source: Tutorials/MCsimanneal/MCSA in GSAS.htm @ 1752

Last change on this file since 1752 was 1745, checked in by vondreele, 8 years ago

changes to various tutorials - mostly getting file references correct & removing hyperlinks
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File size: 114.7 KB
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416  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
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428  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
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431  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
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434  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
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436  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
437  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
438  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
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440  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
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450  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
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452  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
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454  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
455  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
456  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
457  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
458  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
459  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
460  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
461  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
462  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
463  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
464  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
465  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
466  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
467  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
468  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
469  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
470  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
471  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
472  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
473  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
474  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
475  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
476  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
477  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
478  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
479  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
480  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
481  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
482  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
483  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
484  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
485  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
486  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
487  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
488  <w:LsdException Locked="false" Priority="19" QFormat="true"
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491   Name="Intense Emphasis"/>
492  <w:LsdException Locked="false" Priority="31" QFormat="true"
493   Name="Subtle Reference"/>
494  <w:LsdException Locked="false" Priority="32" QFormat="true"
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496  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
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498   UnhideWhenUsed="true" Name="Bibliography"/>
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503  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
504  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
505  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
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509  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
510  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
511  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
512  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
513  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
514  <w:LsdException Locked="false" Priority="46"
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516  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
517  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
518  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
519  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
520  <w:LsdException Locked="false" Priority="51"
521   Name="Grid Table 6 Colorful Accent 1"/>
522  <w:LsdException Locked="false" Priority="52"
523   Name="Grid Table 7 Colorful Accent 1"/>
524  <w:LsdException Locked="false" Priority="46"
525   Name="Grid Table 1 Light Accent 2"/>
526  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
527  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
528  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
529  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
530  <w:LsdException Locked="false" Priority="51"
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532  <w:LsdException Locked="false" Priority="52"
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535   Name="Grid Table 1 Light Accent 3"/>
536  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
537  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
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540  <w:LsdException Locked="false" Priority="51"
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543   Name="Grid Table 7 Colorful Accent 3"/>
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571   Name="Grid Table 6 Colorful Accent 6"/>
572  <w:LsdException Locked="false" Priority="52"
573   Name="Grid Table 7 Colorful Accent 6"/>
574  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
575  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
576  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
577  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
578  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
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580  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
581  <w:LsdException Locked="false" Priority="46"
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586  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
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618   Name="List Table 6 Colorful Accent 4"/>
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620   Name="List Table 7 Colorful Accent 4"/>
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624  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
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626  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
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630   Name="List Table 7 Colorful Accent 5"/>
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639  <w:LsdException Locked="false" Priority="52"
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783        font-size:26.0pt;
784        font-family:"Cambria",serif;
785        mso-fareast-font-family:"Times New Roman";
786        mso-fareast-theme-font:minor-fareast;
787        mso-bidi-font-family:"Times New Roman";
788        color:#17365D;
789        letter-spacing:.25pt;}
790a:link, span.MsoHyperlink
791        {mso-style-noshow:yes;
792        mso-style-priority:99;
793        color:blue;
794        text-decoration:underline;
795        text-underline:single;}
796a:visited, span.MsoHyperlinkFollowed
797        {mso-style-noshow:yes;
798        mso-style-priority:99;
799        color:purple;
800        text-decoration:underline;
801        text-underline:single;}
802p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
803        {mso-style-noshow:yes;
804        mso-style-priority:99;
805        mso-style-link:"Document Map Char";
806        margin:0in;
807        margin-bottom:.0001pt;
808        mso-pagination:widow-orphan;
809        font-size:8.0pt;
810        font-family:"Tahoma",sans-serif;
811        mso-fareast-font-family:"Times New Roman";
812        mso-fareast-theme-font:minor-fareast;}
813p
814        {mso-style-noshow:yes;
815        mso-style-priority:99;
816        mso-margin-top-alt:auto;
817        margin-right:0in;
818        mso-margin-bottom-alt:auto;
819        margin-left:0in;
820        mso-pagination:widow-orphan;
821        font-size:12.0pt;
822        font-family:"Times New Roman",serif;
823        mso-fareast-font-family:"Times New Roman";
824        mso-fareast-theme-font:minor-fareast;}
825pre
826        {mso-style-noshow:yes;
827        mso-style-priority:99;
828        mso-style-link:"HTML Preformatted Char";
829        margin:0in;
830        margin-bottom:.0001pt;
831        mso-pagination:widow-orphan;
832        tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt;
833        font-size:10.0pt;
834        font-family:"Courier New";
835        mso-fareast-font-family:"Times New Roman";
836        mso-fareast-theme-font:minor-fareast;}
837p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
838        {mso-style-noshow:yes;
839        mso-style-priority:99;
840        mso-style-link:"Balloon Text Char";
841        margin:0in;
842        margin-bottom:.0001pt;
843        mso-pagination:widow-orphan;
844        font-size:8.0pt;
845        font-family:"Tahoma",sans-serif;
846        mso-fareast-font-family:"Times New Roman";
847        mso-fareast-theme-font:minor-fareast;}
848span.MsoPlaceholderText
849        {mso-style-noshow:yes;
850        mso-style-priority:99;
851        mso-style-unhide:no;
852        color:gray;}
853p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
854        {mso-style-noshow:yes;
855        mso-style-priority:1;
856        mso-style-unhide:no;
857        mso-style-qformat:yes;
858        margin:0in;
859        margin-bottom:.0001pt;
860        mso-pagination:widow-orphan;
861        font-size:12.0pt;
862        font-family:"Times New Roman",serif;
863        mso-fareast-font-family:"Times New Roman";
