Ignore:
Timestamp:
Jul 20, 2015 1:39:18 PM (8 years ago)
Author:
vondreele
Message:

revised sucrose charge flip tutorial

File:
1 edited

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  • Tutorials/CFsucrose/Charge Flipping - sucrose.htm

    r1730 r1937  
    2525  <o:LastAuthor>Von Dreele</o:LastAuthor>
    2626  <o:Revision>3</o:Revision>
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    28   <o:Created>2015-03-16T21:09:00Z</o:Created>
    29   <o:LastSaved>2015-03-17T19:23:00Z</o:LastSaved>
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     28  <o:Created>2015-07-20T18:13:00Z</o:Created>
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    12181220ol
    … …  
    12791281(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
    12801282
    1281 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
     1283<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
    12821284style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    12831285style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    … …  
    12991301mouse cursor on the plot.</p>
    13001302
    1301 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
     1303<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
    13021304style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    13031305style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    … …  
    13171319We will refine them again later.</p>
    13181320
    1319 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
     1321<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
    13201322style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    13211323style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    … …  
    13311333mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>.</p>
    13321334
    1333 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
     1335<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
    13341336style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    13351337style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
    … …  
    13721374 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
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    13791381
    13801382<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
    13811383style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13821384mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
    1383 for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
     1385for some text. Do <b style='mso-bidi-font-weight:normal'><span
    13841386style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13851387mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
    … …  
    13871389
    13881390<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1389  id="Picture_x0020_2" o:spid="_x0000_i1063" type="#_x0000_t75" style='width:259.5pt;
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     1391 id="Picture_x0020_2" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:240pt;
     1392 height:232.5pt;visibility:visible;mso-wrap-style:square'>
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    13941396
    1395 <p class=MsoNormal>Select either choice; the desired data set will be added to
    1396 this phase for analysis. The data tab now shows the new data set.</p>
    1397 
    1398 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1399  id="_x0000_i1062" type="#_x0000_t75" style='width:359.25pt;height:375pt;
    1400  visibility:visible;mso-wrap-style:square'>
     1397<p class=MsoNormal>Select the only choice and press <b style='mso-bidi-font-weight:
     1398normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1399minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>; the desired data
     1400set will be added to this phase for analysis. The data tab now shows the new
     1401data set.</p>
     1402
     1403<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1404 id="Picture_x0020_3" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:359.25pt;
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    14011406 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image003.png" o:title=""/>
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    14041409
    14051410<p class=MsoNormal>I’ve stretched the window slightly to see the entire
    … …  
    14081413class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
    14091414and extinction corrections. The <span class=SpellE>Babinet</span> correction is
    1410 intended for protein work where a significant region of the structure is
    1411 disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
    1412 surfaces</p>
    1413 
    1414 <p class=MsoNormal><span class=GramE>as</span> well as preferred orientation
    1415 correction curves.</p>
     1415intended for protein work where a significant region of the structure is disordered
     1416solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
     1417surfaces as well as preferred orientation correction curves.</p>
    14161418
    14171419<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
    … …  
    14241426normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    14251427minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>.
    1426 The table should list reflections 0-780. Select and check the refine column
     1428The table should list reflections 0~780. Select and check the refine column
    14271429using the same technique you used for the peak list. </p>
    14281430
    14291431<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1430  id="Picture_x0020_4" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:375pt;
     1432 id="Picture_x0020_4" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:375pt;
    14311433 height:225pt;visibility:visible;mso-wrap-style:square'>
    14321434 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image004.png" o:title=""/>
    … …  
    14481450to recover from a bad refinement. A progress dialog box will appear showing the
    14491451residual as the refinement proceeds. Notice that there was a singular matrix
    1450 warning on the console window and the last reflection (781) was removed from
    1451 the refinement because it was off the end of the used part of the pattern. This
    1452 is the GSAS-II singular matrix recovery mechanism; you can go to the <b
     1452warning on the console window and perhaps the last reflection (781) was removed
     1453from the refinement because it was off the end of the used part of the pattern.
     1454This is the GSAS-II singular matrix recovery mechanism; you can go to the <b
    14531455style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14541456mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
    … …  
    14571459mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
    14581460to make sure it has essentially minimized. My refinement completed with <span
    1459 class=SpellE>Rwp</span> ~26.3%; a dialog box appears asking if you wish to load
     1461class=SpellE>Rwp</span> ~25%; a dialog box appears asking if you wish to load
    14601462the result. Press <b style='mso-bidi-font-weight:normal'><span
    14611463style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    … …  
    14641466
    14651467<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1466  id="Picture_x0020_46" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:525pt;
     1468 id="Picture_x0020_5" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:525pt;
    14671469 height:450pt;visibility:visible;mso-wrap-style:square'>
    14681470 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image005.png" o:title=""/>
    14691471</v:shape><![endif]--><![if !vml]><img width=700 height=600
    1470 src="Charge%20Flipping%20-%20sucrose_files/image005.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
     1472src="Charge%20Flipping%20-%20sucrose_files/image005.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
    14711473
    14721474<p class=MsoNormal>It is evident from examining the plot that some improvement
    … …  
    15041506style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    15051507mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged;
    1506 I obtained an improved residual of ~9.05% with a much better fit at the high
     1508I obtained an improved residual of ~7.3% with a much better fit at the high
    15071509angle part of the pattern but still not fit well for the lower part.</p>
    15081510
    15091511<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1510  id="Picture_x0020_26" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:504.75pt;
     1512 id="Picture_x0020_6" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:504.75pt;
    15111513 height:432.75pt;visibility:visible;mso-wrap-style:square'>
    15121514 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image006.png" o:title=""/>
    15131515</v:shape><![endif]--><![if !vml]><img width=673 height=577
    1514 src="Charge%20Flipping%20-%20sucrose_files/image006.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
     1516src="Charge%20Flipping%20-%20sucrose_files/image006.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
    15151517
    15161518<p class=MsoNormal>What you see is that the background has a substantial
    … …  
    15281530
    15291531<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1530  id="Picture_x0020_27" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:366.75pt;
     1532 id="Picture_x0020_7" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:366.75pt;
    15311533 height:197.25pt;visibility:visible;mso-wrap-style:square'>
    15321534 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image007.png" o:title=""/>
    15331535</v:shape><![endif]--><![if !vml]><img width=489 height=263
    1534 src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span><span
