;z-index:251662336;margin-left:315px;margin-top:308px;
 width:16px;height:35px'><img width=16 height=35
-src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
+src="Charge%20Flipping%20-%20sucrose_files/image052.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
 style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
  o:spid="_x0000_i1054" type="#_x0000_t75" style='width:502.5pt;height:431.25pt;
@@ -1481 +1496 @@
   croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=575
-src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
+src="Charge%20Flipping%20-%20sucrose_files/image053.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
 
 <p class=MsoNormal>The result looks very promising! Charge flipping operates
@@ -1521 +1536 @@
   croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=667 height=566
-src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
+src="Charge%20Flipping%20-%20sucrose_files/image054.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
 
 <h2>Step 4: Obtain solution from charge flip result</h2>
@@ -1528 +1543 @@
 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 <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b>
-column gives the distance of each peak from the origin. The menu items under
-Map peaks give you several tools to aid in the peak selection process; we will
-just use a couple in this example. I have chosen to proceed by sorting the
-atoms by <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>,
-selecting all and then finding the unique ones. </p>
+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:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin'>dzero</span></b></span> column gives the distance of each peak from
+the origin. The menu items under Map peaks give you several tools to aid in the
+peak selection process; we will just use a couple in this example. I have
+chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and then finding
+the unique ones. </p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -1579 +1595 @@
   croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=572
-src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
+src="Charge%20Flipping%20-%20sucrose_files/image055.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
 
 <p class=MsoNormal>Notice that in my case one atom is in a neighboring
@@ -1605 +1621 @@
   croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=578
-src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
+src="Charge%20Flipping%20-%20sucrose_files/image056.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1623 +1639 @@
 them by selecting a row with 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'>Alt</span></b> key down and then selecting a
-position in the table with 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'>Alt</span></b> key still down. After sorting
-by magnitude, my list is now </p>
+mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='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/Ctrl</span></b> keys) down
+and then selecting a position in the table with 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'>Alt</span></b> key still down. On
+Linux machines 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'>Alt</span></b> key may have been hijacked by
+the operating system; 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'>Shift/Ctrl</span></b> instead to move atoms. After
+sorting by magnitude, my list is now </p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1655 +1679 @@
   croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=541
-src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
+src="Charge%20Flipping%20-%20sucrose_files/image057.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
 
 <p class=MsoNormal>The original charge flipping solution is still visible and
@@ -1678 +1702 @@
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
-charge flip map (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'>Clear map</span></b> in the <b
+charge flip map (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'>Clear</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'> map</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>
@@ -1739 +1765 @@
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the
-selections and make note of 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'>Sym Op</span></b> for each one. In my case
-they were “<b style='mso-bidi-font-weight:normal'><span style='font-family:
+selections and make note of 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'>Sym</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'> Op</span></b>
+for each one. In my case they were “<b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>2+1<span class=GramE>,0,0</span></span></b>”
+for O(4) 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'>2+1,0,0</span></b>” for O(4) 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'>2+2,-1,1</span></b>” for O(3).
-The first number is the symmetry operator number and the 3 numbers after 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'>+</span></b>’
-are unit cell translations.</p>
+minor-latin'>2+2,-1,1</span></b>” for O(3). The first number is the symmetry
+operator number and the 3 numbers after 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'>+</span></b>’ are unit cell
+translations.</p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -1763 +1792 @@
 "Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span></span><![endif]>Select an atom in turn that needs to be moved,
-e.g. in my case O(3) or O(4). </p>
+e.g. in my case <span class=GramE>O(</span>3) or O(4). </p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -1770 +1799 @@
 </span></span></span><![endif]>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/Transform atoms</span></b>, select the
-operator and unit cell translations, then press <b style='mso-bidi-font-weight:
+mso-hansi-theme-font:minor-latin'>Edit/Transform <span class=GramE>atoms<span
+style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
+select the operator and unit cell translations, then 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>. The atom
@@ -1783 +1813 @@
 
 <p class=MsoNormal style='margin-left:.5in'>This will complete the molecule
-with the extra atoms. 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/Reload draw atoms</span></b> to see the
-completed molecule. I’ve made it a balls &amp; sticks with names as labels.</p>
+with the extra atoms. <span class=GramE>Do</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'>Edit/Reload draw atoms</span></b>
+to see the completed molecule. I’ve made it a balls &amp; sticks with names as
+labels.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1794 +1825 @@
   cropbottom="28348f" cropleft="41090f" cropright="9483f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=576
-src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
+src="Charge%20Flipping%20-%20sucrose_files/image058.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
 