864        mso-fareast-theme-font:minor-fareast;}
865p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
866        {mso-style-noshow:yes;
867        mso-style-priority:34;
868        mso-style-unhide:no;
869        mso-style-qformat:yes;
870        margin-top:0in;
871        margin-right:0in;
872        margin-bottom:0in;
873        margin-left:.5in;
874        margin-bottom:.0001pt;
875        mso-pagination:widow-orphan;
876        font-size:12.0pt;
877        font-family:"Times New Roman",serif;
878        mso-fareast-font-family:"Times New Roman";
879        mso-fareast-theme-font:minor-fareast;}
880span.MsoIntenseReference
881        {mso-style-priority:32;
882        mso-style-unhide:no;
883        mso-style-qformat:yes;
884        font-variant:small-caps;
885        color:#C0504D;
886        letter-spacing:.25pt;
887        font-weight:bold;
888        text-decoration:underline;
889        text-underline:single;}
890span.Heading1Char
891        {mso-style-name:"Heading 1 Char";
892        mso-style-priority:9;
893        mso-style-unhide:no;
894        mso-style-locked:yes;
895        mso-style-link:"Heading 1";
896        font-family:"Times New Roman",serif;
897        mso-ascii-font-family:"Times New Roman";
898        mso-hansi-font-family:"Times New Roman";
899        mso-bidi-font-family:"Times New Roman";
900        font-weight:bold;}
901span.Heading2Char
902        {mso-style-name:"Heading 2 Char";
903        mso-style-noshow:yes;
904        mso-style-priority:9;
905        mso-style-unhide:no;
906        mso-style-locked:yes;
907        mso-style-link:"Heading 2";
908        font-family:"Times New Roman",serif;
909        mso-ascii-font-family:"Times New Roman";
910        mso-hansi-font-family:"Times New Roman";
911        mso-bidi-font-family:"Times New Roman";
912        font-weight:bold;}
913span.Heading3Char
914        {mso-style-name:"Heading 3 Char";
915        mso-style-noshow:yes;
916        mso-style-priority:9;
917        mso-style-unhide:no;
918        mso-style-locked:yes;
919        mso-style-link:"Heading 3";
920        font-family:"Times New Roman",serif;
921        mso-ascii-font-family:"Times New Roman";
922        mso-hansi-font-family:"Times New Roman";
923        mso-bidi-font-family:"Times New Roman";
924        font-weight:bold;}
925span.Heading4Char
926        {mso-style-name:"Heading 4 Char";
927        mso-style-noshow:yes;
928        mso-style-priority:9;
929        mso-style-unhide:no;
930        mso-style-locked:yes;
931        mso-style-link:"Heading 4";
932        font-family:"Cambria",serif;
933        mso-ascii-font-family:Cambria;
934        mso-hansi-font-family:Cambria;
935        color:#4F81BD;
936        font-weight:bold;
937        font-style:italic;}
938span.Heading5Char
939        {mso-style-name:"Heading 5 Char";
940        mso-style-noshow:yes;
941        mso-style-priority:9;
942        mso-style-unhide:no;
943        mso-style-locked:yes;
944        mso-style-link:"Heading 5";
945        font-family:"Times New Roman",serif;
946        mso-ascii-font-family:"Times New Roman";
947        mso-hansi-font-family:"Times New Roman";
948        mso-bidi-font-family:"Times New Roman";
949        color:#4F4FFF;
950        font-weight:bold;}
951span.HTMLPreformattedChar
952        {mso-style-name:"HTML Preformatted Char";
953        mso-style-noshow:yes;
954        mso-style-priority:99;
955        mso-style-unhide:no;
956        mso-style-locked:yes;
957        mso-style-link:"HTML Preformatted";
958        font-family:"Courier New";
959        mso-ascii-font-family:"Courier New";
960        mso-hansi-font-family:"Courier New";
961        mso-bidi-font-family:"Courier New";}
962span.TitleChar
963        {mso-style-name:"Title Char";
964        mso-style-priority:10;
965        mso-style-unhide:no;
966        mso-style-locked:yes;
967        mso-style-link:Title;
968        font-family:"Cambria",serif;
969        mso-ascii-font-family:Cambria;
970        mso-hansi-font-family:Cambria;
971        color:#17365D;
972        letter-spacing:.25pt;}
973span.DocumentMapChar
974        {mso-style-name:"Document Map Char";
975        mso-style-noshow:yes;
976        mso-style-priority:99;
977        mso-style-unhide:no;
978        mso-style-locked:yes;
979        mso-style-link:"Document Map";
980        font-family:"Tahoma",sans-serif;
981        mso-ascii-font-family:Tahoma;
982        mso-hansi-font-family:Tahoma;
983        mso-bidi-font-family:Tahoma;}
984span.BalloonTextChar
985        {mso-style-name:"Balloon Text Char";
986        mso-style-noshow:yes;
987        mso-style-priority:99;
988        mso-style-unhide:no;
989        mso-style-locked:yes;
990        mso-style-link:"Balloon Text";
991        font-family:"Tahoma",sans-serif;
992        mso-ascii-font-family:Tahoma;
993        mso-hansi-font-family:Tahoma;
994        mso-bidi-font-family:Tahoma;}
995p.msotitlecxspfirst, li.msotitlecxspfirst, div.msotitlecxspfirst
996        {mso-style-name:msotitlecxspfirst;
997        mso-style-noshow:yes;
998        mso-style-priority:99;
999        mso-style-unhide:no;
1000        margin:0in;
1001        margin-bottom:.0001pt;
1002        mso-pagination:widow-orphan;
1003        font-size:26.0pt;
1004        font-family:"Cambria",serif;
1005        mso-fareast-font-family:"Times New Roman";
1006        mso-fareast-theme-font:minor-fareast;
1007        mso-bidi-font-family:"Times New Roman";
1008        color:#17365D;
1009        letter-spacing:.25pt;}
1010p.msotitlecxspmiddle, li.msotitlecxspmiddle, div.msotitlecxspmiddle
1011        {mso-style-name:msotitlecxspmiddle;
1012        mso-style-noshow:yes;
1013        mso-style-priority:99;
1014        mso-style-unhide:no;
1015        margin:0in;
1016        margin-bottom:.0001pt;
1017        mso-pagination:widow-orphan;
1018        font-size:26.0pt;
1019        font-family:"Cambria",serif;
1020        mso-fareast-font-family:"Times New Roman";
1021        mso-fareast-theme-font:minor-fareast;
1022        mso-bidi-font-family:"Times New Roman";
1023        color:#17365D;
1024        letter-spacing:.25pt;}
1025p.msotitlecxsplast, li.msotitlecxsplast, div.msotitlecxsplast
1026        {mso-style-name:msotitlecxsplast;
1027        mso-style-noshow:yes;
1028        mso-style-priority:99;
1029        mso-style-unhide:no;
1030        margin-top:0in;
1031        margin-right:0in;
1032        margin-bottom:15.0pt;
1033        margin-left:0in;
1034        mso-pagination:widow-orphan;
1035        font-size:26.0pt;
1036        font-family:"Cambria",serif;
1037        mso-fareast-font-family:"Times New Roman";
1038        mso-fareast-theme-font:minor-fareast;
1039        mso-bidi-font-family:"Times New Roman";
1040        color:#17365D;
1041        letter-spacing:.25pt;}
1042p.msolistparagraphcxspfirst, li.msolistparagraphcxspfirst, div.msolistparagraphcxspfirst
1043        {mso-style-name:msolistparagraphcxspfirst;
1044        mso-style-noshow:yes;
1045        mso-style-priority:99;
1046        mso-style-unhide:no;
1047        margin-top:0in;
1048        margin-right:0in;
1049        margin-bottom:0in;
1050        margin-left:.5in;
1051        margin-bottom:.0001pt;
1052        mso-pagination:widow-orphan;
1053        font-size:12.0pt;
1054        font-family:"Times New Roman",serif;
1055        mso-fareast-font-family:"Times New Roman";
1056        mso-fareast-theme-font:minor-fareast;}
1057p.msolistparagraphcxspmiddle, li.msolistparagraphcxspmiddle, div.msolistparagraphcxspmiddle
1058        {mso-style-name:msolistparagraphcxspmiddle;
1059        mso-style-noshow:yes;
1060        mso-style-priority:99;
1061        mso-style-unhide:no;
1062        margin-top:0in;
1063        margin-right:0in;
1064        margin-bottom:0in;
1065        margin-left:.5in;
1066        margin-bottom:.0001pt;
1067        mso-pagination:widow-orphan;
1068        font-size:12.0pt;
1069        font-family:"Times New Roman",serif;
1070        mso-fareast-font-family:"Times New Roman";
1071        mso-fareast-theme-font:minor-fareast;}
1072p.msolistparagraphcxsplast, li.msolistparagraphcxsplast, div.msolistparagraphcxsplast
1073        {mso-style-name:msolistparagraphcxsplast;
1074        mso-style-noshow:yes;
1075        mso-style-priority:99;
1076        mso-style-unhide:no;
1077        margin-top:0in;
1078        margin-right:0in;
1079        margin-bottom:0in;
1080        margin-left:.5in;
1081        margin-bottom:.0001pt;
1082        mso-pagination:widow-orphan;
1083        font-size:12.0pt;
1084        font-family:"Times New Roman",serif;
1085        mso-fareast-font-family:"Times New Roman";
1086        mso-fareast-theme-font:minor-fareast;}
1087p.msochpdefault, li.msochpdefault, div.msochpdefault
1088        {mso-style-name:msochpdefault;
1089        mso-style-noshow:yes;
1090        mso-style-priority:99;
1091        mso-style-unhide:no;
1092        mso-margin-top-alt:auto;
1093        margin-right:0in;
1094        mso-margin-bottom-alt:auto;
1095        margin-left:0in;
1096        mso-pagination:widow-orphan;
1097        font-size:10.0pt;
1098        font-family:"Calibri",sans-serif;
1099        mso-fareast-font-family:"Times New Roman";
1100        mso-fareast-theme-font:minor-fareast;
1101        mso-bidi-font-family:Calibri;}
1102span.SpellE
1103        {mso-style-name:"";
1104        mso-spl-e:yes;}
1105span.GramE
1106        {mso-style-name:"";
1107        mso-gram-e:yes;}
1108.MsoChpDefault
1109        {mso-style-type:export-only;
1110        mso-default-props:yes;
1111        font-size:10.0pt;
1112        mso-ansi-font-size:10.0pt;
1113        mso-bidi-font-size:10.0pt;
1114        mso-ascii-font-family:Calibri;
1115        mso-hansi-font-family:Calibri;
1116        mso-bidi-font-family:Calibri;}
1117@page WordSection1
1118        {size:8.5in 11.0in;
1119        margin:1.0in 1.0in 1.0in 1.0in;
1120        mso-header-margin:.5in;
1121        mso-footer-margin:.5in;
1122        mso-paper-source:0;}
1123div.WordSection1
1124        {page:WordSection1;}
1125 /* List Definitions */
1126 @list l0
1127        {mso-list-id:608973138;
1128        mso-list-type:hybrid;
1129        mso-list-template-ids:-1449999034 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1130@list l0:level1
1131        {mso-level-tab-stop:none;
1132        mso-level-number-position:left;
1133        text-indent:-.25in;}
1134@list l0:level2
