Changeset 1941 for Tutorials


Ignore:
Timestamp:
Jul 21, 2015 12:38:59 PM (6 years ago)
Author:
vondreele
Message:
 
Location:
Tutorials/CFsucrose
Files:
2 added
14 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/CFsucrose/Charge Flipping - sucrose.htm

    r1937 r1941  
    2424  <o:Author>Von Dreele</o:Author>
    2525  <o:LastAuthor>Von Dreele</o:LastAuthor>
    26   <o:Revision>3</o:Revision>
    27   <o:TotalTime>1991</o:TotalTime>
     26  <o:Revision>4</o:Revision>
     27  <o:TotalTime>2101</o:TotalTime>
    2828  <o:Created>2015-07-20T18:13:00Z</o:Created>
    29   <o:LastSaved>2015-07-20T18:37:00Z</o:LastSaved>
     29  <o:LastSaved>2015-07-21T17:36:00Z</o:LastSaved>
    3030  <o:Pages>1</o:Pages>
    31   <o:Words>3460</o:Words>
    32   <o:Characters>19722</o:Characters>
     31  <o:Words>3523</o:Words>
     32  <o:Characters>20087</o:Characters>
    3333  <o:Company>Argonne National Laboratory</o:Company>
    34   <o:Lines>164</o:Lines>
    35   <o:Paragraphs>46</o:Paragraphs>
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     34  <o:Lines>167</o:Lines>
     35  <o:Paragraphs>47</o:Paragraphs>
     36  <o:CharactersWithSpaces>23563</o:CharactersWithSpaces>
    3737  <o:Version>15.00</o:Version>
    3838 </o:DocumentProperties>
     
    4242</xml><![endif]-->
    4343<link rel=dataStoreItem
    44 href="Charge%20Flipping%20-%20sucrose_files/item0059.xml"
    45 target="Charge%20Flipping%20-%20sucrose_files/props060.xml">
     44href="Charge%20Flipping%20-%20sucrose_files/item0054.xml"
     45target="Charge%20Flipping%20-%20sucrose_files/props055.xml">
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    663663        {font-family:"Cambria Math";
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    14591460mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
    14601461to make sure it has essentially minimized. My refinement completed with <span
    1461 class=SpellE>Rwp</span> ~25%; a dialog box appears asking if you wish to load
    1462 the result. Press <b style='mso-bidi-font-weight:normal'><span
    1463 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1464 mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
    1465 PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
     1462class=SpellE>Rwp</span> ~25% (NB: here and after succeeding refinements your <span
     1463class=SpellE>Rwp</span> values may be slightly different from what I show here);
     1464a dialog box appears asking if you wish to load the result. Press <b
     1465style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1466mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
     1467To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
     1468the width and height).</p>
    14661469
    14671470<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    15051508if you didn’t do this earlier. Repeat <b style='mso-bidi-font-weight:normal'><span
    15061509style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1507 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged;
    1508 I obtained an improved residual of ~7.3% with a much better fit at the high
    1509 angle part of the pattern but still not fit well for the lower part.</p>
     1510mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged; I
     1511obtained an improved residual of ~7.3% with a much better fit at the high angle
     1512part of the pattern but still not fit well for the lower part.</p>
    15101513
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    18071810width:16px;height:35px'><img width=16 height=35
    18081811src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
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    18121816  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
    18131817</v:shape><![endif]--><![if !vml]><img width=670 height=575
    1814 src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="_x0000_i1052"><![endif]></span></p>
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    18151819
    18161820<p class=MsoNormal>The result looks very promising! Charge flipping operates
     