     1536src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_7"><![endif]></span><span
    15351537style='mso-spacerun:yes'> </span></p>
    15361538
    … …  
    15551557style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    15561558mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>
    1557 for the <span class=SpellE>chebyschev</span> part of the background. The window
     1559for the <span class=SpellE>Chebyschev</span> part of the background. The window
    15581560should look like</p>
    15591561
    15601562<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1561  id="Picture_x0020_28" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:402pt;
    1562  height:197.25pt;visibility:visible;mso-wrap-style:square'>
     1563 id="Picture_x0020_8" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:439.5pt;
     1564 height:199.5pt;visibility:visible;mso-wrap-style:square'>
    15631565 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image008.png" o:title=""/>
    1564 </v:shape><![endif]--><![if !vml]><img width=536 height=263
    1565 src="Charge%20Flipping%20-%20sucrose_files/image008.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
     1566</v:shape><![endif]--><![if !vml]><img width=586 height=266
     1567src="Charge%20Flipping%20-%20sucrose_files/image008.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
    15661568
    15671569<p class=MsoNormal>Go to the <b style='mso-bidi-font-weight:normal'><span
    … …  
    15941596new negatives that may appear. Then set all the Pawley refinement flags back on
    15951597(excluding any that lead to a singular matrix) and repeat the refinement. After
    1596 refinement, mine converged to ~5.3% with very few negatives and <span
    1597 class=SpellE>and</span> the plot looked like</p>
    1598 
    1599 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1600  id="_x0000_i1056" type="#_x0000_t75" style='width:525pt;height:450pt;
    1601  visibility:visible;mso-wrap-style:square'>
     1598refinement, mine converged to ~5.3% with very few negatives and the plot looked
     1599like</p>
     1600
     1601<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1602 id="Picture_x0020_9" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:525pt;
     1603 height:450pt;visibility:visible;mso-wrap-style:square'>
    16021604 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image009.png" o:title=""/>
    16031605</v:shape><![endif]--><![if !vml]><img width=700 height=600
    1604 src="Charge%20Flipping%20-%20sucrose_files/image009.png" v:shapes="_x0000_i1056"><![endif]></span></p>
     1606src="Charge%20Flipping%20-%20sucrose_files/image009.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
    16051607
    16061608<p class=MsoNormal>Let’s see if this is good enough for charge flipping.</p>
    … …  
    16191621
    16201622<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    1621 mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
     1623mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
    16221624"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    16231625</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
    … …  
    16351637
    16361638<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    1637 mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
     1639mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
    16381640"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    16391641</span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span
    … …  
    16951697
    16961698<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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    … …  
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     1769UEsBAi0AFAAGAAgAAAAhADHdX2HSAAAAjwEAAAsAAAAAAAAAAAAAAAAALgEAAF9yZWxzLy5yZWxz
     1770UEsBAi0AFAAGAAgAAAAhADMvBZ5BAAAAOQAAABAAAAAAAAAAAAAAAAAAKQIAAGRycy9zaGFwZXht
     1771bC54bWxQSwECLQAUAAYACAAAACEAjD9v/8MAAADbAAAADwAAAAAAAAAAAAAAAACYAgAAZHJzL2Rv
     1772d25yZXYueG1sUEsFBgAAAAAEAAQA9QAAAIgDAAAAAA==
    17711773" path="m457200,nsc709705,,914400,204695,914400,457200r-457200,l457200,xem457200,nfc709705,,914400,204695,914400,457200e"
    17721774  filled="f" strokecolor="red" strokeweight="1.5pt">
    … …  
    17871789VAy4LM8w09zU50C/9q7/6ZURE31X/kL8TKv1x6wXNXYPAAAA//8DAFBLAwQUAAYACAAAACEAMy8F
    17881790nkEAAAA5AAAAEAAAAGRycy9zaGFwZXhtbC54bWyysa/IzVEoSy0qzszPs1Uy1DNQUkjNS85PycxL
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    1793 +O7y+/6nnm78th/txvfJxk3bs1Kvw371CSJQH57h//ZWK3ifwONL/AFy8QcAAP//AwBQSwECLQAU
    1794 AAYACAAAACEA8PeKu/0AAADiAQAAEwAAAAAAAAAAAAAAAAAAAAAAW0NvbnRlbnRfVHlwZXNdLnht
    1795 bFBLAQItABQABgAIAAAAIQAx3V9h0gAAAI8BAAALAAAAAAAAAAAAAAAAAC4BAABfcmVscy8ucmVs
    1796 c1BLAQItABQABgAIAAAAIQAzLwWeQQAAADkAAAAQAAAAAAAAAAAAAAAAACkCAABkcnMvc2hhcGV4
    1797 bWwueG1sUEsBAi0AFAAGAAgAAAAhAD+osNrEAAAA2wAAAA8AAAAAAAAAAAAAAAAAmAIAAGRycy9k
    1798 b3ducmV2LnhtbFBLBQYAAAAABAAEAPUAAACJAwAAAAA=
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     1792AADbAAAADwAAAGRycy9kb3ducmV2LnhtbESP0WrCQBRE34X+w3ILfdONtgaJrqFUCvahoKkfcMle
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     1794ZtoOfKS+CJWIEPYZKqhD6DIpfVmTQT+zHXH0ztYZDFG6SmqHQ4SbVi6SJJUGG44LNXb0VlN5Lb6N
     1795go++uB0PzXLn9+P8c3F73rlld1Hq6XF8XYMINIb/8L291wpeUvj7En+A3P4CAAD//wMAUEsBAi0A
     1796FAAGAAgAAAAhAPD3irv9AAAA4gEAABMAAAAAAAAAAAAAAAAAAAAAAFtDb250ZW50X1R5cGVzXS54
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     1798bHNQSwECLQAUAAYACAAAACEAMy8FnkEAAAA5AAAAEAAAAAAAAAAAAAAAAAApAgAAZHJzL3NoYXBl
     1799eG1sLnhtbFBLAQItABQABgAIAAAAIQAv3xNCxQAAANsAAAAPAAAAAAAAAAAAAAAAAJgCAABkcnMv
     1800ZG93bnJldi54bWxQSwUGAAAAAAQABAD1AAAAigMAAAAA
    17991801" path="m457200,nsc709705,,914400,204695,914400,457200r-457200,l457200,xem457200,nfc709705,,914400,204695,914400,457200e"
    18001802  filled="f" strokecolor="red" strokeweight="1.5pt">
    … …  
    18051807width:16px;height:35px'><img width=16 height=35
    18061808src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
    1807 style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
    1808  o:spid="_x0000_i1054" type="#_x0000_t75" style='width:502.5pt;height:431.25pt;
    1809  visibility:visible;mso-wrap-style:square'>
     1809style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1052" type="#_x0000_t75"
     1810 style='width:502.5pt;height:431.25pt;visibility:visible;mso-wrap-style:square'>
    18101811 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image012.png" o:title=""
    18111812  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
    18121813</v:shape><![endif]--><![if !vml]><img width=670 height=575
    1813 src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
     1814src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="_x0000_i1052"><![endif]></span></p>
    18141815
    18151816<p class=MsoNormal>The result looks very promising! Charge flipping operates
    … …  
    18461847
    18471848<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1848  id="Picture_x0020_12" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:500.25pt;
     1849 id="Picture_x0020_12" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:500.25pt;
    18491850 height:424.5pt;visibility:visible;mso-wrap-style:square'>
    18501851 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image014.png" o:title=""
    … …  
    18631864minor-latin'>dzero</span></b></span> column gives the distance of each peak
    18641865from the origin. The menu items under Map peaks give you several tools to aid
    1865 in the peak selection process; we will just use a couple in this example. I
    1866 have chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:
    1867 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1868 minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and
    1869 then finding the unique ones. </p>
     1866in the peak selection process; we will just use a couple in this example. I have
     1867chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:normal'><span
     1868style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1869mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and then finding
     1870the unique ones. </p>
    18701871
    18711872<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    1872 mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
     1873mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
    18731874"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    18741875</span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight:
    … …  
    18781879
    18791880<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    1880 mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
     1881mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
    18811882"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    18821883</span></span></span><![endif]>Do a single click on the upper left (empty) box
    … …  
    18841885
    18851886<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    1886 mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
     1887mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
    18871888"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    18881889</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    … …  
    18901891mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That
    18911892should select (grey) 23 out of 46 peak positions in the table and all should be
    1892 near the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
     1893near the top of the list. The console displays this as both the number of unique
     1894peaks and the fraction found (the ideal value for the latter is easily inferred
     1895from the space group). Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
    18931896that would be all the C &amp; O atoms! They will be colored green in the plot.