1135        {mso-level-number-format:alpha-lower;
1136        mso-level-tab-stop:none;
1137        mso-level-number-position:left;
1138        text-indent:-.25in;}
1139@list l0:level3
1140        {mso-level-number-format:roman-lower;
1141        mso-level-tab-stop:none;
1142        mso-level-number-position:right;
1143        text-indent:-9.0pt;}
1144@list l0:level4
1145        {mso-level-tab-stop:none;
1146        mso-level-number-position:left;
1147        text-indent:-.25in;}
1148@list l0:level5
1149        {mso-level-number-format:alpha-lower;
1150        mso-level-tab-stop:none;
1151        mso-level-number-position:left;
1152        text-indent:-.25in;}
1153@list l0:level6
1154        {mso-level-number-format:roman-lower;
1155        mso-level-tab-stop:none;
1156        mso-level-number-position:right;
1157        text-indent:-9.0pt;}
1158@list l0:level7
1159        {mso-level-tab-stop:none;
1160        mso-level-number-position:left;
1161        text-indent:-.25in;}
1162@list l0:level8
1163        {mso-level-number-format:alpha-lower;
1164        mso-level-tab-stop:none;
1165        mso-level-number-position:left;
1166        text-indent:-.25in;}
1167@list l0:level9
1168        {mso-level-number-format:roman-lower;
1169        mso-level-tab-stop:none;
1170        mso-level-number-position:right;
1171        text-indent:-9.0pt;}
1172@list l1
1173        {mso-list-id:1022125565;
1174        mso-list-type:hybrid;
1175        mso-list-template-ids:-482838388 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1176@list l1:level1
1177        {mso-level-tab-stop:none;
1178        mso-level-number-position:left;
1179        margin-left:1.0in;
1180        text-indent:-.25in;}
1181@list l1:level2
1182        {mso-level-number-format:alpha-lower;
1183        mso-level-tab-stop:none;
1184        mso-level-number-position:left;
1185        margin-left:1.5in;
1186        text-indent:-.25in;}
1187@list l1:level3
1188        {mso-level-number-format:roman-lower;
1189        mso-level-tab-stop:none;
1190        mso-level-number-position:right;
1191        margin-left:2.0in;
1192        text-indent:-9.0pt;}
1193@list l1:level4
1194        {mso-level-tab-stop:none;
1195        mso-level-number-position:left;
1196        margin-left:2.5in;
1197        text-indent:-.25in;}
1198@list l1:level5
1199        {mso-level-number-format:alpha-lower;
1200        mso-level-tab-stop:none;
1201        mso-level-number-position:left;
1202        margin-left:3.0in;
1203        text-indent:-.25in;}
1204@list l1:level6
1205        {mso-level-number-format:roman-lower;
1206        mso-level-tab-stop:none;
1207        mso-level-number-position:right;
1208        margin-left:3.5in;
1209        text-indent:-9.0pt;}
1210@list l1:level7
1211        {mso-level-tab-stop:none;
1212        mso-level-number-position:left;
1213        margin-left:4.0in;
1214        text-indent:-.25in;}
1215@list l1:level8
1216        {mso-level-number-format:alpha-lower;
1217        mso-level-tab-stop:none;
1218        mso-level-number-position:left;
1219        margin-left:4.5in;
1220        text-indent:-.25in;}
1221@list l1:level9
1222        {mso-level-number-format:roman-lower;
1223        mso-level-tab-stop:none;
1224        mso-level-number-position:right;
1225        margin-left:5.0in;
1226        text-indent:-9.0pt;}
1227ol
1228        {margin-bottom:0in;}
1229ul
1230        {margin-bottom:0in;}
1231-->
1232</style>
1233<!--[if gte mso 10]>
1234<style>
1235 /* Style Definitions */
1236 table.MsoNormalTable
1237        {mso-style-name:"Table Normal";
1238        mso-tstyle-rowband-size:0;
1239        mso-tstyle-colband-size:0;
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1256</head>
1257
1258<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1259
1260<div class=WordSection1>
1261
1262<h1><span style='mso-fareast-font-family:"Times New Roman"'>MC/SA in GSAS-II<o:p></o:p></span></h1>
1263
1264<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction: <o:p></o:p></span></h2>
1265
1266<p class=MsoNormal>In these exercises you will use GSAS-II to solve the
1267structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
1268diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
1269were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
1270and were originally collected on NSLS beam line X3b1. The MC/SA technique is
1271needed in these cases because as you will see the data does not extend very far
1272in 2&#920; so one cannot use charge flipping to solve them. The steps for each
1273begin with peak selection and fitting, then indexing to identify the lattice
1274parameters. A Pawley refinement is used to obtain a set of structure factors
1275needed for the MC/SA runs. We will use previously developed models for the two
1276molecules; I used the freeware program Avogadro (<a
1277href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
1278to create them.</p>
1279
1280<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1281
1282<h2>Step 1. Import powder data for 3-aminoquinoline</h2>
1283
1284<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1285style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1286style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1287the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1288mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1289Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder
1290data file</span></b> menu item to read the data file into the current GSAS-II
1291project. Change the file directory to <b style='mso-bidi-font-weight:normal'><span
1292style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1293mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1294minor-latin'>exercises/<span class=SpellE>MCsimanneal</span></span></b><span
1295style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1296mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1297minor-latin'> to find the file; you may need to change the file type to <b
1298style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
1299file.</span></p>
1300
1301<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1302style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1303style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1304the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1305style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1306mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1307minor-latin'>Quinoli.gda</span></b></span><span style='font-family:"Calibri",sans-serif;
1308mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1309Calibri;mso-bidi-theme-font:minor-latin'> data</span> file in the first dialog
1310and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1311mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1312Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
1313Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1314style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1315mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1316minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
1317style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1318mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1319minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
1320style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1321mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1322Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
1323proceed.</p>
1324
1325<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1326style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1327style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1328the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1329mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1330Calibri;mso-bidi-theme-font:minor-latin'>BNL-<span class=SpellE>I.instprm</span></span></b>
1331instrument parameter file in the second dialog and press <b style='mso-bidi-font-weight:
1332normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1333minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1334mso-bidi-theme-font:minor-latin'>Open</span></b>. You’ll have to change the
1335file type to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1336"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1337minor-latin'>*.<span class=SpellE>instprm</span></span></b> (GSAS-II instrument
1338parameter file). The powder pattern will immediately appear.</p>
1339
1340<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1341 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
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1344 <v:formulas>
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1356  <v:f eqn="sum @10 21600 0"/>
1357 </v:formulas>
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1360</v:shapetype><v:shape id="Picture_x0020_28" o:spid="_x0000_i1051" type="#_x0000_t75"
1361 style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
1362 <v:imagedata src="MCSA%20in%20GSAS_files/image001.png" o:title=""/>
1363</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1364src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
1365
1366<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1367
1368<p class=MsoListParagraph>Notice that the pattern extends only to a minimum
1369d-spacing of ~1.81Å; this is not far enough to use charge flipping which needs
13701Å or better. </p>
1371
1372<h2>Step 2. Peak picking &amp; fitting</h2>
1373
1374<p class=MsoNormal>Next you need to select limits so that ~20 peaks are
1375selected for indexing; go to <b style='mso-bidi-font-weight:normal'><span
1376style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1377mso-hansi-theme-font:minor-latin'>Limits</span></b> and choose <b
1378style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1379mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>9-25</span></b>°
13802&#920;. Next go to <b style='mso-bidi-font-weight:normal'><span
1381style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1382mso-hansi-theme-font:minor-latin'>Peak List</span></b> and pick all the peaks
1383you can see between the limits. This is most easily done by hand as the <b
1384style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1385mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Auto search</span></b>
1386routine gives a lot of spurious peaks for this rather noisy and weak data; I
