source: Tutorials/CFXraySingleCrystal/CFSingleCrystal.htm @ 2099

Last change on this file since 2099 was 2099, checked in by vondreele, 6 years ago

add single crystal tutorial

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413  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
414  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
415  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
416  <w:LsdException Locked="false" Priority="34" QFormat="true"
417   Name="List Paragraph"/>
418  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
419  <w:LsdException Locked="false" Priority="30" QFormat="true"
420   Name="Intense Quote"/>
421  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
422  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
423  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
424  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
425  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
426  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
427  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
428  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
429  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
430  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
431  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
432  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
433  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
434  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
435  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
436  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
437  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
438  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
439  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
440  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
441  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
442  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
443  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
444  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
445  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
446  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
447  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
448  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
449  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
450  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
451  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
452  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
453  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
454  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
455  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
456  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
457  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
458  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
459  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
460  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
461  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
462  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
463  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
464  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
465  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
466  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
467  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
468  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
469  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
470  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
471  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
472  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
473  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
474  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
475  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
476  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
477  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
478  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
479  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
480  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
481  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
482  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
483  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
484  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
485  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
486  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
487  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
488  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
489  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
490  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
491  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
492  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
493  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
494  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
495  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
496  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
497  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
498  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
499  <w:LsdException Locked="false" Priority="19" QFormat="true"
500   Name="Subtle Emphasis"/>
501  <w:LsdException Locked="false" Priority="21" QFormat="true"
502   Name="Intense Emphasis"/>
503  <w:LsdException Locked="false" Priority="31" QFormat="true"
504   Name="Subtle Reference"/>
505  <w:LsdException Locked="false" Priority="32" QFormat="true"
506   Name="Intense Reference"/>
507  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
508  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
509   UnhideWhenUsed="true" Name="Bibliography"/>
510  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
511   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
512  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
513  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
514  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
515  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
516  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
517  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
518  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
519  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
520  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
521  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
522  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
523  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
524  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
525  <w:LsdException Locked="false" Priority="46"
526   Name="Grid Table 1 Light Accent 1"/>
527  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
528  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
529  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
530  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
531  <w:LsdException Locked="false" Priority="51"
532   Name="Grid Table 6 Colorful Accent 1"/>
533  <w:LsdException Locked="false" Priority="52"
534   Name="Grid Table 7 Colorful Accent 1"/>
535  <w:LsdException Locked="false" Priority="46"
536   Name="Grid Table 1 Light Accent 2"/>
537  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
538  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
539  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
540  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
541  <w:LsdException Locked="false" Priority="51"
542   Name="Grid Table 6 Colorful Accent 2"/>
543  <w:LsdException Locked="false" Priority="52"
544   Name="Grid Table 7 Colorful Accent 2"/>
545  <w:LsdException Locked="false" Priority="46"
546   Name="Grid Table 1 Light Accent 3"/>
547  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
548  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
549  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
550  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
551  <w:LsdException Locked="false" Priority="51"
552   Name="Grid Table 6 Colorful Accent 3"/>
553  <w:LsdException Locked="false" Priority="52"
554   Name="Grid Table 7 Colorful Accent 3"/>
555  <w:LsdException Locked="false" Priority="46"
556   Name="Grid Table 1 Light Accent 4"/>
557  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
558  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
559  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
560  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
561  <w:LsdException Locked="false" Priority="51"
562   Name="Grid Table 6 Colorful Accent 4"/>
563  <w:LsdException Locked="false" Priority="52"
564   Name="Grid Table 7 Colorful Accent 4"/>
565  <w:LsdException Locked="false" Priority="46"
566   Name="Grid Table 1 Light Accent 5"/>
567  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
568  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
569  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
570  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
571  <w:LsdException Locked="false" Priority="51"
572   Name="Grid Table 6 Colorful Accent 5"/>
573  <w:LsdException Locked="false" Priority="52"
574   Name="Grid Table 7 Colorful Accent 5"/>
575  <w:LsdException Locked="false" Priority="46"
576   Name="Grid Table 1 Light Accent 6"/>
577  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
578  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
579  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
580  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
581  <w:LsdException Locked="false" Priority="51"
582   Name="Grid Table 6 Colorful Accent 6"/>
583  <w:LsdException Locked="false" Priority="52"
584   Name="Grid Table 7 Colorful Accent 6"/>
585  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
586  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
587  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
588  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
589  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
590  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
591  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
592  <w:LsdException Locked="false" Priority="46"
593   Name="List Table 1 Light Accent 1"/>