    18941897If more are selected then check the map offset – it may need a slight
    … …  
    18961899
    18971900<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1898  id="Picture_x0020_13" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:337.5pt;
     1901 id="Picture_x0020_13" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:337.5pt;
    18991902 height:411.75pt;visibility:visible;mso-wrap-style:square'>
    19001903 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image016.png" o:title=""/>
    … …  
    19051908
    19061909<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1907  id="Picture_x0020_14" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:7in;
     1910 id="Picture_x0020_14" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:7in;
    19081911 height:429pt;visibility:visible;mso-wrap-style:square'>
    19091912 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image017.png" o:title=""
    … …  
    19311934
    19321935<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1933  id="Picture_x0020_15" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:7in;
     1936 id="Picture_x0020_15" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:7in;
    19341937 height:433.5pt;visibility:visible;mso-wrap-style:square'>
    19351938 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image019.png" o:title=""
    … …  
    19391942
    19401943<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1941  id="Picture_x0020_44" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
     1944 id="Picture_x0020_44" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;
    19421945 height:414.75pt;visibility:visible;mso-wrap-style:square'>
    19431946 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image021.png" o:title=""/>
    … …  
    19561959mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
    19571960normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1958 minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down and
    1959 then selecting a position in the table with the <b style='mso-bidi-font-weight:
     1961minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
     1962and then selecting a position in the table with the <b style='mso-bidi-font-weight:
    19601963normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    19611964minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
    … …  
    19691972
    19701973<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1971  id="Picture_x0020_17" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:525pt;
     1974 id="Picture_x0020_17" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
    19721975 height:417pt;visibility:visible;mso-wrap-style:square'>
    19731976 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image022.png" o:title=""/>
    … …  
    19761979
    19771980<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out
    1978 into two groups with a clear gap between M79 and M64. The higher ones are
    1979 likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit
    1980 of ambiguity in the middle, but just assign the top 11 as O and the rest as C
    1981 and see what happens. You can do this by selecting a block of atoms, go to <b
     1981into two groups with a clear gap between M79 and M64. The higher ones are likely
     1982to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of
     1983ambiguity in the middle, but just assign the top 11 as O and the rest as C and
     1984see what happens. You can do this by selecting a block of atoms, go to <b
    19821985style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19831986mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
    19841987atom parameters</span></b> and select <b style='mso-bidi-font-weight:normal'><span
    19851988style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1986 mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a periodic
    1987 table will appear. Select the desired element and they will be changed in the
    1988 list and drawing.</p>
    1989 
    1990 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1991  id="Picture_x0020_18" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:7in;
    1992  height:405.75pt;visibility:visible;mso-wrap-style:square'>
     1989mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a
     1990periodic table will appear. Select the desired element and they will be changed
     1991in the list and drawing. (NB: I show below the result from a different charge
     1992flipping run which had a different origin choice so the sucrose molecule is
     1993more fragmented).</p>
     1994
     1995<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'>
    19931998 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image023.png" o:title=""
    1994   croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/>
    1995 </v:shape><![endif]--><![if !vml]><img width=672 height=541
     1999  croptop="10802f" cropbottom="17378f" cropleft="37546f" cropright="12910f"/>
     2000</v:shape><![endif]--><![if !vml]><img width=486 height=415
    19962001src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
    19972002
    … …  
    20052010
    20062011<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2007  id="Picture_x0020_19" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:450pt;
    2008  height:415.5pt;visibility:visible;mso-wrap-style:square'>
     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'>
    20092014 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image025.png" o:title=""/>
    2010 </v:shape><![endif]--><![if !vml]><img width=600 height=554
     2015</v:shape><![endif]--><![if !vml]><img width=700 height=599
    20112016src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
    20122017
    … …  
    20242029style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20252030mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    2026 tab). The atom positions I obtained have two atoms (O3 &amp; O4) not connected
    2027 to the sucrose molecule because they belong to neighboring molecules. We need
    2028 to discover the equivalent ones that belong to this molecule. Follow the steps:</p>
     2031tab). The atom positions I obtained in this charge flipping run have the
     2032sucrose molecule fragmented over several neighboring molecules. We need
     2033assemble these into a single molecule. Follow the steps:</p>
    20292034
    20302035<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2031 mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
     2036mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
    20322037"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2033 </span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    2034 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2035 mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> tab and select them
    2036 (hold the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2037 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ctrl</span></b>
    2038 key down and select the appropriate rows). </p>
     2038</span></span></span><![endif]>In the Atoms tab of the Data window do <b
     2039style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2040mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload
     2041draw <span class=GramE>atoms<span style='font-family:"Times New Roman",serif;
     2042font-weight:normal'>.</span></span></span></b> This ensures the drawing is
     2043up-to-date with the Atom list.</p>
    20392044
    20402045<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2041 mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
     2046mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
    20422047"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2043 </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    2044 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2045 mso-hansi-theme-font:minor-latin'>Edit/Fill unit cell</span></b>; new atoms
    2046 will appear at end of list and in the drawing. </p>
     2048</span></span></span><![endif]>Select one atom in one of the fragments (perhaps
     2049<span class=GramE>O(</span>1) in the drawing above as that is likely to be the
     2050bridging O-atom between the two rings of sucrose. With the Atoms table showing
     2051on the data window, use Shift-Left mouse button on the desired atom; it will