1387picked 21 peaks, skipping a few very weak ones. Then use <b style='mso-bidi-font-weight:
1388normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1389minor-latin;mso-hansi-theme-font:minor-latin'>Peak fitting/LSQ <span
1390class=SpellE>PeakFit</span> </span></b>to fit them. You will need to vary at
1391least <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1392mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
1393&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1394mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
1395in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1396mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1397Parameters</span></b> along with <span class=SpellE><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'>pos</span></b></span> &amp; <span
1400class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1401"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1402minor-latin'>int</span></b></span> in the <b style='mso-bidi-font-weight:normal'><span
1403style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1404mso-hansi-theme-font:minor-latin'>Peak List</span></b> to get a reasonable fit
1405suitable for indexing.</p>
1406
1407<h2>Step 3. Indexing</h2>
1408
1409<p class=MsoNormal>Next go to <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'>Index Peak List</span></b> and do <b
1412style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1413mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1414to set up the peaks for indexing. Then go to <b style='mso-bidi-font-weight:
1415normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1416minor-latin;mso-hansi-theme-font:minor-latin'>Unit Cells List</span></b> for
1417indexing. The most likely <span class=SpellE>Bravais</span> lattice for these
1418small organic molecules is either Orthorhombic-P or Monoclinic-P; you can try
1419both and see what comes out (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
1420style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1421mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>). The correct unit
1422cell should almost immediately appear with an M20 ~200 with a=7.748, b=7.651,
1423c=12.736, Vol=755.01. NB: your solution may have <span class=GramE>a &amp;</span>
1424b switched. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1425"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1426minor-latin'>Cell Index/Refine/Copy Cell</span></b>; you can then try various
1427space groups. Press the <b style='mso-bidi-font-weight:normal'><span
1428style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1429mso-hansi-theme-font:minor-latin'>Show HKL positions</span></b> to see the
1430lines with extinctions (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
1431style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1432mso-hansi-theme-font:minor-latin'>P 2<sub>1</sub> 2<sub>1</sub> 2<sub>1</sub></span></b>).
1433You can then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1434"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1435minor-latin'>Cell Index/Refine/Refine Cell</span></b> to improve the lattice
1436parameters with M20 ~380. Finally do <b style='mso-bidi-font-weight:normal'><span
1437style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1438mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Make new phase</span></b>
1439to create the phase; I named it <b style='mso-bidi-font-weight:normal'><span
1440style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1441mso-hansi-theme-font:minor-latin'>3-aminoquinoline</span></b>.</p>
1442
1443<h2>Step 4. Setup for Pawley refinement</h2>
1444
1445<p class=MsoNormal>There are a number of steps that must be done in preparation
1446for a Pawley refinement after having completed the unit cell indexing and new
1447phase creation. These cover two things: one is to prepare the powder pattern
1448(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1449
1450<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1451style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1452style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1453<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1454mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
1455in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1456region at the end of the data is readily seen. This is ~37deg 2<span
1457style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
1458"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
1459style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>;
1460there is a zero point at the end that needs to be excluded. Use the right mouse
1461button and pick a point just inside the end avoiding the zero. Make a note of
1462the exact d-spacing (for me 1.8133) using the mouse cursor on the plot.</p>
1463
1464<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1465style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1466style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1467<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1468mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1469Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1470style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1471mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1472style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1473mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1474profile</span></b> to recover the default values. The peak fitting done earlier
1475is over a more limited range of 2<span style='font-family:Symbol;mso-ascii-font-family:
1476"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
1477mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
1478Symbol'>Q</span></span> giving values that will not extrapolate well over the
1479wider range to be used in the Pawley refinement. We may refine them again
1480later.</p>
1481
1482<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1483style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1484style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1485<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1486mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1487Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1488normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1489minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
1490
1491<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1492style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1493style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1494to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1495mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b>
1496to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1497"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1498minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1499normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1500minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
1501box and enter the d-spacing (1.8133) into the <b style='mso-bidi-font-weight:
1502normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1503minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
1504box.</p>
1505
1506<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1507style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1508mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1509
1510<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1511 id="_x0000_i1050" type="#_x0000_t75" style='width:487.5pt;height:375pt;
1512 visibility:visible;mso-wrap-style:square'>
1513 <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/>
1514</v:shape><![endif]--><![if !vml]><img border=0 width=650 height=500
1515src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="_x0000_i1050"><![endif]></span></p>
1516
1517<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1518
1519<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1520style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1521mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1522for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
1523style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1524mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
1525dialog box will appear</p>
1526
1527<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1528 id="Picture_x0020_3" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:259.5pt;
1529 height:252pt;visibility:visible;mso-wrap-style:square'>
1530 <v:imagedata src="MCSA%20in%20GSAS_files/image005.png" o:title=""/>
1531</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1532src="MCSA%20in%20GSAS_files/image006.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
1533
1534<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1535
1536<p class=MsoNormal>Select either choice; the desired data set will be added to
1537this phase for analysis. The data tab now shows the new data set.</p>
1538
1539<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1540 id="Picture_x0020_30" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:359.25pt;
1541 height:375pt;visibility:visible;mso-wrap-style:square'>
1542 <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/>
1543</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500
1544src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
1545
1546<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1547
1548<p class=MsoNormal>This is the location for all the phase dependent parameters
1549for this histogram. Notice that it includes phase fraction, size &amp; <span
1550class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1551and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1552intended for protein work where a significant region of the structure is
1553disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1554surfaces and preferred orientation correction curves.</p>
1555
1556<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1557style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1558mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1559empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
1560style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1561mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
1562makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
1563normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1564minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>.