    18921896should select (grey) 23 out of 46 peak positions in the table and all should be
    18931897near the top of the list. The console displays this as both the number of unique
    1894 peaks and the fraction found (the ideal value for the latter is easily inferred
    1895 from the space group). Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
    1896 that would be all the C &amp; O atoms! They will be colored green in the plot.
    1897 If more are selected then check the map offset – it may need a slight
    1898 correction.</p>
     1898peaks and the fraction found (the ideal value<span class=GramE>,0.5</span>, for
     1899the latter is easily inferred from the space group). Given the formula for
     1900sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub> that would be all the C
     1901&amp; O atoms! They will be colored green in the plot. If more are selected
     1902then check the map offset – it may need a slight correction.</p>
    18991903
    19001904<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    19421946
    19431947<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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    19461950 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image021.png" o:title=""/>
    19471951</v:shape><![endif]--><![if !vml]><img width=700 height=553
    1948 src="Charge%20Flipping%20-%20sucrose_files/image021.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
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    19491953
    19501954<p class=MsoNormal>The atom names indicate the peak magnitude to aid
     
    19781982src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
    19791983
    1980 <p class=MsoNormal>Notice that in this case the atom list is neatly sorted out
    1981 into two groups with a clear gap between M79 and M64. The higher ones are likely
    1982 to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of
     1984<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out into
     1985two groups with a clear gap between M79 and M64. The higher ones are likely to
     1986be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of
    19831987ambiguity in the middle, but just assign the top 11 as O and the rest as C and
    19841988see what happens. You can do this by selecting a block of atoms, go to <b
     
    19941998
    19951999<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1996  id="Picture_x0020_18" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:364.5pt;
    1997  height:311.25pt;visibility:visible;mso-wrap-style:square'>
     2000 id="Picture_x0020_44" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:363pt;
     2001 height:309.75pt;visibility:visible;mso-wrap-style:square'>
    19982002 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image023.png" o:title=""
    1999   croptop="10802f" cropbottom="17378f" cropleft="37546f" cropright="12910f"/>
    2000 </v:shape><![endif]--><![if !vml]><img width=486 height=415
    2001 src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
     2003  croptop="13142f" cropbottom="15218f" cropleft="37794f" cropright="12724f"/>
     2004</v:shape><![endif]--><![if !vml]><img width=484 height=413
     2005src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_44"><![endif]></span></p>
    20022006
    20032007<p class=MsoNormal>The original charge flipping solution is still visible and
     
    20102014
    20112015<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2012  id="Picture_x0020_19" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:525pt;
    2013  height:449.25pt;visibility:visible;mso-wrap-style:square'>
     2016 id="Picture_x0020_45" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:525pt;
     2017 height:445.5pt;visibility:visible;mso-wrap-style:square'>
    20142018 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image025.png" o:title=""/>
    2015 </v:shape><![endif]--><![if !vml]><img width=700 height=599
    2016 src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
     2019</v:shape><![endif]--><![if !vml]><img width=700 height=594
     2020src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
    20172021
    20182022<p class=MsoNormal>Now one can safely remove the map peaks (do <b
     
    20302034mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    20312035tab). The atom positions I obtained in this charge flipping run have the
    2032 sucrose molecule fragmented over several neighboring molecules. We need
    2033 assemble these into a single molecule. Follow the steps:</p>
     2036sucrose molecule fragmented over several neighboring molecules. We need assemble
     2037these into a single molecule. Follow the steps:</p>
    20342038
    20352039<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    20782082
    20792083<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2080  id="_x0000_i1042" type="#_x0000_t75" style='width:525pt;height:448.5pt;
    2081  visibility:visible;mso-wrap-style:square'>
     2084 id="Picture_x0020_46" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
     2085 height:449.25pt;visibility:visible;mso-wrap-style:square'>
    20822086 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/>
    2083 </v:shape><![endif]--><![if !vml]><img width=700 height=598
    2084 src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="_x0000_i1042"><![endif]></span></p>
     2087</v:shape><![endif]--><![if !vml]><img width=700 height=599
     2088src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
     2089
     2090<p class=MsoNormal>If it happens that the Assemble molecule routine leaves one
     2091or two atoms out, rerun it adjusting the Bond search factor to a slightly
     2092larger value (e.g. 0.9 vs 0.85). That should pick up the outliers.</p>
    20852093
    20862094<p class=MsoNormal>To rename the atoms, select all the atoms (double click in
     
