Changeset 873


Ignore:
Timestamp:
Mar 22, 2013 10:30:00 AM (9 years ago)
Author:
vondreele
Message:

a bit more in tutorial

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/help/Charge Flipping - sucrose.htm

    r872 r873  
    2424  <o:Author>Von Dreele</o:Author>
    2525  <o:LastAuthor>Von Dreele</o:LastAuthor>
    26   <o:Revision>14</o:Revision>
    27   <o:TotalTime>1423</o:TotalTime>
     26  <o:Revision>15</o:Revision>
     27  <o:TotalTime>1426</o:TotalTime>
    2828  <o:Created>2013-03-15T18:32:00Z</o:Created>
    29   <o:LastSaved>2013-03-22T15:24:00Z</o:LastSaved>
     29  <o:LastSaved>2013-03-22T15:29:00Z</o:LastSaved>
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    3333  <o:Company>Argonne National Laboratory</o:Company>
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    971971symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
    972972relatively clear of peaks that makes a good place to end the calculations with
    973 a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution needed
    974 for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span
     973a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution
     974needed for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span
    975975style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    976976mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span class=SpellE><b
     
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    15781578select (grey) 23 out of 46 peak positions in the table and all should be near
    15791579the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
    1580 that would be all the C &amp; O atoms! They will be colored green in the plot.
    1581 If more are selected then check the map offset – it may need a slight
    1582 correction.</p>
     1580that would be all the C &amp; O atoms! They will be colored green in the plot. If
     1581more are selected then check the map offset – it may need a slight correction.</p>
    15831582
    15841583<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16551654
    16561655<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out
    1657 into two groups with a clear gap between M79 and M64. The higher ones are
    1658 likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit
    1659 of ambiguity in the middle, but just assign the top 11 as O and the rest as C
    1660 and see what happens. You can do this by selecting a block of atoms, go to <b
     1656into two groups with a clear gap between M79 and M64. The higher ones are likely
     1657to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of
     1658ambiguity in the middle, but just assign the top 11 as O and the rest as C and
     1659see what happens. You can do this by selecting a block of atoms, go to <b
    16611660style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    16621661mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
     
    17041703mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    17051704tab). The atom positions I obtained have two atoms (O3 &amp; O4) not connected
    1706 to the sucrose molecule because they belong to neighboring molecules. We need to
    1707 discover the equivalent ones that belong to this molecule. Follow the steps:</p>
     1705to the sucrose molecule because they belong to neighboring molecules. We need
     1706to discover the equivalent ones that belong to this molecule. Follow the steps:</p>
    17081707
    17091708<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    17501749for the first one &amp; <b style='mso-bidi-font-weight:normal'><span
    17511750style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1752 mso-hansi-theme-font:minor-latin'>Shift right</span></b> for <span
    1753 class=SpellE>the</span> rest, they will show in green. </p>
     1751mso-hansi-theme-font:minor-latin'>Shift right</span></b> for the rest, they
     1752will show in green. </p>
    17541753
    17551754<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    17971796select the operator and unit cell translations, then press <b style='mso-bidi-font-weight:
    17981797normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1799 minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom
    1800 coordinates will be transformed.</p>
     1798minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom coordinates
     1799will be transformed.</p>
    18011800
    18021801<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    21342133level</span></b> and <b style='mso-bidi-font-weight:normal'><span
    21352134style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2136 mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for
    2137 the remaining H-atoms; you may have to guess positions for some of them using
    2138 known stereochemistry rules. My model looked like</p>
     2135mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for the
     2136remaining H-atoms; you may have to guess positions for some of them using known
     2137stereochemistry rules. My model looked like</p>
    21392138
    21402139<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    23942393and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    23952394mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b>
    2396 restraints to give a final <span class=SpellE>Rwp</span> ~7.1%.</p>
     2395restraints to give a final <span class=SpellE>Rwp</span> ~7.1%. NB: the H-atom
     2396positions may not be correct even though the refinement apparently succeeded.
     2397You should check that the OH ones all give reasonable H-bonds to neighboring
     2398O-atoms. As this is powder data such changes will hardly affect the fit but
     2399will be more satisfying. At present such checking is outside the scope of
     2400GSAS-II.</p>
    23972401
    23982402<p class=MsoNormal><o:p>&nbsp;</o:p></p>
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