1565The table should list reflections 0-91. Select and check the <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'>refine</span></b>
1568column using the same technique you used for the peak list. </p>
1569
1570<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1571 id="Picture_x0020_5" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;
1572 height:225pt;visibility:visible;mso-wrap-style:square'>
1573 <v:imagedata src="MCSA%20in%20GSAS_files/image009.png" o:title=""/>
1574</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
1575src="MCSA%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
1576
1577<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1578
1579<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1580you didn’t skip a step as it might not work correctly if you did.</p>
1581
1582<h2>Step 5. Pawley refinement</h2>
1583
1584<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1585normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1586minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1587the main GSAS-II data tree window. Before it begins a backup of the project
1588file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
1589style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1590mso-hansi-theme-font:minor-latin'>aminoquinoline.bck0.gpx</span></b>. It can be
1591used to recover from a bad refinement. A progress dialog box will appear
1592showing the residual as the refinement proceeds. My refinement completed with <span
1593class=SpellE>Rwp</span> ~12.9%; a dialog box appears asking if you wish to load
1594the result. Press <b style='mso-bidi-font-weight:normal'><span
1595style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1596mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
1597PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
1598
1599<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1600 id="_x0000_i1046" type="#_x0000_t75" style='width:525pt;height:450pt;
1601 visibility:visible;mso-wrap-style:square'>
1602 <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/>
1603</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1604src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="_x0000_i1046"><![endif]></span></p>
1605
1606<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1607
1608<p class=MsoNormal>I’ve expanded the vertical scale to show the fit; it is
1609evident from examining the plot that improvement can be had by improving the
1610background model. One easy way to fit that broad hump is to add a peak to the
1611background. Go to <b style='mso-bidi-font-weight:normal'><span
1612style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1613mso-hansi-theme-font:minor-latin'>Background</span></b> and set <b
1614style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1615mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. peaks</span></b>
1616to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1617mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>,
1618then change <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1619style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1620mso-hansi-theme-font:minor-latin'>pos</span></b></span> to <b style='mso-bidi-font-weight:
1621normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1622minor-latin;mso-hansi-theme-font:minor-latin'>19</span></b>, <span
1623class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1624"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1625minor-latin'>int</span></b></span> to <b style='mso-bidi-font-weight:normal'><span
1626style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1627mso-hansi-theme-font:minor-latin'>100000</span></b> and <b style='mso-bidi-font-weight:
1628normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1629minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> to <b
1630style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1631mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>;
1632for the peak only refine <b style='mso-bidi-font-weight:normal'><span
1633style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1634mso-hansi-theme-font:minor-latin'>int</span></b>. I also set <b
1635style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1636mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
1637class=SpellE>coeff</span>.</span></b> <span class=GramE>to</span> <b
1638style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1639mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>;
1640the window shows</p>
1641
1642<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1643 id="Picture_x0020_33" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:402pt;
1644 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1645 <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/>
1646</v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
1647src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
1648
1649<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1650
1651<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
1652style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1653mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
1654class=SpellE>Rwp</span> fell to ~8.5%. In <b style='mso-bidi-font-weight:normal'><span
1655style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1656mso-hansi-theme-font:minor-latin'>Background</span></b> select <span
1657class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1658"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1659minor-latin'>pos</span></b></span> &amp; <b style='mso-bidi-font-weight:normal'><span
1660style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1661mso-hansi-theme-font:minor-latin'>sig</span></b> for refinement and in <b
1662style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1663mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1664Parameters</span></b> select <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'>X</span></b> &amp; <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'>Y</span></b> for refinement; then
1669do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1670style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1671mso-hansi-theme-font:minor-latin'>Calculate</span></b></span><b
1672style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1673mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> /Refine</span></b>
1674again. I got Rwp~7.5% at convergence and the fit looked like</p>
1675
1676<p class=MsoNormal><span style='mso-no-proof:yes'>c<!--[if gte vml 1]><v:shape
1677 id="_x0000_i1044" type="#_x0000_t75" style='width:525pt;height:450pt;
1678 visibility:visible;mso-wrap-style:square'>
1679 <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/>
1680</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1681src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="_x0000_i1044"><![endif]></span></p>
1682
1683<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1684
1685<p class=MsoNormal>This may be good enough to try Monte Carlo/Simulated
1686Annealing.</p>
1687
1688<h2>Step 6. Setup for Monte Carlo/Simulated Annealing</h2>
1689
1690<p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic
1691rings with one N-substituted position and an amino side group</p>
1692
1693<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1694 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:142.5pt;
1695 height:93.75pt;visibility:visible;mso-wrap-style:square'>
1696 <v:imagedata src="MCSA%20in%20GSAS_files/image017.png" o:title="" croptop="20629f"
1697  cropbottom="17428f" cropleft="9893f" cropright="13874f"/>
1698</v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125
1699src="MCSA%20in%20GSAS_files/image018.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
1700
1701<p class=MsoNormal>MC/SA structure solution consists of optimizing the position
1702and orientation of this object in the unit cell; it has no internal degrees of
1703freedom. Thus we need to determine essentially six parameters. To do this in
1704GSAS-II we need to put a model of this molecule in as a rigid body. One must
1705create the model outside of GSAS-II, it has no facilities for model building. I
1706used the Avogadro (<a href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
1707package for this and created a simple xyz Cartesian coordinate file for it (if
1708you have Avogadro or something equivalent you can try this for yourself). To
1709start go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1710"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1711minor-latin'>Rigid bodies</span></b> in the main GSAS-II data tree. You will
1712see a window with two tabs; select <b style='mso-bidi-font-weight:normal'><span
1713style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1714mso-hansi-theme-font:minor-latin'>Residue rigid bodies</span></b> and then do <b
1715style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1716mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Body/Import
1717XYZ</span></b>. Change the file type to <b style='mso-bidi-font-weight:normal'><span
1718style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1719mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and select <span
1720class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1721"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1722minor-latin'>aminoquinoline.xyz</span></b></span>. The <b style='mso-bidi-font-weight:
1723normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1724minor-latin;mso-hansi-theme-font:minor-latin'>Rigid <span class=GramE>bodies</span></span></b>
1725window will show</p>
1726
1727<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1728 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:300pt;
1729 height:320.25pt;visibility:visible;mso-wrap-style:square'>
1730 <v:imagedata src="MCSA%20in%20GSAS_files/image019.png" o:title=""/>
1731</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=427
1732src="MCSA%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