594  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
595  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
596  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
597  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
598  <w:LsdException Locked="false" Priority="51"
599   Name="List Table 6 Colorful Accent 1"/>
600  <w:LsdException Locked="false" Priority="52"
601   Name="List Table 7 Colorful Accent 1"/>
602  <w:LsdException Locked="false" Priority="46"
603   Name="List Table 1 Light Accent 2"/>
604  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
605  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
606  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
607  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
608  <w:LsdException Locked="false" Priority="51"
609   Name="List Table 6 Colorful Accent 2"/>
610  <w:LsdException Locked="false" Priority="52"
611   Name="List Table 7 Colorful Accent 2"/>
612  <w:LsdException Locked="false" Priority="46"
613   Name="List Table 1 Light Accent 3"/>
614  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
615  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
616  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
617  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
618  <w:LsdException Locked="false" Priority="51"
619   Name="List Table 6 Colorful Accent 3"/>
620  <w:LsdException Locked="false" Priority="52"
621   Name="List Table 7 Colorful Accent 3"/>
622  <w:LsdException Locked="false" Priority="46"
623   Name="List Table 1 Light Accent 4"/>
624  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
625  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
626  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
627  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
628  <w:LsdException Locked="false" Priority="51"
629   Name="List Table 6 Colorful Accent 4"/>
630  <w:LsdException Locked="false" Priority="52"
631   Name="List Table 7 Colorful Accent 4"/>
632  <w:LsdException Locked="false" Priority="46"
633   Name="List Table 1 Light Accent 5"/>
634  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
635  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
636  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
637  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
638  <w:LsdException Locked="false" Priority="51"
639   Name="List Table 6 Colorful Accent 5"/>
640  <w:LsdException Locked="false" Priority="52"
641   Name="List Table 7 Colorful Accent 5"/>
642  <w:LsdException Locked="false" Priority="46"
643   Name="List Table 1 Light Accent 6"/>
644  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
645  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
646  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
647  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
648  <w:LsdException Locked="false" Priority="51"
649   Name="List Table 6 Colorful Accent 6"/>
650  <w:LsdException Locked="false" Priority="52"
651   Name="List Table 7 Colorful Accent 6"/>
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1031</head>
1032
1033<body lang=EN-US style='tab-interval:.5in'>
1034
1035<div class=WordSection1>
1036
1037<h1>Single crystal structure determination and refinement with X-ray data in
1038GSAS-II</h1>
1039
1040<h2>Introduction</h2>
1041
1042<p class=MsoNormal>In this exercise we will use a set of X-ray single crystal
1043structure factors to solve the structure of <span class=SpellE>dipyridyl</span>
1044disulfide by charge flipping and then refine the structure by least-squares.
1045The structure will be completed by adding the requisite hydrogen atoms and by
1046using anisotropic thermal parameters for the heavier atoms. The structure was
1047originally solved by <span class=SpellE>Raghavan</span> &amp; <span
1048class=SpellE>Seff</span>, <span class=SpellE>Acta</span> <span class=SpellE>Cryst</span>.
1049B33, 386-391 (1977) in the space group P2<sub>1</sub>/c with one disordered
1050pyridine ring with indications that the true space group was P2<sub>1</sub>. It
1051was subsequently reinvestigated by Young (2014….) who found that the true space
1052group was P2<sub>1</sub> with 4 molecules in the asymmetric unit. The data used
1053in the latter analysis is what is used here and is provided as <span
1054class=GramE>a</span> “<span class=SpellE>fcf</span>” file obtained after
1055structure analysis by Shelx-97; the structure factors are scaled to those
1056calculated from the structure. We will solve the P 2<sub>1</sub>/c structure
1057first.</p>
1058
1059<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1060
1061<p class=MsoNormal>Note that menu entries and user input are shown in bold face
1062below as <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1063mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1064Calibri;mso-bidi-theme-font:minor-latin'>Help/About GSAS-II</span></b>, which
1065lists first the name of the menu (here <b style='mso-bidi-font-weight:normal'><span
1066style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1067mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1068minor-latin'>Help</span></b>) and second the name of the entry in the menu
1069(here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1070mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1071Calibri;mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>). If you have
1072not done so already, start GSAS-II</p>
1073
1074<h2>Step 1. Input phase information</h2>
1075
1076<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
1077style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1078style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1079the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1080mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1081Calibri;mso-bidi-theme-font:minor-latin'>Data/Add phase</span></b> menu item
1082add a new phase into the current GSAS-II project. A popup window will appear
1083asking for a phase name; I entered <b style='mso-bidi-font-weight:normal'><span
1084style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1085mso-hansi-theme-font:minor-latin'>SS <span class=SpellE>dipyridyl</span></span></b>;
1086press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1087mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
1088when done. Select <b style='mso-bidi-font-weight:normal'><span
1089style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1090mso-hansi-theme-font:minor-latin'>Loaded Data/Phases/SS <span class=SpellE>dipyridyl</span></span></b>
1091from the GSAS-II Data tree window. The General tab for Phase Data will appear.</p>
1092
1093<p class=MsoListParagraph><span style='mso-no-proof:yes'><v:shapetype id="_x0000_t75"
1094 coordsize="21600,21600" o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe"
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1111 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1112 <o:lock v:ext="edit" aspectratio="t"/>
1113</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1042" type="#_x0000_t75"
1114 style='width:393pt;height:230.25pt;visibility:visible;mso-wrap-style:square'>
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1117
1118<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
1119style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1120style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
1121the space group <b style='mso-bidi-font-weight:normal'><span style='font-family:
1122"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1123minor-latin'>P 21/c</span></b> (don’t forget the space between P &amp; 21/c)
1124&amp; press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1125"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1126minor-latin'>Enter</span></b>. A Space Group Information popup window will
1127appear; press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1128"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1129minor-latin'>OK</span></b>. The General window will be refreshed showing only
1130the needed lattice <span style='mso-no-proof:yes'>parameters for P 21/c.</span></p>
1131
1132<p class=MsoListParagraph><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_3"
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1134 visibility:visible;mso-wrap-style:square'>
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1136</v:shape></span></p>
1137
1138<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
1139style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1140style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
1141<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1142mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>15.8489</span></b>,
1143<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1144mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5.5008</span></b>,
1145<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1146mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>23.118</span></b>,
1147and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1148mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>96.9160</span></b>
1149for a, b, c and beta, respectively; the unit cell volume will be recalculated
1150at each entry.</p>
1151
1152<h2>Step 2. Import structure factors </h2>
1153
1154<p class=MsoNormal>There are two parts to this step: one is to import the data
1155and the second is to connect the data with the phase within GSAS-II.</p>
1156
1157<p class=MsoNormal>To do these, do <b style='mso-bidi-font-weight:normal'><span
1158style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1159mso-hansi-theme-font:minor-latin'>Import/Structure factor/from CIF file</span></b>
1160from the main GSAS-II data tree window menu. A file selection dialog will
1161appear; find <b style='mso-bidi-font-weight:normal'><span style='font-family:
1162"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1163minor-latin'>exercises\CF <span class=SpellE>Xray</span> single
1164crystal\S2dipyridyl.fcf</span></b> and press <b style='mso-bidi-font-weight:
1165normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1166minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>. A popup window
1167asking if this is the file you want; press <span class=GramE><b
1168style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1169mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b></span>.
