Changeset 873

Timestamp:

Mar 22, 2013 10:30:00 AM (11 years ago)

Author:

vondreele

Message:

a bit more in tutorial

File:

• trunk/help/Charge Flipping - sucrose.htm (modified) (11 diffs)

trunk/help/Charge Flipping - sucrose.htm

@@ -24 +24 @@
   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>14</o:Revision>
-  <o:TotalTime>1423</o:TotalTime>
+  <o:Revision>15</o:Revision>
+  <o:TotalTime>1426</o:TotalTime>
   <o:Created>2013-03-15T18:32:00Z</o:Created>
-  <o:LastSaved>2013-03-22T15:24:00Z</o:LastSaved>
+  <o:LastSaved>2013-03-22T15:29:00Z</o:LastSaved>
   <o:Pages>17</o:Pages>
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+  <o:Words>3416</o:Words>
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   <o:Company>Argonne National Laboratory</o:Company>
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@@ -971 +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 <span class=SpellE>d<sub>min</sub></span> ~1Å resolution needed
-for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span
+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
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@@ -1578 +1578 @@
 select (grey) 23 out of 46 peak positions in the table and all should be near
 the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
-that would be all the C &amp; O atoms! They will be colored green in the plot.
-If more are selected then check the map offset – it may need a slight
-correction.</p>
+that would be all the C &amp; O atoms! They will be colored green in the plot. If
+more are selected then check the map offset – it may need a slight correction.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1655 +1654 @@
 
 <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
+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
@@ -1704 +1703 @@
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
 tab). The atom positions I obtained have two atoms (O3 &amp; O4) not connected
-to the sucrose molecule because they belong to neighboring molecules. We need to
-discover the equivalent ones that belong to this molecule. Follow the steps:</p>
+to the sucrose molecule because they belong to neighboring molecules. We need
+to discover the equivalent ones that belong to this molecule. Follow the steps:</p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -1750 +1749 @@
 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>
+mso-hansi-theme-font:minor-latin'>Shift right</span></b> for the rest, they
+will show in green. </p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -1797 +1796 @@
 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
-coordinates will be transformed.</p>
+minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom coordinates
+will be transformed.</p>
 
 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
@@ -2134 +2133 @@
 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-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
@@ -2394 +2393 @@
 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 <span class=SpellE>Rwp</span> ~7.1%.</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>