1733
1734<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1735
1736<p class=MsoNormal>If you select the <b style='mso-bidi-font-weight:normal'><span
1737style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1738mso-hansi-theme-font:minor-latin'>Plot?</span></b> <span class=GramE>box</span>
1739a drawing will appear</p>
1740
1741<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1742 id="_x0000_i1041" type="#_x0000_t75" style='width:286.5pt;height:234pt;
1743 visibility:visible;mso-wrap-style:square'>
1744 <v:imagedata src="MCSA%20in%20GSAS_files/image021.png" o:title="" croptop="13685f"
1745  cropbottom="15961f" cropleft="36898f" cropright="13504f"/>
1746</v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312
1747src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="_x0000_i1041"><![endif]></span></p>
1748
1749<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1750
1751<p class=MsoNormal>The orientation is determined by rotation and translation
1752about a coordinate system centered on C1 and defined by the vectors C1-C2 and
1753C1-C3; you can change these via the pull downs (you can’t pick the same atom
1754for two of these so pick them appropriately; I chose C2, C3 &amp; C6). My new
1755model is</p>
1756
1757<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1758 id="Picture_x0020_36" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:4in;
1759 height:234.75pt;visibility:visible;mso-wrap-style:square'>
1760 <v:imagedata src="MCSA%20in%20GSAS_files/image023.png" o:title="" croptop="13609f"
1761  cropbottom="16027f" cropleft="37724f" cropright="12673f"/>
1762</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=313
1763src="MCSA%20in%20GSAS_files/image024.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
1764
1765<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1766
1767<p class=MsoNormal>Notice that the model includes H-atoms; they are not really
1768needed for MC/SA and will just make computation times a bit longer than
1769necessary. You should change the <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'>Residue name</span></b> to something
1772meaningful, I used <b style='mso-bidi-font-weight:normal'><span
1773style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1774mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
1775
1776<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
1777style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1778mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b> and select
1779the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1780mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA</span></b>
1781tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1782"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1783minor-latin'>MC/SA/Add rigid body</span></b>; select the only choice (<b
1784style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1785mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>)
1786from the popup selection box. The MC/SA window shows</p>
1787
1788<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1789 id="Picture_x0020_37" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:448.5pt;
1790 height:251.25pt;visibility:visible;mso-wrap-style:square'>
1791 <v:imagedata src="MCSA%20in%20GSAS_files/image025.png" o:title=""/>
1792</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=335
1793src="MCSA%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
1794
1795<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1796
1797<p class=MsoNormal>And the plot shows the arbitrarily positioned molecules.</p>
1798
1799<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1800 id="Picture_x0020_14" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:4in;
1801 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1802 <v:imagedata src="MCSA%20in%20GSAS_files/image027.png" o:title="" croptop="17592f"
1803  cropbottom="12829f" cropleft="38911f" cropright="11642f"/>
1804</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=310
1805src="MCSA%20in%20GSAS_files/image028.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
1806
1807<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1808
1809<p class=MsoNormal>You see the four equivalent molecules for space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>
1810whose centers fall within the unit cell; the reference one is that in the lower
1811left corner with C1 at the origin. You can enter values in the <span
1812class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1813"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1814minor-latin'>x<span class=GramE>,y,z</span></span></b></span> boxes and see how
1815the structure changes. Similarly, you can enter an angle in <span class=SpellE><b
1816style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1817mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>
1818or a vector in the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1819style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1820mso-hansi-theme-font:minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><span
1821style='mso-spacerun:yes'>  </span>box to see the effects of rotating the
1822molecule. Each of these parameters has a defined range for the MC/SA
1823optimization run we are about to do; they define the multidimensional search
1824volume. Within that volume will be a number of correct solutions to the
1825structure problem all related by translational and space group symmetry. One
1826can limit this volume by choosing more limited ranges, but here we’ll just go
1827with the default. We want to optimize the position and orientation of this
1828molecule; check the <b style='mso-bidi-font-weight:normal'><span
1829style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1830mso-hansi-theme-font:minor-latin'>x</span></b>, <b style='mso-bidi-font-weight:
1831normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1832minor-latin;mso-hansi-theme-font:minor-latin'>y</span></b> &amp; <b
1833style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1834mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>
1835boxes and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1836"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1837minor-latin'>AV</span></b> from the <span class=SpellE><b style='mso-bidi-font-weight:
1838normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1839minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>, <span
1840class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1841"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1842minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><b
1843style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1844mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Vary?</span></b>
1845<span class=GramE>pulldown</span>. The MC/SA window should look like</p>
1846
1847<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1848 id="_x0000_i1037" type="#_x0000_t75" style='width:448.5pt;height:193.5pt;
1849 visibility:visible;mso-wrap-style:square'>
1850 <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/>
1851</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258
1852src="MCSA%20in%20GSAS_files/image030.gif" v:shapes="_x0000_i1037"><![endif]></span><span
1853style='mso-spacerun:yes'> </span></p>
1854
1855<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1856
1857<p class=MsoNormal>This completes the set up for MC/SA processing. </p>
1858
1859<h2>Step 7. Monte Carlo/Simulated Annealing</h2>
1860
1861<p class=MsoNormal>Now go to the <b style='mso-bidi-font-weight:normal'><span
1862style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1863mso-hansi-theme-font:minor-latin'>General</span></b> tab; the MC/SA controls
1864are at the bottom of the window. To begin the setup of these controls, select a
1865source of the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1866"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1867minor-latin'>Reflection set</span></b> to be used in the MC/SA runs. The choice
1868is to use either the Pawley reflections or the Reflection List for the PWDR
1869data set. If you choose <b style='mso-bidi-font-weight:normal'><span
1870style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1871mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> then the
1872structure factors will be Pawley model values, <span class=SpellE><span
1873class=GramE>Fsq</span></span><span class=GramE>(</span><span class=SpellE>hkl</span>)
1874in Pawley table, and the covariance matrix developed from the refinement will
1875be used for peak overlap effects in the MC/SA calculations. Alternatively, if
1876you choose <b style='mso-bidi-font-weight:normal'><span style='font-family:
1877"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1878minor-latin'>PWDR <span class=SpellE>Quinoli.gda</span> Bank 1 </span></b>then
1879the structure factors will be those, <span class=SpellE>Fosq</span> in
1880Reflection table, extracted during the Pawley refinement and the peak FWHMs
1881will be used for peak overlap effects in the MC/SA calculations. Notice that
1882the Pawley <span class=SpellE><span class=GramE>Fsq</span></span><span
1883class=GramE>(</span><span class=SpellE>hkl</span>) values are the same as the <span
1884class=SpellE>Fcsq</span> Reflection List values. Here I chose <b
1885style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1886mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR <span
1887class=SpellE>Quinoli.gda</span> Bank 1 </span></b>for the <b style='mso-bidi-font-weight:
1888normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1889minor-latin;mso-hansi-theme-font:minor-latin'>Reflection set</span></b> as it
1890give slightly better performance in MC/SA.</p>
1891
1892<p class=MsoNormal>Next, you need to set the minimum d-spacing (<b
1893style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1894mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>d-min</span></b>).