1170After a pause while the file is read a new popup will appear offering the
1171chance to rename the structure factor set; press <b style='mso-bidi-font-weight:
1172normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1173minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. After some time a
1174new popup will appear to <span style='mso-bidi-font-family:"Times New Roman"'>Add
1175the new structure factor set</span> to the SS <span class=SpellE>dipyridyl</span>
1176phase. Select the phase and press <b style='mso-bidi-font-weight:normal'><span
1177style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1178mso-hansi-theme-font:minor-latin'>OK</span></b>. The plot will show a rectangular
1179array of circles for the hk0 reflection layer; select the plot &amp; press <b
1180style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1181mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k</span></b>
1182to get an h0l layer.</p>
1183
1184<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_2"
1185 o:spid="_x0000_i1040" type="#_x0000_t75" style='width:5in;height:309pt;
1186 visibility:visible;mso-wrap-style:square'>
1187 <v:imagedata src="CFSingleCrystal_files/image003.png" o:title=""/>
1188</v:shape></span></p>
1189
1190<p class=MsoNormal>Because the <span class=SpellE>fcf</span> file has both
1191observed and calculated structure factors, the plot shows a small R value for
1192the layer. The observed structure factors are shown as blue rings, the
1193calculated ones as green rings and a small green or red dot may appear at each
1194ring center showing <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>. If
1195the reflection data file had only observed structure factors then only blue
1196rings will be seen. You can explore the plot options in the ‘<b
1197style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1198mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>K</span></b>’
1199box in the plot toolbar.</p>
1200
1201<h2>Step 3. Setup for charge flipping</h2>
1202
1203<p class=MsoNormal>To solve (again) this crystal structure we will use charge
1204flipping. Charge flipping in GSAS-II is implemented to solve the crystal
1205structure without consideration of space group symmetry. To do this it operates
1206on the entire unit cell volume to a selected resolution (usually 0.5<span
1207style='mso-bidi-font-family:"Times New Roman"'>Å</span>) using fast <span
1208class=SpellE><span class=GramE>fourier</span></span> transform techniques. This
1209requires a set of structure factors in an array of the same dimensions as the
1210density array covering the unit cell (i.e. a box bounded by ~0.5<span
1211style='mso-bidi-font-family:"Times New Roman"'>Å</span> resolution). The space
1212group symmetry is applied to the observed structure factors to create a full
1213sphere which is then zero filled out to the 0.5<span style='mso-bidi-font-family:
1214"Times New Roman"'>Å</span> resolution bounded box. To be reasonably assured of
1215success, the observed structure factors should extend to ~1<span
1216style='mso-bidi-font-family:"Times New Roman"'>Å</span> resolution; we have
1217that here for this example. To begin select <b style='mso-bidi-font-weight:
1218normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1219minor-latin;mso-hansi-theme-font:minor-latin'>Phases/SS <span class=SpellE>dipyridyl</span></span></b>
1220from the GSAS-II data tree; the General tab will be shown</p>
1221
1222<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_4"
1223 o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;height:300.75pt;
1224 visibility:visible;mso-wrap-style:square'>
1225 <v:imagedata src="CFSingleCrystal_files/image004.png" o:title=""/>
1226</v:shape></span></p>
1227
1228<p class=MsoNormal>Find the <b style='mso-bidi-font-weight:normal'><span
1229style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1230mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> and change
1231the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1232mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak cutoff
1233%</span></b> to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1234"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1235minor-latin'>10</span></b>; then immediately below find the <b
1236style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1237mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Charge flip
1238controls</span></b>. Press <b style='mso-bidi-font-weight:normal'><span
1239style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1240mso-hansi-theme-font:minor-latin'>Select reflection sets</span></b>, pick <b
1241style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1242mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>HKLF
1243S2dipyridyl.fcf:1a</span></b> from the list (the only one) and press <b