     2052turn green indicating selection.</p>
    20472053
    20482054<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2049 mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
     2055mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
    20502056"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2051 </span></span></span><![endif]>Select all the atoms in the <b style='mso-bidi-font-weight:
     2057</span></span></span><![endif]>Then in the Atoms menu do <b style='mso-bidi-font-weight:
    20522058normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2053 minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table by a
    2054 double click on upper left corner box of the table.</p>
    2055 
    2056 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2057 mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
    2058 "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2059 </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    2060 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2061 mso-hansi-theme-font:minor-latin'>Edit/Fill CN-sphere</span></b>; new atoms
    2062 will appear that are bonded to the molecule.</p>
    2063 
    2064 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2065 mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
    2066 "Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2067 </span></span></span><![endif]>Select these new atoms that are in the molecule;
    2068 they will probably be outside the unit cell box. Do this on the drawing with <b
    2069 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2070 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift left</span></b>
    2071 for the first one &amp; <b style='mso-bidi-font-weight:normal'><span
    2072 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2073 mso-hansi-theme-font:minor-latin'>Shift right</span></b> for the rest, they
    2074 will show in green. </p>
    2075 
    2076 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2077 mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
    2078 "Times New Roman"'><span style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2079 </span></span></span><![endif]>Look at the <b style='mso-bidi-font-weight:normal'><span
    2080 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2081 mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the
    2082 selections and make note of the <span class=SpellE><b style='mso-bidi-font-weight:
    2083 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2084 minor-latin;mso-hansi-theme-font:minor-latin'>Sym</span></b></span><b
    2085 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2086 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Op</span></b>
    2087 for each one. In my case they were “<b style='mso-bidi-font-weight:normal'><span
    2088 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2089 mso-hansi-theme-font:minor-latin'>2+1<span class=GramE>,0,0</span></span></b>”
    2090 for O(4) and “<b style='mso-bidi-font-weight:normal'><span style='font-family:
     2059minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b>;
     2060a popup dialog offering choices of distances (&amp; angles – not used). Press <b
     2061style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2062mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.</p>
     2063
     2064<p class=MsoNormal style='margin-left:.5in'>The atoms will automatically be
     2065reorganized into a single molecule and are ordered in the table according to
     2066connectivity.</p>
     2067
     2068<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2069 id="Picture_x0020_20" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:360.75pt;
     2070 height:312pt;visibility:visible;mso-wrap-style:square'>
     2071 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image026.png" o:title=""
     2072  croptop="14042f" cropbottom="14048f" cropleft="39221f" cropright="11359f"/>
     2073</v:shape><![endif]--><![if !vml]><img width=481 height=416
     2074src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
     2075
     2076<p class=MsoNormal>I’ve changed the style to balls &amp; sticks and added the
     2077atom names as labels.</p>
     2078
     2079<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'>
     2082 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/>
     2083</v:shape><![endif]--><![if !vml]><img width=700 height=598
     2084src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="_x0000_i1042"><![endif]></span></p>
     2085
     2086<p class=MsoNormal>To rename the atoms, select all the atoms (double click in
     2087the empty left upper square of the Atom table; the entries will turn blue or
     2088grey. Then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
    20912089"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2092 minor-latin'>2+2,-1,1</span></b>” for O(3). The first number is the symmetry
    2093 operator number and the 3 numbers after the ‘<b style='mso-bidi-font-weight:
    2094 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2095 minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’ are unit cell
    2096 translations.</p>
    2097 
    2098 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2099 mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
    2100 "Times New Roman"'><span style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2101 </span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    2102 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2103 mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab.</p>
    2104 
    2105 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2106 mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
    2107 "Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2108 </span></span></span><![endif]>Select an atom in turn that needs to be moved,
    2109 e.g. in my case <span class=GramE>O(</span>3) or O(4). </p>
    2110 
    2111 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2112 mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
    2113 "Times New Roman"'><span style='mso-list:Ignore'>9.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2114 </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    2115 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2116 mso-hansi-theme-font:minor-latin'>Edit/Transform atoms</span></b>, select the
    2117 operator and unit cell translations, then press <b style='mso-bidi-font-weight:
    2118 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2119 minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom
    2120 coordinates will be transformed.</p>
    2121 
    2122 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2123 mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
    2124 "Times New Roman"'><span style='mso-list:Ignore'>10.<span style='font:7.0pt "Times New Roman"'>&nbsp;
    2125 </span></span></span><![endif]>Repeat 8 &amp; 9 for any other atoms to be
    2126 moved.</p>
    2127 
    2128 <p class=MsoNormal style='margin-left:.5in'>This will complete the molecule
    2129 with the extra atoms. Do <b style='mso-bidi-font-weight:normal'><span
    2130 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2131 mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b> to see the
    2132 completed <span class=GramE>molecule.</span> I’ve made it a balls &amp; sticks
    2133 with names as labels.</p>
    2134 
    2135 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2136  id="Picture_x0020_20" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:7in;
    2137  height:6in;visibility:visible;mso-wrap-style:square'>
    2138  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image026.png" o:title=""
    2139   cropbottom="28348f" cropleft="41090f" cropright="9483f"/>
    2140 </v:shape><![endif]--><![if !vml]><img width=672 height=576
    2141 src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
     2090minor-latin'>Edit/Modify atom parameters</span></b>. Select <b
     2091style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2092mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Name</span></b>
     2093from the popup window and press <b style='mso-bidi-font-weight:normal'><span
     2094style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2095mso-hansi-theme-font:minor-latin'>OK</span></b>; you will be asked to confirm.