    20972105
    20982106<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2099  id="Picture_x0020_22" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;
    2100  height:448.5pt;visibility:visible;mso-wrap-style:square'>
     2107 id="Picture_x0020_47" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;
     2108 height:450.75pt;visibility:visible;mso-wrap-style:square'>
    21012109 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/>
    2102 </v:shape><![endif]--><![if !vml]><img width=700 height=598
    2103 src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
     2110</v:shape><![endif]--><![if !vml]><img width=700 height=601
     2111src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
    21042112
    21052113<p class=MsoNormal>You can also reorder the atoms to make the connectivity
     
    21612169mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
    21622170GSAS-II data tree menu; only scale and background are refined. I got <span
    2163 class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear
    2164 intensity differences; the atom positions obviously need refinement.</p>
     2171class=SpellE>Rwp</span> ~20%. The plot shows clear intensity differences; the
     2172atom positions obviously need refinement.</p>
    21652173
    21662174<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21912199
    21922200<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2193  id="Picture_x0020_24" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
     2201 id="Picture_x0020_48" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
    21942202 height:225pt;visibility:visible;mso-wrap-style:square'>
    21952203 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/>
    21962204</v:shape><![endif]--><![if !vml]><img width=700 height=300
    2197 src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
     2205src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
    21982206
    21992207<p class=MsoNormal>To deal with the warning we need to set a “Hold” on one atom
    22002208y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span
    22012209style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2202 mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II
    2203 data tree.</p>
     2210mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II data
     2211tree.</p>
    22042212
    22052213<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22152223style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    22162224mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
    2217 class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will fix
    2218 the shift along y for the <span class=GramE>O(</span>1) atom.</p>
    2219 
    2220 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2221  id="Picture_x0020_26" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:259.5pt;
    2222  height:271.5pt;visibility:visible;mso-wrap-style:square'>
     2225class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. Notice the
     2226use of a filter to shorten the list. This will fix the shift along y for the <span
     2227class=GramE>O(</span>1) atom.</p>
     2228
     2229<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2230 id="Picture_x0020_49" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468.75pt;
     2231 height:300pt;visibility:visible;mso-wrap-style:square'>
    22232232 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title=""/>
    2224 </v:shape><![endif]--><![if !vml]><img width=346 height=362
    2225 src="Charge%20Flipping%20-%20sucrose_files/image033.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
     2233</v:shape><![endif]--><![if !vml]><img width=625 height=400
     2234src="Charge%20Flipping%20-%20sucrose_files/image033.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
    22262235
    22272236<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
     
    22852294minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>. A new popup window
    22862295will appear.<br>
    2287 <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_45"
     2296<span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_50"
    22882297 o:spid="_x0000_i1035" type="#_x0000_t75" style='width:300pt;height:363.75pt;
    22892298 visibility:visible;mso-wrap-style:square'>
    22902299 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""/>
    22912300</v:shape><![endif]--><![if !vml]><img width=400 height=485
    2292 src="Charge%20Flipping%20-%20sucrose_files/image035.png" v:shapes="Picture_x0020_45"><![endif]></span><br>
     2301src="Charge%20Flipping%20-%20sucrose_files/image035.png" v:shapes="Picture_x0020_50"><![endif]></span><br>
    22932302This offers the choice of how many H-atoms to be added for each atom in the
    22942303table; the maximum is chosen for each atom. If the bonds are sufficiently short
     