1244style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1245mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1246If you had multiple data sets for this phase, you can pick more than one and
1247GSAS-II will use a “last one in” process for assembling the reflection set to
1248use for charge flipping. There are four more settings to consider: 1) <span
1249class=SpellE>kMax</span> controls the upper cutoff for charge flipping; if the
1250density is &gt; k-Max*<span style='font-family:Symbol'>s</span><sub><span
1251style='font-family:Symbol;mso-bidi-font-family:"Times New Roman"'>r</span></sub>
1252(map standard deviation) then flip the charge. This prevents the “Uranium
1253solution” sometimes found where all the density is concentrated in a single
1254peak. A useful guide is to use twice the largest atomic number of any element
1255in your structure. For equal atom problems use 12-15; adjust upward for
1256structures with heavy &amp; light atoms. In this case, set <b style='mso-bidi-font-weight:
1257normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1258minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b> to <b
1259style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1260mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>30.0</span></b>
1261to allow the S atom to appear. 2) k-Factor controls the lower level for charge
1262flipping; if the density is &lt; k-Factor*<span style='font-family:Symbol'>s</span><sub><span
1263style='font-family:Symbol;mso-bidi-font-family:"Times New Roman"'>r</span></sub><span
1264style='mso-bidi-font-family:"Times New Roman"'> then flip the charge. The
1265default value seems to work pretty well; I’d only change it if the charge
1266flipping is having trouble solving the structure. 3) Resolution selects the
1267spacing between map points. 0.5Å is sufficient in most cases. Choosing a
1268smaller value requires more map points (NB: GSAS-II uses the entire unit cell
1269volume for charge flipping) and thus will require more structure factors since
1270the fast <span class=SpellE>fourier</span> algorithm requires the same size
1271arrays in both real space and reciprocal space. This will slow down the charge
1272flip process. 4) Normalizing element selects a form factor to rescale the
1273structure factors thus “sharpening” the density map. I suggest trying </span><span
1274class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1275"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1276minor-latin;mso-bidi-font-family:"Times New Roman"'>None</span></b></span><span
1277style='mso-bidi-font-family:"Times New Roman"'> first, otherwise select a
1278representative element (really doesn’t matter which).<o:p></o:p></span></p>
1279
1280<h2 style='page-break-after:avoid'>Step 4. Charge flipping</h2>
1281
1282<p class=MsoNormal>With the controls all set you can now do charge flipping;
1283from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1284mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1285tab do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1286mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1287flipping</span></b>. A progress bar popup will appear showing the residual
1288between the observed structure factors and those obtained from the inverse <span
1289class=SpellE><span class=GramE>fourier</span></span> transform of the last
1290flipped density map. It should quickly decrease to the ~20% range and level out
1291indicating a good charge flip solution. When it has reached this, press <span
1292class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1293"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1294minor-latin'>Cancel</span></b></span> to stop the process.</p>
1295
1296<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_6"
1297 o:spid="_x0000_i1038" type="#_x0000_t75" style='width:274.5pt;height:135pt;
1298 visibility:visible;mso-wrap-style:square'>
1299 <v:imagedata src="CFSingleCrystal_files/image005.png" o:title=""/>
1300</v:shape></span></p>
1301
1302<p class=MsoNormal>The console window will show something like</p>
1303
1304<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_7"
1305 o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;height:124.5pt;
1306 visibility:visible;mso-wrap-style:square'>
1307 <v:imagedata src="CFSingleCrystal_files/image006.png" o:title=""/>
1308</v:shape></span></p>
1309
1310<p class=MsoNormal>There may be a pause at <b style='mso-bidi-font-weight:normal'><span
1311style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1312mso-hansi-theme-font:minor-latin'>Begin <span class=SpellE><span class=GramE>fourier</span></span>
1313map search</span></b> before it finishes. Provided is a summary of the charge
1314flip calculation (time, map size, density range &amp; structure factor
1315residual). The map offset is discovered by an analysis of the reflection phases
1316with respect to how they should be distributed for your chosen space group.