1895Smaller values gives minima in the MC/SA minimization surface that are more
1896sharply defined (thus harder to locate), while larger values yield insufficient
1897numbers of reflections to give sufficient redundancy in the calculations. One
1898should have 5-8 reflections for each MC/SA parameter; in this case 35-50
1899reflections are needed. If you examine the reflection list (either <b
1900style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1901mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley</span></b>
1902or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1903mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1904List</span></b>) you’ll see that a <b style='mso-bidi-font-weight:normal'><span
1905style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1906mso-hansi-theme-font:minor-latin'>d-min</span></b> of <b style='mso-bidi-font-weight:
1907normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1908minor-latin;mso-hansi-theme-font:minor-latin'>2.5</span></b> will give
1909sufficient reflections.</p>
1910
1911<p class=MsoNormal>Lastly, you need to set the run controls. I used <b
1912style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1913mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>500</span></b>
1914for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1915mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. trials</span></b>;
1916this is the number of random tries at each “temperature” in the annealing
1917schedule. I also used <b style='mso-bidi-font-weight:normal'><span
1918style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1919mso-hansi-theme-font:minor-latin'>4 MC/SA runs</span></b> <span class=GramE>When</span>
1920done the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1921mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1922window should look like</p>
1923
1924<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1925 id="Picture_x0020_38" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:7in;
1926 height:375pt;visibility:visible;mso-wrap-style:square'>
1927 <v:imagedata src="MCSA%20in%20GSAS_files/image031.png" o:title=""/>
1928</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500
1929src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_38"><![endif]></span></p>
1930
1931<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1932
1933<p class=MsoNormal>When ready, you can start the MC/SA calculation by doing <b
1934style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1935mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>
1936from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1937mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1938window menu. A progress bar will appear that shows the MC/SA residual (an
1939R-factor) as the calculation progresses through the annealing schedule as well
1940as indicating which MC/SA run is being done. When it finishes, control is
1941shifted to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1942"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1943minor-latin'>MC/SA</span></b> window which gives a list of the solutions it
1944found at the bottom of the window (scroll down to see them).</p>
1945
1946<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1947 id="Picture_x0020_39" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:564pt;
1948 height:273.75pt;visibility:visible;mso-wrap-style:square'>
1949 <v:imagedata src="MCSA%20in%20GSAS_files/image033.png" o:title=""/>
1950</v:shape><![endif]--><![if !vml]><img border=0 width=752 height=365
1951src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
1952
1953<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1954
1955<p class=MsoNormal>The one with the lowest residual is already chosen and the
1956corresponding structure is drawn</p>
1957
1958<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1959 id="Picture_x0020_1" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:364.5pt;
1960 height:298.5pt;visibility:visible;mso-wrap-style:square'>
1961 <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title="" croptop="8643f"
1962  cropbottom="21002f" cropleft="39996f" cropright="10456f"/>
1963</v:shape><![endif]--><![if !vml]><img border=0 width=486 height=398
1964src="MCSA%20in%20GSAS_files/image036.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
1965
1966<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1967
1968<p class=MsoNormal>If you are lucky (like I was!) then the result is clearly a
1969good solution with a very low Residual (~4.8%). This problem typically gives
1970suitable solutions with Residuals of 4-5%. If your cell indexing resulted in <span
1971class=GramE>a &amp;</span> b swapped, you should view the structure along b
1972(green). If no good solution appears (e.g. molecules clashing), then you should
1973just rerun MC/SA perhaps using more runs or more trials. Be sure to set the <b
1974style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1975mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Keep</span></b>
1976box for any solutions you want to retain; the others will be cleared before the
1977next MC/SA run starts. When you think you have a good one, <span class=GramE><b
1978style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1979mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select</span></b></span>
1980it; the parameters will be copied to the appropriate boxes in the upper part of
1981the MC/SA window and the structure is drawn again. Next we want to refine this
1982solution so go back to the <b style='mso-bidi-font-weight:normal'><span
1983style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1984mso-hansi-theme-font:minor-latin'>General</span></b> tab.</p>
1985
1986<p class=MsoNormal>MC/SA refinement is achieved by narrowing the search ranges
1987and rerunning the MC/SA calculations. This is done by checking the <b
1988style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1989mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA Refine</span></b>
1990box. Using 10% of the ranges reduces the search volume in this case by ~6
1991orders of magnitude so that the true minimum is much easier to find. Now rerun <b
1992style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1993mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>;
1994be sure to select the best one before starting. The residual should drop to a
1995much lower level. This refinement can be repeated with tighter restriction on
1996the ranges; I used 5% for a final run and got</p>
1997
1998<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1999 id="Picture_x0020_40" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:448.5pt;
2000 height:273.75pt;visibility:visible;mso-wrap-style:square'>
2001 <v:imagedata src="MCSA%20in%20GSAS_files/image037.png" o:title=""/>
2002</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=365
2003src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
2004
2005<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2006
2007<p class=MsoNormal>This is clearly a good result (R ~ <span class=GramE>2.6%</span>!)
2008and the structure</p>
2009
2010<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2011 id="Picture_x0020_23" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:288.75pt;
2012 height:248.25pt;visibility:visible;mso-wrap-style:square'>
2013 <v:imagedata src="MCSA%20in%20GSAS_files/image039.png" o:title="" croptop="11555f"
2014  cropbottom="16469f" cropleft="37988f" cropright="12498f"/>
2015</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=331
2016src="MCSA%20in%20GSAS_files/image040.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
2017
2018<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2019
2020<p class=MsoNormal><span class=GramE>is</span> identical to the published one</p>
2021
2022<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2023 id="Picture_x0020_24" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:288.75pt;
2024 height:225.75pt;visibility:visible;mso-wrap-style:square'>
2025 <v:imagedata src="MCSA%20in%20GSAS_files/image041.png" o:title="" croptop="14378f"
2026  cropbottom="21852f" cropleft="3509f" cropright="49103f"/>
2027</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301
2028src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
2029
2030<p class=MsoNormal><span class=GramE>as</span> drawn by the Mercury program </p>
2031
2032<p class=MsoNormal>(<a
2033href="https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx">https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx</a>).