 <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>
+structure by finding H-atoms and then do the final <span class=SpellE>Rietveld</span>
+refinements.</p>
 
 <h2>Step 5: Complete the structure</h2>
 
 <p class=MsoNormal>To complete the structure you will need to perform a
-preliminary Rietveld refinement. This will make the atom positions more
-accurate and prepare a set of calculated structure factors needed to generate a
-difference Fourier map good enough to maybe reveal the H atoms. There are a
-number of steps needed to set all the controls from the previous Pawley
-refinement to get a successful start for the Rietveld refinement.</p>
+preliminary <span class=SpellE>Rietveld</span> refinement. This will make the
+atom positions more accurate and prepare a set of calculated structure factors
+needed to generate a difference Fourier map good enough to maybe reveal the H
+atoms. There are a number of steps needed to set all the controls from the
+previous Pawley refinement to get a successful start for the <span
+class=SpellE>Rietveld</span> refinement.</p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -1829 +1862 @@
 scale factor</span></b> box. This is the scale factor for the data set. Uncheck
 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'>Sample X
-displ</span></b>.</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
+class=SpellE>displ</span></span></b>.</p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -1849 +1882 @@
 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; only scale and background are refined. I got a Rwp
-~20%. The plot shows clear intensity differences; the atom positions obviously
-need refinement.</p>
+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>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1903 +1936 @@
 mso-hansi-theme-font:minor-latin'>Edit/Add hold</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'>0::dAy:0 for
-O(1)</span></b>’ from the dialog box. This will fix the shift along y for the
-O(1) atom.</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
+class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will
+fix the shift along y for the <span class=GramE>O(</span>1) atom.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1928 +1961 @@
 <p class=MsoNormal>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; my Rwp is
-now ~10.3%. You can now safely refine lattice parameters (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 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
+class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice
+parameters (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 for <b
+style='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/sucrose</span></b>),
 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
@@ -1948 +1982 @@
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
 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'>Sample X
-displ</span></b>. You can also include refinement of atom thermal motion (U<sub>iso</sub>)
-parameters. My refinement improved slightly to Rwp~10.0%. Let’s see if a
-difference Fourier map will show anything.<br>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
+class=SpellE>displ</span></span></b>. You can also include refinement of atom
+thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
+refinement improved slightly to Rwp~10.0%. Let’s see if a difference Fourier
+map will show anything.<br>
 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'>Phases/sucrose
@@ -1962 +1997 @@
 mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]>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'>delt-F</span></b> for the <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+</span></span></span><![endif]>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'>delt</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'>-F</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'>Map type</span></b>.</p>
 
@@ -2014 +2051 @@
   croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=581
-src="Charge%20Flipping%20-%20sucrose_files/image034.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
-
-<p class=MsoNormal>What is drawn here are green dots whose size are
-proportional to the electron density. There are peaks that might be H-atom
-positions as well as features that suggest C &amp; O-atoms out of 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>
+src="Charge%20Flipping%20-%20sucrose_files/image059.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
+
+<p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots
+whose size are proportional to the electron density. There are peaks that might
+be H-atom positions as well as features that suggest C &amp; O-atoms out of
+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>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -2028 +2065 @@
 </span></span></span><![endif]>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'>Phases/sucrose<span
-style='mso-spacerun:yes'>  </span>Draw Atoms</span></b> tab.</p>
+mso-hansi-theme-font:minor-latin'>Phases/<span class=GramE>sucrose<span
+style='mso-spacerun:yes'>  </span>Draw</span> Atoms</span></b> tab.</p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -2060 +2097 @@
   croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=581
-src="Charge%20Flipping%20-%20sucrose_files/image036.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
+src="Charge%20Flipping%20-%20sucrose_files/image060.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -2082 +2119 @@
   croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=570
-src="Charge%20Flipping%20-%20sucrose_files/image038.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
+src="Charge%20Flipping%20-%20sucrose_files/image061.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -2095 +2132 @@
 style='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>;
-there should be a drop in Rwp. Then repeat 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'>Compute/Fourier map</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>
-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
+there should be a drop in <span class=SpellE>Rwp</span>. Then repeat 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'>Compute/Fourier
+map</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> 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
@@ -2114 +2152 @@
   croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=562
-src="Charge%20Flipping%20-%20sucrose_files/image040.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
+src="Charge%20Flipping%20-%20sucrose_files/image062.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
 