1317These offsets are then applied to shift the map so that the symmetry elements
1318are properly located in the unit cell. The quality of this fit (chi**2) is
1319given. This process is not necessarily perfect; you are given an opportunity to
1320hand-tune the offset. Finally the number of peaks found in the map is listed,
1321the structure is drawn (I’ve made the view down the b-axis)</p>
1322
1323<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_11"
1324 o:spid="_x0000_i1036" type="#_x0000_t75" style='width:358.5pt;height:301.5pt;
1325 visibility:visible;mso-wrap-style:square'>
1326 <v:imagedata src="CFSingleCrystal_files/image007.png" o:title="" croptop="12490f"
1327  cropbottom="16795f" cropleft="47577f" cropright="3045f"/>
1328</v:shape></span></p>
1329
1330<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>and</span>
1331the Phase data window will show the map peaks tab</p>
1332
1333<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_12"
1334 o:spid="_x0000_i1035" type="#_x0000_t75" style='width:375pt;height:225pt;
1335 visibility:visible;mso-wrap-style:square'>
1336 <v:imagedata src="CFSingleCrystal_files/image008.png" o:title=""/>
1337</v:shape></span></p>
1338
1339<p class=MsoNormal>These are listed in order of magnitude; a double click on any
1340of the table headings will sort the list according to that parameter. My list
1341has 112 entries; <span class=SpellE>dipyridyl</span> disulfide has 14 C &amp; S
1342atoms so this list is appropriate for 8 molecules in the unit cell and thus all
1343atoms were found in this charge flipping result.</p>
1344
1345<p class=MsoNormal>If all went well then the drawing should nicely show all the
1346atoms in the structure placed properly with respect to the locations of the inversion
1347centers (they are at all the corners, edge centers, face centers and cell
1348center). If not then you can shift the map &amp; peaks with the <b
1349style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1350mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>,
1351<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1352mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>,
1353<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1354mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
1355&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1356mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
1357keys (NB: rotate the drawing so the axes are ~horizontal/vertical); the
1358map/peaks will move in resolution steps (0.5A). The table is also updated with
1359new peak positions. You could also just repeat the charge flipping and hope to
1360get a better map offset solution (examine the map offset chi**2 to get a sense
1361of this). You can also show the map density (highest point is shown as a green
1362dot somewhere in the map – on <span class=GramE>a</span> S-atom position);
1363select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1364"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1365minor-latin'>Draw Options</span></b> tab and use the <b style='mso-bidi-font-weight:
1366normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1367minor-latin;mso-hansi-theme-font:minor-latin'>Contour level</span></b> slider.
1368The drawing will show green dots at each set map point with size in proportion
1369to the density. The mouse <b style='mso-bidi-font-weight:normal'><span
1370style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1371mso-hansi-theme-font:minor-latin'>RB</span></b> can be used to slide the
1372structure around; the density is always drawn in a space surrounding the view
1373point (multicolored cross at the center). While here you can also change the <b
1374style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1375mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond search
1376factor</span></b> to <b style='mso-bidi-font-weight:normal'><span
1377style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1378mso-hansi-theme-font:minor-latin'>0.90</span></b> to ensure all S-C bonds are
1379shown.</p>
1380
1381<p class=MsoNormal>If the charge flipping has failed (high residual &amp; no
1382recognizable structure) the process should be just repeated. This gives it a
1383new random start for the structure factor phases which may lead to a good
1384solution. After a few attempts, you can try different control settings to see
1385if that will coax out a good solution; first be sure <b style='mso-bidi-font-weight:
1386normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1387minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b> is properly set
1388and then perhaps try different <b style='mso-bidi-font-weight:normal'><span
1389style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1390mso-hansi-theme-font:minor-latin'>k-Factors</span></b> and do <b
1391style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1392mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing</span></b>
1393by some element form factor. If it seemed to work but very few peaks were
1394found, make sure <b style='mso-bidi-font-weight:normal'><span style='font-family:
1395"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1396minor-latin'>Peak cutoff</span></b> was properly set; you can then repeat the
1397peak search by doing <b style='mso-bidi-font-weight:normal'><span
1398style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1399mso-hansi-theme-font:minor-latin'>Compute/Search map</span></b>.</p>
1400
1401<h2>Step 5. Extract solution and make molecules</h2>
1402
1403<p class=MsoNormal>Assuming that the map &amp; peak positions are properly
1404placed with respect to the symmetry elements of the space group, we can now
1405select those peaks which describe the structure. Select the <b
1406style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1407mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
1408tab and double LB click the blank upper left corner of the table; all entries
1409will be highlighted in blue. Then do <b style='mso-bidi-font-weight:normal'><span
1410style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1411mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>; after a
1412bit of time 1/4 of the peaks in the list will be highlighted and the
1413corresponding peaks in the drawing will be green (NB: if you navigate away from
1414this tab, this selection will be lost and you’ll have to repeat it!). Next, do <b
1415style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1416mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1417peaks/Move peaks</span></b>; these peaks will be transferred to the <b
1418style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1419mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1420list as H-atoms named according to their position in the magnitude column.</p>
1421
1422<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_13"
1423 o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;height:200.25pt;
1424 visibility:visible;mso-wrap-style:square'>
1425 <v:imagedata src="CFSingleCrystal_files/image009.png" o:title=""/>
1426</v:shape></span></p>
1427
1428<p class=MsoNormal>The drawing will show white balls at the atom positions
1429scattered over several molecules.</p>
1430
1431<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_14"
1432 o:spid="_x0000_i1033" type="#_x0000_t75" style='width:355.5pt;height:306.75pt;
1433 visibility:visible;mso-wrap-style:square'>
1434 <v:imagedata src="CFSingleCrystal_files/image010.png" o:title="" croptop="9479f"
1435  cropbottom="18319f" cropleft="42631f" cropright="7857f"/>
1436</v:shape></span></p>
1437
1438<p class=MsoNormal>Notice that 4 atoms have magnitudes ~90+, these are the S
1439atoms. The rest are C &amp; N atoms. In the <b style='mso-bidi-font-weight:
1440normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1441minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab select the
1442first 4 atoms (press LB on the 1<sup>st</sup> &amp; shift LB on the 4<sup>th</sup>
1443one). Then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1444"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1445minor-latin'>Edit/Modify atom parameters</span></b>; a popup window will
1446appear. Select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1447"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1448minor-latin'>Type</span></b> &amp; press <b style='mso-bidi-font-weight:normal'><span
1449style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1450mso-hansi-theme-font:minor-latin'>OK</span></b>; a Periodic Table will appear.