    23012310normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    23022311minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>. The structure will
    2303 be redrawn with H-atoms shown as van der Waals spheres; they are appended to
    2304 the end of the Atom list.</p>
    2305 
    2306 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2307  id="Picture_x0020_46" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:360.75pt;
    2308  height:312.75pt;visibility:visible;mso-wrap-style:square'>
     2312be redrawn with H-atoms shown as van der Waals spheres; they are inserted in
     2313the Atom list immediately after the C-atom they are bound to and they are named
     2314accordingly. </p>
     2315
     2316<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2317 id="Picture_x0020_51" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:362.25pt;
     2318 height:312pt;visibility:visible;mso-wrap-style:square'>
    23092319 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image036.png" o:title=""
    2310   croptop="12872f" cropbottom="15128f" cropleft="40027f" cropright="10552f"/>
    2311 </v:shape><![endif]--><![if !vml]><img width=481 height=417
    2312 src="Charge%20Flipping%20-%20sucrose_files/image037.jpg" v:shapes="Picture_x0020_46"><![endif]></span></p>
     2320  croptop="15482f" cropbottom="12608f" cropleft="37236f" cropright="13314f"/>
     2321</v:shape><![endif]--><![if !vml]><img width=483 height=416
     2322src="Charge%20Flipping%20-%20sucrose_files/image037.jpg" v:shapes="Picture_x0020_51"><![endif]></span></p>
    23132323
    23142324<p class=MsoNormal>These hydrogen atoms will better describe the scattering
     
    23222332
    23232333<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2324  id="Picture_x0020_47" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:363pt;
    2325  height:312pt;visibility:visible;mso-wrap-style:square'>
     2334 id="Picture_x0020_52" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:363pt;
     2335 height:311.25pt;visibility:visible;mso-wrap-style:square'>
    23262336 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image038.png" o:title=""
    2327   croptop="12872f" cropbottom="15218f" cropleft="40028f" cropright="10490f"/>
    2328 </v:shape><![endif]--><![if !vml]><img width=484 height=416
    2329 src="Charge%20Flipping%20-%20sucrose_files/image039.jpg" v:shapes="Picture_x0020_47"><![endif]></span></p>
     2337  croptop="15482f" cropbottom="12698f" cropleft="37236f" cropright="13252f"/>
     2338</v:shape><![endif]--><![if !vml]><img width=484 height=415
     2339src="Charge%20Flipping%20-%20sucrose_files/image039.jpg" v:shapes="Picture_x0020_52"><![endif]></span></p>
    23302340
    23312341<p class=MsoNormal>Because the C-atoms have probably moved; the H-atoms (which
     
    24162426Recall that the refinement was just done without any H-atoms on the oxygen
    24172427atoms; it will make the best fit compensating for the missing H-atoms by
    2418 displacing the O atoms in the direction of the missing H-atoms. To add the OH
    2419 atoms do the following:</p>
     2428displacing the O atoms in the direction of the missing H-atoms. To add the OH atoms
     2429do the following:</p>
    24202430
    24212431<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    24292439mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
    24302440"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2431 </span></span></span><![endif]>Select all O-atoms in the table (double click the
    2432 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2441</span></span></span><![endif]>Select all O-atoms in the table (double click
     2442the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    24332443mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b>
    24342444column heading &amp; select <b style='mso-bidi-font-weight:normal'><span
     
    24662476<p class=MsoNormal style='margin-left:.5in'>These OH hydrogens are found by
    24672477finding the highest point in the delta-F map for all possible orientations of
    2468 this bond at a fixed angle (109.5°). The new hydrogen atoms are named in
    2469 sequence and are appended to the end of the Atom list.</p>
     2478this bond at a fixed angle (109.5°). The new hydrogen atoms are named in sequence
     2479and are appended to the end of the Atom list.</p>
    24702480
    24712481<p class=MsoNormal style='margin-left:.5in'><o:p>&nbsp;</o:p></p>
     
    25512561style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    25522562mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
    2553 phenomenological model for <span class=SpellE>microstrain</span> which has 9
    2554 terms for monoclinic structures. Check all the boxes for it and press <b
     2563phenomenological model for <span class=SpellE>microstrain</span> which has 9 terms
     2564for monoclinic structures. Check all the boxes for it and press <b
    25552565style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    25562566mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reset</span></b>.
  • Tutorials/CFsucrose/Charge Flipping - sucrose_files/filelist.xml

    r1937 r1941  
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