 <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> to finish this
-stage in the structure analysis. My Rwp was ~8.02% with all the H-atoms
-included (but not refined). The fit looks pretty good</p>
+stage in the structure analysis. My <span class=SpellE>Rwp</span> was ~8.02%
+with all the H-atoms included (but not refined). The fit looks pretty good</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2133 +2171 @@
 <p class=MsoNormal>Looking at the fit, there may be room for improvement and
 we’d like to refine the H-atom positions. First we need to change the profile
-model to include crystallite size and mustrain broadening. 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'>Instrument
-Parameters</span></b>, 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'>X</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'>Y</span></b> to <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+model to include crystallite size and <span class=SpellE>mustrain</span>
+broadening. 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'>Instrument Parameters</span></b>, 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'>X</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'>Y</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'>zero</span></b>
 and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
@@ -2155 +2193 @@
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the
-boxes for 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> 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'>microstrain</span></b>.</p>
+boxes for 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>
+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'>microstrain</span></b></span>.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2170 +2211 @@
 <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>; the Rwp will
-start out high but should converge to where it was 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>
+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 <b style='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
@@ -2185 +2226 @@
 <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 <b
-style='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
-model</span></b>; this is the Stephens phenomenological model for microstrain
-which has 9 terms for monoclinic structures. Check all the boxes for it.</p>
+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
@@ -2200 +2244 @@
 <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>; the Rwp will
-start out high but should converge lower than 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 <b style='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>
-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
-mustrain surface plot for ground sucrose.</p>
+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 <b style='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
@@ -2235 +2280 @@
 no bond restraints for sucrose. 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/Add restraints</span></b>, a dialog box
-will appear asking for the origin atom for the bond. </p>
+mso-hansi-theme-font:minor-latin'>Edit/Add <span class=GramE>restraints<span
+style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
+a dialog box will appear asking for the origin atom for the bond. </p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -2344 +2390 @@
 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 Rwp 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 Rwp. In the end I chose <b style='mso-bidi-font-weight:
+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
+class=SpellE>Rwp</span>. In the end 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'>2.0</span></b> for both <b
@@ -2355 +2402 @@
 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'>Angle</span></b>
-restraints to give a final Rwp ~7.1%. NB: the H-atom positions may not be
-correct even though the refinement apparently succeeded. You should check that
-the OH ones all give reasonable H-bonds to neighboring O-atoms. As this is
-powder data such changes will hardly affect the fit but will be more
-satisfying. At present such checking is outside the scope of GSAS-II.</p>
+restraints to give a final <span class=SpellE>Rwp</span> ~7.1%. NB: the H-atom
+positions may not be correct even though the refinement apparently succeeded.
+You should check that the OH ones all give reasonable H-bonds to neighboring
+O-atoms. As this is powder data such changes will hardly affect the fit but
+will be more satisfying. At present such checking is outside the scope of
+GSAS-II.</p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>

trunk/help/Charge Flipping - sucrose_files/filelist.xml ¶

@@ -13 +13 @@
  <o:File HRef="image009.png"/>
  <o:File HRef="image010.png"/>
- <o:File HRef="image011.png"/>
+ <o:File HRef="image052.png"/>
  <o:File HRef="image012.png"/>
- <o:File HRef="image013.jpg"/>
+ <o:File HRef="image053.jpg"/>
  <o:File HRef="image014.png"/>
- <o:File HRef="image015.jpg"/>
+ <o:File HRef="image054.jpg"/>
  <o:File HRef="image016.png"/>
  <o:File HRef="image017.png"/>
- <o:File HRef="image018.jpg"/>
+ <o:File HRef="image055.jpg"/>
  <o:File HRef="image019.png"/>
- <o:File HRef="image020.jpg"/>
+ <o:File HRef="image056.jpg"/>
  <o:File HRef="image021.png"/>
  <o:File HRef="image022.png"/>
  <o:File HRef="image023.png"/>
- <o:File HRef="image024.jpg"/>
+ <o:File HRef="image057.jpg"/>
  <o:File HRef="image025.png"/>
  <o:File HRef="image026.png"/>
- <o:File HRef="image027.jpg"/>
+ <o:File HRef="image058.jpg"/>
  <o:File HRef="image028.png"/>
  <o:File HRef="image029.png"/>
@@ -36 +36 @@
  <o:File HRef="image032.png"/>
  <o:File HRef="image033.png"/>
- <o:File HRef="image034.jpg"/>
+ <o:File HRef="image059.jpg"/>
  <o:File HRef="image035.png"/>
- <o:File HRef="image036.jpg"/>
+ <o:File HRef="image060.jpg"/>
  <o:File HRef="image037.png"/>
- <o:File HRef="image038.jpg"/>
+ <o:File HRef="image061.jpg"/>
  <o:File HRef="image039.png"/>
- <o:File HRef="image040.jpg"/>
+ <o:File HRef="image062.jpg"/>
  <o:File HRef="image041.png"/>
  <o:File HRef="image042.png"/>