1451Select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1452mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>S</span></b>;
1453the atoms will be renames and their Type changed to S. Next select the remaining
1454H atoms (a quick way it to double LB click the <b style='mso-bidi-font-weight:
1455normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1456minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column heading
1457and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1458"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1459minor-latin'>H</span></b> from the popup window). Then do <b style='mso-bidi-font-weight:
1460normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1461minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b>
1462and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1463mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b>
1464from the popup; select <b style='mso-bidi-font-weight:normal'><span
1465style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1466mso-hansi-theme-font:minor-latin'>C</span></b> from the Periodic Table as we
1467don’t know which ones are N. The drawing will change (you may have to wiggle it
1468a bit to force the update).</p>
1469
1470<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_17"
1471 o:spid="_x0000_i1032" type="#_x0000_t75" style='width:5in;height:292.5pt;
1472 visibility:visible;mso-wrap-style:square'>
1473 <v:imagedata src="CFSingleCrystal_files/image011.png" o:title="" croptop="12086f"
1474  cropbottom="17505f" cropleft="42193f" cropright="8105f"/>
1475</v:shape></span></p>
1476
1477<p class=MsoNormal>Notice that the atoms are scattered over several molecules;
1478we want to assemble them into 2 conveniently placed ones. Begin by selecting an
1479atom (make sure the <b style='mso-bidi-font-weight:normal'><span
1480style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1481mso-hansi-theme-font:minor-latin'>Atom</span></b> tab is displayed &amp; do
1482shift LB on an atom in the drawing – I chose the S atom near the upper middle);
1483it will turn green and a line in the Atom table will be highlighted. Next do <b
1484style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1485mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assemble
1486molecule</span></b>; a popup window will appear. Change the <b
1487style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1488mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond search
1489factor</span></b> to <b style='mso-bidi-font-weight:normal'><span
1490style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1491mso-hansi-theme-font:minor-latin'>0.90</span></b> to be sure all S-C bonds are
1492found.</p>
1493
1494<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_16"
1495 o:spid="_x0000_i1031" type="#_x0000_t75" style='width:198.75pt;height:167.25pt;
1496 visibility:visible;mso-wrap-style:square'>
1497 <v:imagedata src="CFSingleCrystal_files/image012.png" o:title=""/>
1498</v:shape></span><span style='mso-spacerun:yes'> </span></p>
1499
1500<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1501style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1502mso-hansi-theme-font:minor-latin'>OK</span></b>; atoms will be collected into a
1503<span class=SpellE>well positioned</span> group, but others are not. Next
1504select one of the unassembled atoms (I chose a C-atom in a nearby SS-<span
1505class=SpellE>dipyridyl</span>) and do <b style='mso-bidi-font-weight:normal'><span
1506style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1507mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b>; there will
1508be two nicely assembled SS-<span class=SpellE>dipyridyls</span>.</p>
1509
1510<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_5"
1511 o:spid="_x0000_i1030" type="#_x0000_t75" style='width:5in;height:4in;
1512 visibility:visible;mso-wrap-style:square'>
1513 <v:imagedata src="CFSingleCrystal_files/image013.png" o:title="" croptop="11447f"
1514  cropbottom="19102f" cropleft="41491f" cropright="8984f"/>
1515</v:shape></span></p>
1516
1517<p class=MsoNormal>You should probably save this project as it contains your
1518solved crystal structure.</p>
1519
1520<h2>Step 6. Initial refinement</h2>
1521
1522<p class=MsoNormal>Since we now have a structural model, we can do the initial
1523structure refinement. By default this will only refine the scale factor; do <b
1524style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1525mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1526from the main GSAS-II data tree window. Convergence will quickly occur with <span
1527class=SpellE>Rw</span> ~35%. More useful is to refine the atom positions and
1528isotropic thermal parameters. Select the <b style='mso-bidi-font-weight:normal'><span
1529style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1530mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab from the Phase window.