     2096The atoms will be renamed. </p>
     2097
     2098<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'>
     2101 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/>
     2102</v:shape><![endif]--><![if !vml]><img width=700 height=598
     2103src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
     2104
     2105<p class=MsoNormal>You can also reorder the atoms to make the connectivity
     2106conform to usual chemical naming rules; use the Alt key to pick &amp; place
     2107each atom to be moved just as we did with the Map peak results above.</p>
    21422108
    21432109<p class=MsoNormal>Save the project file; the next step is to complete the
    … …  
    21502116accurate and prepare a set of calculated structure factors needed to generate a
    21512117difference Fourier map good enough to maybe reveal the H atoms. There are a
    2152 number of steps needed to set all the controls from the previous Pawley refinement
    2153 to get a successful start for the Rietveld refinement.</p>
     2118number of steps needed to set all the controls from the previous Pawley
     2119refinement to get a successful start for the Rietveld refinement.</p>
    21542120
    21552121<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2156 mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
     2122mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
    21572123"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    21582124</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    … …  
    21652131
    21662132<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2167 mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
     2133mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
    21682134"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    21692135</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
    … …  
    21782144
    21792145<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2180 mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
     2146mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
    21812147"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    21822148</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
    … …  
    21992165
    22002166<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2201  id="_x0000_i1044" type="#_x0000_t75" style='width:525pt;height:450pt;
    2202  visibility:visible;mso-wrap-style:square'>
    2203  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/>
     2167 id="Picture_x0020_21" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
     2168 height:450pt;visibility:visible;mso-wrap-style:square'>
     2169 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image030.png" o:title=""/>
    22042170</v:shape><![endif]--><![if !vml]><img width=700 height=600
    2205 src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="_x0000_i1044"><![endif]></span></p>
     2171src="Charge%20Flipping%20-%20sucrose_files/image030.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
    22062172
    22072173<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
    … …  
    22252191
    22262192<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2227  id="Picture_x0020_22" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
     2193 id="Picture_x0020_24" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
    22282194 height:225pt;visibility:visible;mso-wrap-style:square'>
    2229  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/>
     2195 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/>
    22302196</v:shape><![endif]--><![if !vml]><img width=700 height=300
    2231 src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
     2197src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
    22322198
    22332199<p class=MsoNormal>To deal with the warning we need to set a “Hold” on one atom
    … …  
    22382204
    22392205<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2240  id="Picture_x0020_23" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:225pt;
    2241  height:187.5pt;visibility:visible;mso-wrap-style:square'>
    2242  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image030.png" o:title=""/>
    2243 </v:shape><![endif]--><![if !vml]><img width=300 height=250
    2244 src="Charge%20Flipping%20-%20sucrose_files/image030.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
    2245 
    2246 <p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
    2247 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2248 mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
    2249 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2250 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
    2251 class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will
    2252 fix the shift along y for the <span class=GramE>O(</span>1) atom.</p>
    2253 
    2254 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2255  id="Picture_x0020_53" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:259.5pt;
    2256  height:271.5pt;visibility:visible;mso-wrap-style:square'>
    2257  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/>
    2258 </v:shape><![endif]--><![if !vml]><img width=346 height=362
    2259 src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
    2260 
    2261 <p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
    2262 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2263 mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will
    2264 show the hold</p>
    2265 
    2266 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2267  id="Picture_x0020_54" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:225pt;
     2206 id="Picture_x0020_23" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:225pt;
    22682207 height:187.5pt;visibility:visible;mso-wrap-style:square'>
    22692208 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image032.png" o:title=""/>
    22702209</v:shape><![endif]--><![if !vml]><img width=300 height=250
    2271 src="Charge%20Flipping%20-%20sucrose_files/image032.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
     2210src="Charge%20Flipping%20-%20sucrose_files/image032.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
     2211
     2212<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
     2213style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2214mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
     2215style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2216mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
     2217class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will fix
     2218the 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'>
     2223 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title=""/>
     2224</v:shape><![endif]--><![if !vml]><img width=346 height=362
     2225src="Charge%20Flipping%20-%20sucrose_files/image033.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
     2226
     2227<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
     2228style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2229mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will
     2230show the hold</p>
     2231
     2232<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2233 id="Picture_x0020_27" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:225pt;
     2234 height:187.5pt;visibility:visible;mso-wrap-style:square'>
     2235 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image034.png" o:title=""/>
     2236</v:shape><![endif]--><![if !vml]><img width=300 height=250
     2237src="Charge%20Flipping%20-%20sucrose_files/image034.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
    22722238
    22732239<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
    … …  
    22972263class=SpellE>displ</span></span></b>. You can also include refinement of atom
    22982264thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
    2299 refinement improved slightly to Rwp~10.0%. Let’s see if a difference Fourier
    2300 map will show anything.<br>
    2301 Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2265refinement improved slightly to Rwp~10.0%. Next we should add the hydrogen
     2266atoms that are on carbon as these can be located from the molecular geometry.
     2267To do this do the following:</p>
     2268
     2269<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     2270
     2271<p class=MsoNormal>Go to the Atoms tab and select the <b style='mso-bidi-font-weight:
     2272normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2273minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column; a popup
     2274will appear. Select just the <b style='mso-bidi-font-weight:normal'><span
     2275style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2276mso-hansi-theme-font:minor-latin'>C</span></b> atoms; these will be highlighted
     2277in grey in the Atom table.</p>
     2278
     2279<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
     2280style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2281mso-hansi-theme-font:minor-latin'>Edit/Insert H atoms</span></b> from the Atoms
     2282menu; a Distance Angle Controls popup will appear. You can change radii and
     2283Bond search factor if needed (rarely). Press <b style='mso-bidi-font-weight:
     2284normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2285minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>. A new popup window
     2286will appear.<br>
     2287<span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_45"
     2288 o:spid="_x0000_i1035" type="#_x0000_t75" style='width:300pt;height:363.75pt;
     2289 visibility:visible;mso-wrap-style:square'>
     2290 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""/>
     2291</v:shape><![endif]--><![if !vml]><img width=400 height=485
     2292src="Charge%20Flipping%20-%20sucrose_files/image035.png" v:shapes="Picture_x0020_45"><![endif]></span><br>
     2293This offers the choice of how many H-atoms to be added for each atom in the
     2294table; the maximum is chosen for each atom. If the bonds are sufficiently short
     2295this may be fewer reflecting the possibility of sp<sup>2</sup> or <span
     2296class=SpellE>sp</span> bonding on the atom. You can override the choices made
     2297by default. You also can deselect some of the other attached atoms so they will
     2298not be used in the geometry calculations for H-atom placement (e.g. a metal
     2299atom in certain organometallics). When you are satisfied with the choices
     2300(actually no changes are needed in this case), press <b style='mso-bidi-font-weight:
     2301normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2302minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>. The structure will
     2303be redrawn with H-atoms shown as van der Waals spheres; they are appended to
     2304the 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'>
     2309 <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
     2312src="Charge%20Flipping%20-%20sucrose_files/image037.jpg" v:shapes="Picture_x0020_46"><![endif]></span></p>
     2313
     2314<p class=MsoNormal>These hydrogen atoms will better describe the scattering
     2315density in the vicinity of the carbon atoms; their positions need to be refined
     2316to find their better locations. Do <b style='mso-bidi-font-weight:normal'><span
     2317style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2318mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (the refinement
     2319flags are already set for this – NB: don’t be tempted to refine the H-atom
     2320positions as they are likely to move erratically). My result was Rwp~9.2% and
     2321the drawing is updated with the new atom positions (as van der Waals spheres).</p>
     2322
     2323<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'>
     2326 <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
     2329src="Charge%20Flipping%20-%20sucrose_files/image039.jpg" v:shapes="Picture_x0020_47"><![endif]></span></p>
     2330
     2331<p class=MsoNormal>Because the C-atoms have probably moved; the H-atoms (which
     2332were fixed) are now no longer in their optimal locations. From the Atom tab
     2333menu, do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2334mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/ Update
     2335H atoms</span></b>. This will shift their positions slightly. Repeat <b
     2336style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2337mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
     2338and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2339mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Update
     2340H atoms</span></b>; you should see no shift this time. (<span class=SpellE>Rwp</span>
     2341may be slightly higher; I got ~9.3%).</p>
     2342
     2343<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     2344
     2345<p class=MsoNormal>Now we have to find the hydrogens that are on oxygen; these
     2346cannot be geometrically located except that they are somewhere on a circle at
     2347the bonding distance from the O-atom. We need a difference Fourier map. Go to
     2348the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23022349mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose
    23032350General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
    23042351style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2305 mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway down
    2306 the window.</p>
     2352mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway
     2353down the window.</p>
    23072354
    23082355<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2309 mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
     2356mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
    23102357"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    23112358</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
    … …  
    23182365
    23192366<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2320 mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
     2367mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
    23212368"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    23222369</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
    … …  
    23262373mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
    23272374set from</span></b> item (the only choice). The Fourier calculation will use
    2328 the structure factors shown in the <b style='mso-bidi-font-weight:normal'><span
    2329 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2330 mso-hansi-theme-font:minor-latin'>Reflection list</span></b> item for this PWDR
    2331 data set.</p>
     2375the structure factors shown in the Reflection list item for this PWDR data set.</p>
    23322376
    23332377<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2334 mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
     2378mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
    23352379"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    23362380</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    … …  
    23452389
    23462390<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2347 mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
     2391mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
    23482392"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    23492393</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    … …  
    23552399the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23562400mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
    2357 to help clarify the view.</p>
    2358 
    2359 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2360  id="Picture_x0020_35" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:502.5pt;
    2361  height:435.75pt;visibility:visible;mso-wrap-style:square'>
    2362  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title=""
    2363   croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/>
    2364 </v:shape><![endif]--><![if !vml]><img width=670 height=581
    2365 src="Charge%20Flipping%20-%20sucrose_files/image034.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
    2366 
    2367 <p class=MsoNormal>What is drawn here are green dots whose size are
    2368 proportional to the electron density. There are peaks that might be H-atom
    2369 positions as well as features that suggest C &amp; O-atoms out of position.