2034To save this solution to the <b style='mso-bidi-font-weight:normal'><span
2035style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2036mso-hansi-theme-font:minor-latin'>Atoms</span></b> list do <b style='mso-bidi-font-weight:
2037normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2038minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA/Move MC/SA solution</span></b>;
2039the drawing will show the new atom positions</p>
2040
2041<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2042 id="Picture_x0020_25" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:4in;
2043 height:243.75pt;visibility:visible;mso-wrap-style:square'>
2044 <v:imagedata src="MCSA%20in%20GSAS_files/image043.png" o:title="" croptop="12581f"
2045  cropbottom="15938f" cropleft="37111f" cropright="13377f"/>
2046</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=325
2047src="MCSA%20in%20GSAS_files/image044.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
2048
2049<p class=MsoNormal>And they will be listed in the Atoms table.</p>
2050
2051<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2052 id="Picture_x0020_26" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
2053 height:225pt;visibility:visible;mso-wrap-style:square'>
2054 <v:imagedata src="MCSA%20in%20GSAS_files/image045.png" o:title=""/>
2055</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
2056src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
2057
2058<p class=MsoNormal>It is now ready for Rietveld refinement; this needs to use
2059the rigid body as the data will not support independent atom position
2060refinement.</p>
2061
2062<h2>Step 8. Initial Rietveld refinement</h2>
2063
2064<p class=MsoNormal>After a few simple steps the 3-aminoquinoline structure will
2065be ready for the first Rietveld refinement: 1) On the <b style='mso-bidi-font-weight:
2066normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2067minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab uncheck
2068the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2069mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley
2070refinement?</span></b> box, 2) check the <b style='mso-bidi-font-weight:normal'><span
2071style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2072mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> box in <b
2073style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2074mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
2075Parameters</span></b> and 3) zero both <b style='mso-bidi-font-weight:normal'><span
2076style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2077mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
2078normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2079minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> and uncheck their
2080refine boxes in <b style='mso-bidi-font-weight:normal'><span style='font-family:
2081"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2082minor-latin'>Instrument Parameters</span></b>. Then do <b style='mso-bidi-font-weight:
2083normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2084minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
2085the main GSAS-II data tree window; my <span class=SpellE>R<sub>wp</sub></span>
2086was ~9%. Next check the <b style='mso-bidi-font-weight:normal'><span
2087style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2088mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> in the <b
2089style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2090mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2091window and in the <b style='mso-bidi-font-weight:normal'><span
2092style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2093mso-hansi-theme-font:minor-latin'>Data</span></b> window, using the <b
2094style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2095mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>uniaxial</span></b>
2096model for <span class=SpellE>mustrain</span>, check both <span class=SpellE><b
2097style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2098mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b
2099style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2100mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span
2101class=GramE>size</span></span></b> &amp; <span class=SpellE><b
2102style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2103mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b></span>
2104boxes and do another <b style='mso-bidi-font-weight:normal'><span
2105style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2106mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I got an <span
2107class=SpellE>R<sub>wp</sub></span> ~8.5% for this. We’ve not refined atom
2108positions or thermal parameters; to do this we need to describe the structure
2109as a rigid body.</p>
2110
2111<h2>Step 9. Rigid body model</h2>
2112
2113<p class=MsoNormal>The rigid body itself has already been defined; it was used
2114for the MC/SA structure solution. Now we have to place it in the unit cell
2115matching the atom positions obtained from the MC/SA runs. First go to the <b
2116style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2117mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
2118tab and change the <b style='mso-bidi-font-weight:normal'><span
2119style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2120mso-hansi-theme-font:minor-latin'>Style</span></b> to <b style='mso-bidi-font-weight:
2121normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2122minor-latin;mso-hansi-theme-font:minor-latin'>balls &amp; sticks</span></b> and
2123the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2124mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Label</span></b>
2125to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2126mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>name</span></b>.
2127Double click on the column headings and select the item from the popup control.
2128Next go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2129"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2130minor-latin'>RB Models</span></b> tab; it will be empty. Do <b
2131style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2132mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assign
2133atoms to rigid body</span></b>; then select <b style='mso-bidi-font-weight:
2134normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2135minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b> in the <b
2136style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2137mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select rigid
2138body model</span></b> pull down (the only choice). The <b style='mso-bidi-font-weight:
2139normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2140minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window will
2141show</p>
2142
2143<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2144 id="Picture_x0020_27" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:337.5pt;
2145 height:218.25pt;visibility:visible;mso-wrap-style:square'>
2146 <v:imagedata src="MCSA%20in%20GSAS_files/image047.png" o:title=""/>
2147</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=291
2148src="MCSA%20in%20GSAS_files/image048.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
2149
2150<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2151
2152<p class=MsoNormal>You will orient the rigid body against the atoms by matching
2153up the 3 reference atoms in the rigid body (C1, C2 &amp; C5) to the
2154corresponding atoms in the structure (C(2), C(3) &amp; C(6)). Do these in
2155order; the drawing will show the shift of molecular origin and then its
2156reorientation as the three atoms are selected. Press <span class=GramE><b
2157style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2158mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ready</span></b></span>
2159when done; the structure will be drawn with yellow bonds indicating that it is
2160now a rigid body and not independent atoms. The <b style='mso-bidi-font-weight:
2161normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2162minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window shows
2163the new rigid body</p>
2164
2165<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2166 id="Picture_x0020_29" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:474.75pt;
2167 height:210pt;visibility:visible;mso-wrap-style:square'>
2168 <v:imagedata src="MCSA%20in%20GSAS_files/image049.png" o:title=""/>
2169</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=280
2170src="MCSA%20in%20GSAS_files/image050.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
2171
2172<p class=MsoNormal>To refine the rigid body parameters check the <b
2173style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2174mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
2175<span class=GramE>box</span>, select <b style='mso-bidi-font-weight:normal'><span
2176style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2177mso-hansi-theme-font:minor-latin'>AV</span></b> from the pull down, choose <span
2178class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2179"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2180minor-latin'>Uiso</span></b></span> from the thermal parameter model and check
2181its <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2182mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
2183<span class=GramE>box</span>. Then do <b style='mso-bidi-font-weight:normal'><span
2184style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2185mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; after a couple
2186of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span> ~7.9% and
2187the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2188style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2189mso-hansi-theme-font:minor-latin'>RBModels</span></b></span> window shows the
2190new parameters</p>
2191
2192<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2193 id="Picture_x0020_32" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:474.75pt;
2194 height:225.75pt;visibility:visible;mso-wrap-style:square'>
2195 <v:imagedata src="MCSA%20in%20GSAS_files/image051.png" o:title=""/>
2196</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=301
2197src="MCSA%20in%20GSAS_files/image052.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
2198
2199<p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
2200
2201<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2202 id="Picture_x0020_31" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
2203 height:450pt;visibility:visible;mso-wrap-style:square'>
2204 <v:imagedata src="MCSA%20in%20GSAS_files/image053.png" o:title=""/>
2205</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2206src="MCSA%20in%20GSAS_files/image054.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
2207
2208<p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.
2209Next is a more complex case involving some internal degrees of freedom in the
2210molecule of a-d-<span class=GramE>lactose.</span></p>
2211
2212</div>
2213
2214</body>
2215
2216</html>
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