1531Then LB double click the <b style='mso-bidi-font-weight:normal'><span
1532style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1533mso-hansi-theme-font:minor-latin'>refine</span></b> column heading; a popup
1534window will appear. Select <b style='mso-bidi-font-weight:normal'><span
1535style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1536mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
1537normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1538minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> and press <b
1539style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1540mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1541The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1542mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1543window will show <b style='mso-bidi-font-weight:normal'><span style='font-family:
1544"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1545minor-latin'>XU</span></b> for each atom in the refine column. Then do <b
1546style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1547mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1548(twice to get convergence) and the <span class=SpellE>Rw</span> ~12%.</p>
1549
1550<h2>Step 7. Determine C/N choice</h2>
1551
1552<p class=MsoNormal>We know from the chemistry that the N atom is in the 2
1553position of the pyridine ring, i.e. next to the point of attachment to the
1554S-atom. However, we don’t know which one that is and we have 8 atoms of which 4
1555are C and 4 are N.</p>
1556
1557<p class=MsoNormal>To work out the C/N problem above we need the atoms to be in
1558a chemically sensible order. The assemble molecule routine did construct chains
1559of atoms but this ordering is not really satisfactory. The ordering can quickly
1560be done by hand by following a labelled drawing. First go to the <b
1561style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1562mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
1563tab and double LB click the <b style='mso-bidi-font-weight:normal'><span
1564style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1565mso-hansi-theme-font:minor-latin'>Style</span></b> column; select <b
1566style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1567mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>balls &amp;
1568sticks</span></b> from the popup box. Press <b style='mso-bidi-font-weight:
1569normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1570minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. Next, double LB
1571click the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1572mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Label</span></b>
1573column and select <b style='mso-bidi-font-weight:normal'><span
1574style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1575mso-hansi-theme-font:minor-latin'>name</span></b> from the popup box; press <b
1576style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1577mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1578Then go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1579"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1580minor-latin'>Draw options</span></b> tab and adjust the <b style='mso-bidi-font-weight:
1581normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1582minor-latin;mso-hansi-theme-font:minor-latin'>Ball scale</span></b> &amp; <b
1583style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1584mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond radius </span></b>to
1585allow the labels to be easily seen. After shifting the view point the drawing
1586should look something like</p>
1587
1588<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1589
1590<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_9"
1591 o:spid="_x0000_i1029" type="#_x0000_t75" style='width:355.5pt;height:289.5pt;
1592 visibility:visible;mso-wrap-style:square'>
1593 <v:imagedata src="CFSingleCrystal_files/image014.png" o:title="" croptop="11765f"
1594  cropbottom="18146f" cropleft="38895f" cropright="11572f"/>
1595</v:shape></span></p>
1596
1597<p class=MsoNormal>Now go to the <b style='mso-bidi-font-weight:normal'><span
1598style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1599mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab. If you look carefully,
1600you can see that the atoms in each SS-<span class=SpellE>dipyridyl</span> are
1601grouped together in the table but they are not in chemically sensible order. The
1602atoms can be reordered by selecting one row with the <b style='mso-bidi-font-weight:
1603normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1604minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key down (the
1605status line will tell which atom is selected to move) and then with the <b
1606style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1607mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b>
1608key still down pick a row below where you want to insert it. I ordered them so
1609each S-atom was followed by the C-atoms in order around the ring; my list
1610looked like (I show just the 1<sup>st</sup> SS <span class=SpellE>dipyridyl</span>
1611molecule)</p>
1612
1613<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_10"
1614 o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;height:306pt;
1615 visibility:visible;mso-wrap-style:square'>
1616 <v:imagedata src="CFSingleCrystal_files/image015.png" o:title=""/>
1617</v:shape></span></p>
1618
1619<p class=MsoNormal>Once you have reordered the atoms to your satisfaction they
1620can be renamed to be in order. To do this select all the atoms (double LB click
1621the empty corner box) and then do <b style='mso-bidi-font-weight:normal'><span
1622style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1623mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b>.
1624Select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1625mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Name</span></b>
1626and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1627mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1628press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1629style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1630mso-hansi-theme-font:minor-latin'>Yes</span></b></span> to the popup question.
1631The atoms will be renamed in numerical order. Do <b style='mso-bidi-font-weight:
1632normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1633minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>;
1634the labels will change. In my numbering scheme, half of the C3, C7, C10, C14,
1635C17, C21, C24 and C28 carbon atoms are really nitrogen (if they are ordered).
1636Select these and do <b style='mso-bidi-font-weight:normal'><span
1637style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1638mso-hansi-theme-font:minor-latin'>Edit/Set atom refinement flags</span></b>;
1639select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1640mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>F</span></b>,
1641<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1642mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
1643&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1644mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
1645for these. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1646"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1647minor-latin'>Calculate/Refine</span></b>; the <span class=SpellE>Rw</span> will
1648drop to ~10% and 4 of the atom <span class=SpellE><b style='mso-bidi-font-weight:
1649normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1650minor-latin;mso-hansi-theme-font:minor-latin'>frac</span></b></span> values
1651will be ~1.25 while the others are ~1.0. The former are N-atoms and the latter
1652are C-atoms. Change the <b style='mso-bidi-font-weight:normal'><span