    2370 Recall that the refinement was just done without any H-atoms; it will make the
    2371 best fit compensating for the missing H-atoms by displacing the C &amp; O atoms
    2372 in the direction of the missing H-atoms. </p>
     2401and shift the View Point (use right mouse button) to help clarify the view.
     2402Note that the map continues to show the density around the View Point even if
     2403it is outside the unit cell box.</p>
     2404
     2405<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2406 id="Picture_x0020_31" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:362.25pt;
     2407 height:308.25pt;visibility:visible;mso-wrap-style:square'>
     2408 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image040.png" o:title=""
     2409  croptop="10982f" cropbottom="17558f" cropleft="37484f" cropright="13065f"/>
     2410</v:shape><![endif]--><![if !vml]><img width=483 height=411
     2411src="Charge%20Flipping%20-%20sucrose_files/image041.jpg" v:shapes="Picture_x0020_31"><![endif]></span></p>
     2412
     2413<p class=MsoNormal>What is drawn here are green (&amp; red for negative) dots
     2414whose size are proportional to the electron density. There are peaks that might
     2415be H-atom positions as well as features that suggest O-atoms out of position.
     2416Recall that the refinement was just done without any H-atoms on the oxygen
     2417atoms; it will make the best fit compensating for the missing H-atoms by
     2418displacing the O atoms in the direction of the missing H-atoms. To add the OH
     2419atoms do the following:</p>
    23732420
    23742421<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2375 mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
     2422mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
    23762423"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    23772424</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    23782425style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2379 mso-hansi-theme-font:minor-latin'>Phases/sucrose Draw Atoms</span></b> tab.</p>
     2426mso-hansi-theme-font:minor-latin'>Phases/sucrose Atoms</span></b> tab.</p>
    23802427
    23812428<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2382 mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
     2429mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
    23832430"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2384 </span></span></span><![endif]>Select a C or O atom with possible H-atom
    2385 density nearby. It will appear green. Do <b style='mso-bidi-font-weight:normal'><span
    2386 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2387 mso-hansi-theme-font:minor-latin'>Edit/View point</span></b>; this will
    2388 position the cross on the selected atom.</p>
     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;
     2433mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b>
     2434column heading &amp; select <b style='mso-bidi-font-weight:normal'><span
     2435style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2436mso-hansi-theme-font:minor-latin'>O</span></b> atoms from the popup); all will
     2437turn grey.</p>
    23892438
    23902439<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2391 mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
     2440mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
    23922441"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2393 </span></span></span><![endif]>Using the mouse, position the multicolored cross
    2394 directly in the center of the nearby H atom peak. Rotate the drawing around
    2395 with the left mouse button and shift the cross with the right mouse button. You
    2396 can zoom in using the roll wheel on the mouse (or else use the <b
    2397 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2398 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Camera
    2399 distance</span></b> slider in the <b style='mso-bidi-font-weight:normal'><span
    2400 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2401 mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab if your mouse
    2402 lacks a wheel).</p>
    2403 
    2404 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2405  id="Picture_x0020_36" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:7in;
    2406  height:435.75pt;visibility:visible;mso-wrap-style:square'>
    2407  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""
    2408   croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/>
    2409 </v:shape><![endif]--><![if !vml]><img width=672 height=581
    2410 src="Charge%20Flipping%20-%20sucrose_files/image036.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
    2411 
    2412 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2413 mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
    2414 "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2415 </span></span></span><![endif]>Go to the Atoms tab and do <b style='mso-bidi-font-weight:
     2442</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
     2443style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2444mso-hansi-theme-font:minor-latin'>Edit/Insert H atoms</span></b> from the menu;
     2445a Distance Angle Controls popup will appear. You can change radii and Bond
     2446search factor if needed (rarely). Press <b style='mso-bidi-font-weight:normal'><span
     2447style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2448mso-hansi-theme-font:minor-latin'>Ok</span></b>. A new popup window will appear</p>
     2449
     2450<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2451 id="Picture_x0020_32" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:300pt;
     2452 height:363.75pt;visibility:visible;mso-wrap-style:square'>
     2453 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/>
     2454</v:shape><![endif]--><![if !vml]><img width=400 height=485
     2455src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
     2456
     2457<p class=MsoNormal style='margin-left:.5in'>This offers the choice of how many
     2458H-atoms to be added for each O-atom in the table; one is chosen in this case
     2459for each atom. Press <b style='mso-bidi-font-weight:normal'><span
     2460style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2461mso-hansi-theme-font:minor-latin'>Ok</span></b>. The structure will be redrawn
     2462showing the added H-atoms.</p>
     2463
     2464<p class=MsoNormal style='margin-left:.5in'><o:p>&nbsp;</o:p></p>
     2465
     2466<p class=MsoNormal style='margin-left:.5in'>These OH hydrogens are found by
     2467finding the highest point in the delta-F map for all possible orientations of
     2468this bond at a fixed angle (109.5°). The new hydrogen atoms are named in
     2469sequence and are appended to the end of the Atom list.</p>
     2470
     2471<p class=MsoNormal style='margin-left:.5in'><o:p>&nbsp;</o:p></p>
     2472
     2473<p class=MsoNormal>Do the set of <b style='mso-bidi-font-weight:normal'><span
     2474style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2475mso-hansi-theme-font:minor-latin'>Calculate/Refine, Edit/Update H atoms</span></b>
     2476at least twice to finish this stage in the structure analysis; end with a <b
     2477style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2478mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>.