trunk/help/Charge Flipping in GSAS.htm ¶

@@ -23 +23 @@
   <o:Author>vondreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>2</o:Revision>
-  <o:TotalTime>1</o:TotalTime>
+  <o:Revision>4</o:Revision>
+  <o:TotalTime>14</o:TotalTime>
   <o:Created>2014-07-21T14:56:00Z</o:Created>
-  <o:LastSaved>2014-07-21T14:56:00Z</o:LastSaved>
+  <o:LastSaved>2014-07-23T17:41:00Z</o:LastSaved>
   <o:Pages>10</o:Pages>
-  <o:Words>2223</o:Words>
-  <o:Characters>12672</o:Characters>
+  <o:Words>2239</o:Words>
+  <o:Characters>12763</o:Characters>
   <o:Company>Argonne National Laboratory</o:Company>
-  <o:Lines>105</o:Lines>
+  <o:Lines>106</o:Lines>
   <o:Paragraphs>29</o:Paragraphs>
-  <o:CharactersWithSpaces>14866</o:CharactersWithSpaces>
+  <o:CharactersWithSpaces>14973</o:CharactersWithSpaces>
   <o:Version>14.00</o:Version>
  </o:DocumentProperties>
@@ -45 +45 @@
  <w:WordDocument>
   <w:Zoom>156</w:Zoom>
+  <w:SpellingState>Clean</w:SpellingState>
+  <w:GrammarState>Clean</w:GrammarState>
   <w:TrackMoves>false</w:TrackMoves>
   <w:TrackFormatting/>
@@ -786 +788 @@
         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;
@@ -1226 +1234 @@
 
 <h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in
-GSAS-II - jadarite<o:p></o:p></span></h1>
+GSAS-II - <span class=SpellE>jadarite</span><o:p></o:p></span></h1>
 
 <h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1>
 
 <p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
-of jadarite (aka “kryptonite”) from powder diffraction data via charge flipping.
-This structure was originally solved by Pam Whitfield from laboratory powder
-data in the space group P2<sub>1</sub>/c. </p>
+of <span class=SpellE>jadarite</span> (aka “kryptonite”) from powder
+diffraction data via charge flipping. This structure was originally solved by
+Pam Whitfield from laboratory powder data in the space group P2<sub>1</sub>/c. </p>
 
 <p class=MsoNormal>If you have not done so already, <a
 href="Starting%20GSAS.htm">start GSAS-II</a> and open the GSAS-II project file
-(I called it jadarite.gpx) you saved from the second part of the <a
-href="Fit%20Peaks.htm#kryptonite_peak_fit">peak fitting-indexing exercise</a>.
-If you didn’t do that exercise, do it now.</p>
-
-<h2>Step 1. Setup for Pawley refinement</h2>
+(I called it <span class=SpellE>jadarite.gpx</span>) you saved from the second
+part of the <a href="Fit%20Peaks.htm#kryptonite_peak_fit">peak 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>
 
 <p class=MsoNormal>There are a number of steps that must be done in preparation
@@ -1261 +1269 @@
 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'>24</span></b> for <b
-style='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>
-as the upper limit and make a note of the exact d-spacing (0.9945Å) using the
-mouse cursor on the plot.</p>
+minor-latin;mso-hansi-theme-font:minor-latin'>24</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 (0.9945Å) using the mouse cursor on the plot.</p>
 
 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
@@ -1289 +1297 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>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'>Sample Parameters</span></b>
-and uncheck refinement of <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
+Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
 