1653style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1654mso-hansi-theme-font:minor-latin'>Type</span></b> for the N-atoms and repeat <b
1655style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1656mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
1657the <span class=SpellE>Rw</span> will be high to start, but immediately fall to
1658~10%. In the Atom table all 8 refined <span class=SpellE>frac</span> values are
1659be now ~1.0. To finish this part of the refinement, set all <span class=SpellE><b
1660style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1661mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>frac</span></b></span>
1662values to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1663mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.0</span></b>
1664and all refine flags to <b style='mso-bidi-font-weight:normal'><span
1665style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1666mso-hansi-theme-font:minor-latin'>XU</span></b>. Do <b style='mso-bidi-font-weight:
1667normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1668minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the
1669final <span class=SpellE>Rw</span> ~10.5%</p>
1670
1671<h2>Step 8. Anisotropic thermal motion refinement</h2>
1672
1673<p class=MsoNormal>Given reasonable measured structure factors one can improve
1674a crystal model by using anisotropic thermal motion models for all the <span
1675class=SpellE>nonhydrogen</span> atoms. To convert all the atoms here select the
1676Atoms tab and then do a double LB click on <span class=GramE>the I</span>/A
1677column heading. Select Anisotropic from the popup and press OK; the Atom table
1678will be redrawn with <span class=SpellE>Uij</span> values equivalent to the
1679corresponding <span class=SpellE>Uiso</span> (now hidden). Do <b
1680style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1681mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
1682the final <span class=SpellE>Rw</span> ~8.2%</p>
1683
1684<h2 style='page-break-after:avoid'>Step 9. H-atom placement &amp; final
1685refinement</h2>
1686
1687<p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per
1688pyridine ring (16 in all). One could do this (painfully) by hand by looking for
1689them in <span style='font-family:Symbol'>D</span>F maps, but it is simpler to
1690just place them knowing the bonding chemistry of the rings. To start this
1691select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1692"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1693minor-latin'>Atoms</span></b> tab for the phase. Then select the C-atoms by a
1694double LB click on the <b style='mso-bidi-font-weight:normal'><span
1695style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1696mso-hansi-theme-font:minor-latin'>Type</span></b> column heading and select <b
1697style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1698mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b>
1699from the popup; press <b style='mso-bidi-font-weight:normal'><span
1700style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1701mso-hansi-theme-font:minor-latin'>OK</span></b>. The C-atoms will be
1702highlighted. Next do <b style='mso-bidi-font-weight:normal'><span
1703style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1704mso-hansi-theme-font:minor-latin'>Edit/Insert H atoms</span></b>; a <b
1705style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1706mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Distance
1707Angle Controls</span></b> popup will appear; the numbers should be as before.
1708Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1709mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
1710a new popup will appear</p>
1711
1712<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_8"
1713 o:spid="_x0000_i1027" type="#_x0000_t75" style='width:300pt;height:363.75pt;
1714 visibility:visible;mso-wrap-style:square'>
1715 <v:imagedata src="CFSingleCrystal_files/image016.png" o:title=""/>
1716</v:shape></span></p>
1717
1718<p class=MsoNormal>This is the hydrogen add control; it shows both the expected
1719number of H-atoms to add to each C-atom and the neighboring atoms used to
1720determine the geometry of the C-H bond. Check to make sure that 4 H-atoms will
1721be added for each ring. Note that C2, C9, C16 &amp; C23 will not have an H-atom
1722added as these are the S-atom attachment points in SS-<span class=SpellE>dipyridyl</span>.
1723Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1724mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>;
1725the H-atoms will be inserted immediately after the corresponding C-atoms and
1726the drawing is updated showing van der Waals spheres for all atoms.</p>
1727
1728<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_15"
1729 o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;height:297pt;
1730 visibility:visible;mso-wrap-style:square'>
1731 <v:imagedata src="CFSingleCrystal_files/image017.png" o:title=""/>
1732</v:shape></span></p>
1733
1734<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1735
1736<p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_18"
1737 o:spid="_x0000_i1025" type="#_x0000_t75" style='width:362.25pt;height:295.5pt;
1738 visibility:visible;mso-wrap-style:square'>
1739 <v:imagedata src="CFSingleCrystal_files/image018.png" o:title="" croptop="12402f"
1740  cropbottom="17514f" cropleft="39344f" cropright="11175f"/>
1741</v:shape></span></p>
1742
1743<p class=MsoNormal>Next, do <b style='mso-bidi-font-weight:normal'><span
1744style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1745mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; there will be an
1746immediate drop in <span class=SpellE>Rw</span> ~3.2%. Note that we did not
1747refine the H-atom positions or thermal parameters. The H-atom insertion process
1748retains the mechanisms for creating them in the first place and these tools can
1749be used to move them to reflect the changes in the C-atom parameters thus
1750forcing them to ride on the C-atoms. Do <b style='mso-bidi-font-weight:normal'><span
1751style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1752mso-hansi-theme-font:minor-latin'>Edit/Update H atoms</span></b>; the H-atom
1753positions &amp; <span class=SpellE>Uisos</span> will be <span class=GramE>revised.</span>
1754Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1755mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
1756there will be a slight improvement in <span class=SpellE>Rw</span>. Repeat
1757these two steps (twice); <span class=SpellE>Rw</span> should not change on the
1758last round. This completes the refinement of the SS-<span class=SpellE>dipyridyl</span>
1759structure. You can generate a final <span style='font-family:Symbol'>D</span>F
1760map from the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1761"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1762minor-latin'>General</span></b> tab; in <b style='mso-bidi-font-weight:normal'><span
1763style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1764mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> select the <b
1765style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1766mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>
1767and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1768mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1769sets</span></b>, then do <b style='mso-bidi-font-weight:normal'><span
1770style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1771mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b>. The <span
1772style='font-family:Symbol'>r</span><sub>max</sub> (=0.33) and <span
1773style='font-family:Symbol'>r</span><sub>min</sub> (=-0.31) are listed on the
1774console; these seem to be concentrated around the S-atoms.</p>
1775
1776</div>
1777
1778</body>
1779
1780</html>
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