     2479My <span class=SpellE>Rwp</span> was ~8.14% with all the H-atoms included (but
     2480not refined). The fit looks pretty good</p>
     2481
     2482<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2483 id="Picture_x0020_40" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
     2484 height:450pt;visibility:visible;mso-wrap-style:square'>
     2485 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image043.png" o:title=""/>
     2486</v:shape><![endif]--><![if !vml]><img width=700 height=600
     2487src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
     2488
     2489<h2>Step 6: Final refinement</h2>
     2490
     2491<p class=MsoNormal>Looking at the fit, there may be room for improvement. First
     2492we need to change the profile model to include crystallite size and <span
     2493class=SpellE>mustrain</span> broadening. Go to <b style='mso-bidi-font-weight:
    24162494normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2417 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>,
    2418 a white ball will appear at the selected position and an H-atom (name = <b
    2419 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2420 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>)
    2421 will be appended to the end of the atom list. Repeat steps 1-4 for as many
    2422 recognizable H-atom positions you can find; the goal is to find all 22 of them
    2423 (you probably will find less than that, but you could guess many of the rest).
    2424 I easily found all but 5 of them.</p>
    2425 
    2426 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2427  id="Picture_x0020_38" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:7in;
    2428  height:427.5pt;visibility:visible;mso-wrap-style:square'>
    2429  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image037.png" o:title=""
    2430   croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/>
    2431 </v:shape><![endif]--><![if !vml]><img width=672 height=570
    2432 src="Charge%20Flipping%20-%20sucrose_files/image038.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
    2433 
    2434 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    2435 mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
    2436 "Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2437 </span></span></span><![endif]>Change their <b style='mso-bidi-font-weight:
    2438 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2439 minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> to <b
    2440 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2441 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>,
    2442 they will be renamed and make then all ball &amp; stick. Do a <b
    2443 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2444 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    2445 there should be a drop in <span class=SpellE>Rwp</span>. Then repeat the <b
    2446 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2447 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier
    2448 map</span></b> in the <b style='mso-bidi-font-weight:normal'><span
    2449 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2450 mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust the <b
    2451 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2452 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
    2453 level</span></b> and <b style='mso-bidi-font-weight:normal'><span
    2454 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2455 mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for
    2456 the remaining H-atoms; you may have to guess positions for some of them using
    2457 known stereochemistry rules. My model looked like</p>
    2458 
    2459 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2460  id="Picture_x0020_39" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:502.5pt;
    2461  height:421.5pt;visibility:visible;mso-wrap-style:square'>
    2462  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image039.png" o:title=""
    2463   croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/>
    2464 </v:shape><![endif]--><![if !vml]><img width=670 height=562
    2465 src="Charge%20Flipping%20-%20sucrose_files/image040.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
    2466 
    2467 <p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    2468 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2469 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> to finish this
    2470 stage in the structure analysis. My <span class=SpellE>Rwp</span> was ~8.02%
    2471 with all the H-atoms included (but not refined). The fit looks pretty good</p>
    2472 
    2473 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2474  id="Picture_x0020_40" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
    2475  height:450pt;visibility:visible;mso-wrap-style:square'>
    2476  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image041.png" o:title=""/>
    2477 </v:shape><![endif]--><![if !vml]><img width=700 height=600
    2478 src="Charge%20Flipping%20-%20sucrose_files/image041.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
    2479 
    2480 <h2>Step 6: Final refinement</h2>
    2481 
    2482 <p class=MsoNormal>Looking at the fit, there may be room for improvement and
    2483 we’d like to refine the H-atom positions. First we need to change the profile
    2484 model to include crystallite size and <span class=SpellE>mustrain</span>
    2485 broadening. Go to <b style='mso-bidi-font-weight:normal'><span
    2486 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2487 mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>, set <b
    2488 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2495minor-latin;mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>,
     2496set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    24892497mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
    24902498and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    … …  
    25142522
    25152523<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2516  id="Picture_x0020_41" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:480pt;
     2524 id="Picture_x0020_41" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:480pt;
    25172525 height:339pt;visibility:visible;mso-wrap-style:square'>
    2518  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/>
     2526 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image044.png" o:title=""/>
    25192527</v:shape><![endif]--><![if !vml]><img width=640 height=452
    2520 src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
     2528src="Charge%20Flipping%20-%20sucrose_files/image044.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
    25212529
    25222530<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    … …  
    25242532mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
    25252533class=SpellE>Rwp</span> will start out high but should converge to where it was
    2526 before this change. I got 8.08% and the <b style='mso-bidi-font-weight:normal'><span
     2534before this change. I got 8.09% and the <b style='mso-bidi-font-weight:normal'><span
    25272535style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    25282536mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>
    25292537
    25302538<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2531  id="Picture_x0020_42" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:480pt;
     2539 id="Picture_x0020_42" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:480pt;
    25322540 height:334.5pt;visibility:visible;mso-wrap-style:square'>
    2533  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image043.png" o:title=""/>
     2541 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image045.png" o:title=""/>
    25342542</v:shape><![endif]--><![if !vml]><img width=640 height=446
    2535 src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
     2543src="Charge%20Flipping%20-%20sucrose_files/image045.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
    25362544
    25372545<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
    … …  
    25442552mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
    25452553phenomenological model for <span class=SpellE>microstrain</span> which has 9
    2546 terms for monoclinic structures. Check all the boxes for it.</p>
    2547 
    2548 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2549  id="Picture_x0020_43" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:480pt;
    2550  height:303.75pt;visibility:visible;mso-wrap-style:square'>
    2551  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image044.png" o:title=""/>
    2552 </v:shape><![endif]--><![if !vml]><img width=640 height=405
    2553 src="Charge%20Flipping%20-%20sucrose_files/image044.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
     2554terms for monoclinic structures. Check all the boxes for it and press <b
     2555style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2556mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reset</span></b>.