 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
@@ -1306 +1314 @@
 box and enter the d-spacing (0.9945) 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
@@ -1368 +1377 @@
 <p class=MsoNormal>I’ve stretched the window slightly to see the entire
 contents. 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</p>
-
-<p class=MsoNormal>and preferred orientation correction curves.</p>
+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</p>
+
+<p class=MsoNormal><span class=GramE>and</span> preferred orientation
+correction curves.</p>
 
 <p class=MsoNormal>Next find 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; it will be
-empty except for column headings. 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'>Operations/Pawley create</span></b>; this
-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 0-629. 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>
+empty except for column headings. <span class=GramE>Do</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'>Operations/Pawley
+create</span></b>; this 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 <span
+class=SpellE>dmin</span></span></b>. The table should list reflections 0-629.
+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
@@ -1408 +1420 @@
 file is made; the name will be jadarite.bck0.gpx. 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 ~15.5%; 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>
+as the refinement proceeds. My refinement completed with <span class=SpellE>Rwp</span>
+~15.5%; 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_7" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
- height:450pt;visibility:visible;mso-wrap-style:square'>
+ id="_x0000_i1043" type="#_x0000_t75" style='width:525pt;height:450pt;
+ visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image009.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Charge%20Flipping%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
+src="Charge%20Flipping%20in%20GSAS_files/image010.gif" v:shapes="_x0000_i1043"><![endif]></span></p>
 
 <p class=MsoNormal>It is evident from examining the plot that improvement can
@@ -1444 +1456 @@
 mso-ascii-theme-font:minor-latin;mso-hansi-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'> 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>.
-Repeat <b style='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 obtained an improved residual of 9.7% with a much better fit at the high
-angle part of the pattern.</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
+class=GramE>X</span> </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>. Repeat <b style='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
+obtained an improved residual of 9.7% with a much better fit at the high angle
+part of the pattern.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1535 +1548 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="_x0000_i1041" type="#_x0000_t75" style='width:337.5pt;height:225pt;
- visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_7" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:337.5pt;
+ height:225pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image013.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
-src="Charge%20Flipping%20in%20GSAS_files/image014.gif" v:shapes="_x0000_i1041"><![endif]></span></p>
+src="Charge%20Flipping%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1584 +1597 @@
 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
-headings in the table by a single click on the desired heading. 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'>dzero</span></b>
-column gives the distance of each peak from the origin. The menu items under
-Map peaks give you several tools to aid in the peak selection process, we will
-just use a couple in this example. I have chosen to proceed by sorting the
-atoms by <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b>,
-selecting all and then finding the unique ones. </p>
+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:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin'>dzero</span></b></span> column gives the distance of each peak
+from the origin. The menu items under Map peaks give you several tools to aid
+in the peak selection <span class=GramE>process,</span> we will just use a
+couple in this example. I have chosen to proceed by sorting the atoms by <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'>dzero</span></b></span>, selecting all and then finding the unique
+ones. </p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
 mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]>Do a 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'>dzero</span></b> column heading.
-This will sort the peaks in increasing distance from the origin.</p>
+</span></span></span><![endif]>Do a single click on 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'>dzero</span></b></span>
+column heading. This will sort the peaks in increasing distance from the origin.</p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -1653 +1668 @@
 identification (M100 for the largest 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'>Map peaks</span></b> table which
-may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
+minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which may
+not be one of those moved 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'>Atoms</span></b> table). You can hand sort
 them by selecting a row with 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'>Alt</span></b> key down and then selecting a
-position in the table with 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'>Alt</span></b> key still down. My list is now
-</p>
+mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='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/Ctrl</span></b> keys) down
+and then selecting a position in the table with 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'>Alt</span></b> key still down. On
+Linux machines 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'>Alt</span></b> key may have been hijacked by
+the operating system; 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'>Shift/Ctrl</span></b> instead to move atoms. My
+list is now </p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1739 +1762 @@
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
-charge flip map (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'>Clear map</span></b> in the <b
+charge flip map (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'>Clear</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'> map</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>
@@ -1757 +1782 @@
 
 <p class=MsoNormal>Save the project file; the next step is to complete the
-structure by finding the Li and H atoms and then doing the Rietveld refinement
-on the completed structure.</p>
+structure by finding the Li and H atoms and then doing the <span class=SpellE>Rietveld</span>
+refinement on the completed structure.</p>
 