     2557This will convert the isotropic strain value to the equivalent generalized
     2558values.</p>
     2559
     2560<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2561 id="Picture_x0020_55" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:402pt;
     2562 height:375pt;visibility:visible;mso-wrap-style:square'>
     2563 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image046.png" o:title=""/>
     2564</v:shape><![endif]--><![if !vml]><img width=536 height=500
     2565src="Charge%20Flipping%20-%20sucrose_files/image046.png" v:shapes="Picture_x0020_55"><![endif]></span></p>
    25542566
    25552567<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    … …  
    25692581
    25702582<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2571  id="Picture_x0020_45" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:480pt;
    2572  height:305.25pt;visibility:visible;mso-wrap-style:square'>
    2573  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image045.png" o:title=""/>
    2574 </v:shape><![endif]--><![if !vml]><img width=640 height=407
    2575 src="Charge%20Flipping%20-%20sucrose_files/image045.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
    2576 
    2577 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    2578 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2579 mso-hansi-theme-font:minor-latin;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2580  id="Picture_x0020_47" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
     2583 id="Picture_x0020_56" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:402pt;
     2584 height:375pt;visibility:visible;mso-wrap-style:square'>
     2585 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image047.png" o:title=""/>
     2586</v:shape><![endif]--><![if !vml]><img width=536 height=500
     2587src="Charge%20Flipping%20-%20sucrose_files/image047.png" v:shapes="Picture_x0020_56"><![endif]></span></p>
     2588
     2589<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2590 id="Picture_x0020_58" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
    25812591 height:450pt;visibility:visible;mso-wrap-style:square'>
    2582  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image046.png" o:title=""/>
     2592 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image048.png" o:title=""/>
    25832593</v:shape><![endif]--><![if !vml]><img width=700 height=600
    2584 src="Charge%20Flipping%20-%20sucrose_files/image046.png" v:shapes="Picture_x0020_47"><![endif]></span></b></p>
    2585 
    2586 <p class=MsoNormal>Before refining H-atom positions it would be wise to create
    2587 restraints on their bond distances and angles. Locate <b style='mso-bidi-font-weight:
    2588 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2589 minor-latin;mso-hansi-theme-font:minor-latin'>Restraints</span></b> in the main
    2590 GSAS-II data tree; there will be an almost blank window telling you there are
    2591 no bond restraints for sucrose. Do <b style='mso-bidi-font-weight:normal'><span
    2592 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2593 mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
    2594 will appear asking for the origin atom for the bond. </p>
    2595 
    2596 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2597  id="Picture_x0020_48" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:259.5pt;
    2598  height:252pt;visibility:visible;mso-wrap-style:square'>
    2599  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image047.png" o:title=""/>
    2600 </v:shape><![endif]--><![if !vml]><img width=346 height=336
    2601 src="Charge%20Flipping%20-%20sucrose_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
    2602 
    2603 <p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
    2604 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2605 mso-hansi-theme-font:minor-latin'>all H</span></b> and press <b
    2606 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2607 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    2608 A new dialog box will appear asking for the target atoms for the bonds.</p>
    2609 
    2610 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2611  id="Picture_x0020_49" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:259.5pt;
    2612  height:252pt;visibility:visible;mso-wrap-style:square'>
    2613  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image048.png" o:title=""/>
    2614 </v:shape><![endif]--><![if !vml]><img width=346 height=336
    2615 src="Charge%20Flipping%20-%20sucrose_files/image048.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
    2616 
    2617 <p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
    2618 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2619 mso-hansi-theme-font:minor-latin'>all C</span></b> and <b style='mso-bidi-font-weight:
    2620 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2621 minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b> and a third
    2622 dialog box appears asking for the bond length</p>
    2623 
    2624 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2625  id="Picture_x0020_50" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:147pt;
    2626  height:78.75pt;visibility:visible;mso-wrap-style:square'>
    2627  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image049.png" o:title=""/>
    2628 </v:shape><![endif]--><![if !vml]><img width=196 height=105
    2629 src="Charge%20Flipping%20-%20sucrose_files/image049.png" v:shapes="Picture_x0020_50"><![endif]></span><span
    2630 style='mso-spacerun:yes'> </span></p>
    2631 
    2632 <p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
    2633 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2634 mso-hansi-theme-font:minor-latin'>1.09</span></b> and press <b
    2635 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2636 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    2637 I got a short list of 8 H-C and H-O restraints, but I expect 22 of them. Change
    2638 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2639 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Search range</span></b>
    2640 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2641 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.5</span></b>
    2642 and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2643 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2644 minor-latin'>Edit/Add restraints</span></b>. There are now 22 restraints on H-C
    2645 and H-O bond lengths.</p>
    2646 
    2647 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2648  id="Picture_x0020_51" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:450pt;
    2649  height:423pt;visibility:visible;mso-wrap-style:square'>
    2650  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image050.png" o:title=""/>
    2651 </v:shape><![endif]--><![if !vml]><img width=600 height=564
    2652 src="Charge%20Flipping%20-%20sucrose_files/image050.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
    2653 
    2654 <p class=MsoNormal>Next select the <b style='mso-bidi-font-weight:normal'><span
    2655 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2656 mso-hansi-theme-font:minor-latin'>Angle restraints</span></b> tab and again
    2657 there aren’t any. Do <b style='mso-bidi-font-weight:normal'><span
    2658 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2659 mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
    2660 will appear asking for the A atom in the angle A-B-C. Select <b
    2661 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2662 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all H</span></b>.
    2663 The next dialog asks for the B atom in the A-B-C angle, select <b
    2664 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2665 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all C</span></b>
    2666 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2667 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b>.
    2668 The third dialog asks for the angle and has a default of <b style='mso-bidi-font-weight:
    2669 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2670 minor-latin;mso-hansi-theme-font:minor-latin'>109.54</span></b>. This is the
    2671 tetrahedral angle so just press <b style='mso-bidi-font-weight:normal'><span
    2672 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2673 mso-hansi-theme-font:minor-latin'>OK</span></b>. 36 restraints will be listed;
    2674 they are listed in order of the B atom. O-atoms should have one angle apiece;
    2675 C-atoms will have more. </p>
    2676 
    2677 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2678  id="Picture_x0020_52" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:450pt;
    2679  height:365.25pt;visibility:visible;mso-wrap-style:square'>
    2680  <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image051.png" o:title=""/>
    2681 </v:shape><![endif]--><![if !vml]><img width=600 height=487
    2682 src="Charge%20Flipping%20-%20sucrose_files/image051.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
    2683 
    2684 <p class=MsoNormal>Now go back the <b style='mso-bidi-font-weight:normal'><span
    2685 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2686 mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab in <b style='mso-bidi-font-weight:
    2687 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2688 minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>, select
    2689 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2690 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>
    2691 from the dialog box by double clicking on the <b style='mso-bidi-font-weight:
    2692 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2693 minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column. Then do <b
    2694 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2695 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Set
    2696 atom refinement flags</span></b>. Select <b style='mso-bidi-font-weight:normal'><span
    2697 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2698 mso-hansi-theme-font:minor-latin'>X-coordinates</span></b>; this will set those
    2699 for all H-atoms. Now do <b style='mso-bidi-font-weight:normal'><span
    2700 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2701 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>, the console will
    2702 list progress on the “Penalty function” (i.e. the restraints) and the <span
    2703 class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase the <b
    2704 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2705 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Restraint
    2706 weight factors</span></b> to tighten them up at some expense in <span
    2707 class=SpellE>Rwp</span>. In the end I chose <b style='mso-bidi-font-weight:
    2708 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2709 minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b> for both <b
    2710 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2711 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond</span></b>
    2712 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2713 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b>
    2714 restraints to give a final <span class=SpellE>Rwp</span> ~7.1%. NB: the H-atom
    2715 positions may not be correct even though the refinement apparently succeeded.
    2716 You should check that the OH ones all give reasonable H-bonds to neighboring O-atoms.
    2717 As this is powder data such changes will hardly affect the fit but will be more
    2718 satisfying. At present such checking is outside the scope of GSAS-II.</p>
    2719 
    2720 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    2721 
    2722 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
     2594src="Charge%20Flipping%20-%20sucrose_files/image048.png" v:shapes="Picture_x0020_58"><![endif]></span></p>
     2595
     2596<p class=MsoNormal>This completes the exercise.</p>
    27232597
    27242598</div>
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