 <h2>Step 5 Complete the structure</h2>
 
 <p class=MsoNormal>To complete the structure you will need to perform a
-preliminary Rietveld refinement. This will make the atom positions more
-accurate and prepare a set of calculated structure factors needed to generate a
-difference Fourier map good enough to reveal the Li atom position and maybe the
-H-atom as well. There are a number of steps needed to set all the controls from
-the previous Pawley refinement to get a successful start for the Rietveld
-refinement.</p>
+preliminary <span class=SpellE>Rietveld</span> refinement. This will make the
+atom positions more accurate and prepare a set of calculated structure factors
+needed to generate a difference Fourier map good enough to reveal the Li atom
+position and maybe the H-atom as well. There are a number of steps needed to
+set all the controls from the previous Pawley refinement to get a successful
+start for the <span class=SpellE>Rietveld</span> refinement.</p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -1815 +1840 @@
 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 a
-Rwp ~31%. The plot shows clear intensity differences; the atom positions
-obviously need refinement.</p>
+GSAS-II data tree menu; all that was refined is scale and background. I got <span
+class=GramE>a</span> <span class=SpellE>Rwp</span> ~31%. The plot shows clear
+intensity differences; the atom positions obviously need refinement.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1853 +1878 @@
 <p class=MsoNormal>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; my Rwp is
-now ~15%. You can now safely refine lattice parameters (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 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
+class=SpellE>Rwp</span> is now ~15%. You can now safely refine lattice
+parameters (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 for <b
+style='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>)
 and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
@@ -1868 +1894 @@
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-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'>X</span></b>
-&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+<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'>X</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'>Y</span></b>.
 My refinement improved slightly to Rwp~14.5%. Let’s see if a difference Fourier
@@ -1876 +1903 @@
 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'>Phases/kryptonite
-General</span></b> tab ; 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'>Fourier map controls</span></b> are midway
-down the window.</p>
+General</span></b> <span class=GramE>tab ;</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'>Fourier map controls</span></b>
+are midway down the window.</p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
 mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]>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'>delt-F</span></b> for the <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+</span></span></span><![endif]>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'>delt</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'>-F</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'>Map type</span></b>.</p>
 
@@ -1942 +1971 @@
 src="Charge%20Flipping%20in%20GSAS_files/image038.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
 
-<p class=MsoNormal>What is drawn here are green dots whose size are
-proportional to the electron density. These are the Li atom positions. There
-are several ways within GSAS-II to add it to the atom list. One is to 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'>Compute/Search
-map</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> tab and then find them 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'>Map peaks</span></b>
-tab much the same way we did earlier in this exercise. Another is to get the
-atom position directly from the map, we will do that now.</p>
+<p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots
+whose size are proportional to the electron density. These are the Li atom
+positions. There are several ways within GSAS-II to add it to the atom list.
+One is to 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'>Compute/Search map</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> tab and then
+find them 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'>Map peaks</span></b> tab much the same way we did earlier in this
+exercise. Another is to get the atom position directly from the map, we will do
+that now.</p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -2028 +2058 @@
 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 residual Rwp dropped to ~11.3%. Next set all <b
-style='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>
-flags to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+GSAS-II data tree window. My residual <span class=SpellE>Rwp</span> dropped to
+~11.3%. Next set all <b style='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> flags 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'>XU</span></b>
 and repeat <b style='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 residual is now Rwp ~10.8%. Maybe
-we can find the H-atom.</p>
+minor-latin'>Calculate/Refine</span></b>. My residual is now <span
+class=SpellE>Rwp</span> ~10.8%. Maybe we can find the H-atom.</p>
 
 <p class=MsoNormal>From the <b style='mso-bidi-font-weight:normal'><span
@@ -2072 +2103 @@
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>UNK</span></b>). Repeat the Calculate/Refine
-without varying any of the H-atom parameters; my final Rwp = 10.69% (you don’t
-get much improvement for adding an H-atom to an oxide structure).</p>
+without varying any of the H-atom parameters; my final <span class=SpellE>Rwp</span>
+= 10.69% (you don’t get much improvement for adding an H-atom to an oxide
+structure).</p>
 
 </div>

trunk/help/Charge Flipping in GSAS_files/props053.xml ¶

@@ -1 +1 @@
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