source: Tutorials/MCsimanneal/MCSA in GSAS.htm @ 1705

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380        margin-right:0in;
381        mso-margin-bottom-alt:auto;
382        margin-left:0in;
383        mso-pagination:widow-orphan;
384        mso-outline-level:1;
385        font-size:24.0pt;
386        font-family:"Times New Roman","serif";
387        mso-fareast-font-family:"Times New Roman";
388        mso-fareast-theme-font:minor-fareast;
389        font-weight:bold;}
390h2
391        {mso-style-priority:9;
392        mso-style-unhide:no;
393        mso-style-qformat:yes;
394        mso-style-link:"Heading 2 Char";
395        mso-margin-top-alt:auto;
396        margin-right:0in;
397        mso-margin-bottom-alt:auto;
398        margin-left:0in;
399        mso-pagination:widow-orphan;
400        mso-outline-level:2;
401        font-size:18.0pt;
402        font-family:"Times New Roman","serif";
403        mso-fareast-font-family:"Times New Roman";
404        mso-fareast-theme-font:minor-fareast;
405        font-weight:bold;}
406h3
407        {mso-style-priority:9;
408        mso-style-unhide:no;
409        mso-style-qformat:yes;
410        mso-style-link:"Heading 3 Char";
411        mso-margin-top-alt:auto;
412        margin-right:0in;
413        mso-margin-bottom-alt:auto;
414        margin-left:0in;
415        mso-pagination:widow-orphan;
416        mso-outline-level:3;
417        font-size:13.5pt;
418        font-family:"Times New Roman","serif";
419        mso-fareast-font-family:"Times New Roman";
420        mso-fareast-theme-font:minor-fareast;
421        font-weight:bold;}
422h4
423        {mso-style-priority:9;
424        mso-style-unhide:no;
425        mso-style-qformat:yes;
426        mso-style-link:"Heading 4 Char";
427        margin-top:10.0pt;
428        margin-right:0in;
429        margin-bottom:0in;
430        margin-left:0in;
431        margin-bottom:.0001pt;
432        mso-pagination:widow-orphan;
433        page-break-after:avoid;
434        mso-outline-level:4;
435        font-size:13.0pt;
436        font-family:"Cambria","serif";
437        mso-fareast-font-family:"Times New Roman";
438        mso-fareast-theme-font:minor-fareast;
439        mso-bidi-font-family:"Times New Roman";
440        color:#4F81BD;
441        font-weight:bold;
442        font-style:italic;}
443h5
444        {mso-style-priority:9;
445        mso-style-unhide:no;
446        mso-style-qformat:yes;
447        mso-style-link:"Heading 5 Char";
448        mso-margin-top-alt:auto;
449        margin-right:0in;
450        mso-margin-bottom-alt:auto;
451        margin-left:0in;
452        mso-pagination:widow-orphan;
453        mso-outline-level:5;
454        font-size:12.0pt;
455        font-family:"Times New Roman","serif";
456        mso-fareast-font-family:"Times New Roman";
457        mso-fareast-theme-font:minor-fareast;
458        color:#4F4FFF;
459        font-weight:bold;}
460p.MsoTitle, li.MsoTitle, div.MsoTitle
461        {mso-style-noshow:yes;
462        mso-style-priority:10;
463        mso-style-unhide:no;
464        mso-style-qformat:yes;
465        mso-style-link:"Title Char";
466        margin-top:0in;
467        margin-right:0in;
468        margin-bottom:15.0pt;
469        margin-left:0in;
470        mso-pagination:widow-orphan;
471        font-size:26.0pt;
472        font-family:"Cambria","serif";
473        mso-fareast-font-family:"Times New Roman";
474        mso-fareast-theme-font:minor-fareast;
475        mso-bidi-font-family:"Times New Roman";
476        color:#17365D;
477        letter-spacing:.25pt;}
478a:link, span.MsoHyperlink
479        {mso-style-noshow:yes;
480        mso-style-priority:99;
481        color:blue;
482        text-decoration:underline;
483        text-underline:single;}
484a:visited, span.MsoHyperlinkFollowed
485        {mso-style-noshow:yes;
486        mso-style-priority:99;
487        color:purple;
488        text-decoration:underline;
489        text-underline:single;}
490p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
491        {mso-style-noshow:yes;
492        mso-style-priority:99;
493        mso-style-link:"Document Map Char";
494        margin:0in;
495        margin-bottom:.0001pt;
496        mso-pagination:widow-orphan;
497        font-size:8.0pt;
498        font-family:"Tahoma","sans-serif";
499        mso-fareast-font-family:"Times New Roman";
500        mso-fareast-theme-font:minor-fareast;}
501p
502        {mso-style-noshow:yes;
503        mso-style-priority:99;
504        mso-margin-top-alt:auto;
505        margin-right:0in;
506        mso-margin-bottom-alt:auto;
507        margin-left:0in;
508        mso-pagination:widow-orphan;
509        font-size:12.0pt;
510        font-family:"Times New Roman","serif";
511        mso-fareast-font-family:"Times New Roman";
512        mso-fareast-theme-font:minor-fareast;}
513pre
514        {mso-style-noshow:yes;
515        mso-style-priority:99;
516        mso-style-link:"HTML Preformatted Char";
517        margin:0in;
518        margin-bottom:.0001pt;
519        mso-pagination:widow-orphan;
520        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;
521        font-size:10.0pt;
522        font-family:"Courier New";
523        mso-fareast-font-family:"Times New Roman";
524        mso-fareast-theme-font:minor-fareast;}
525p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
526        {mso-style-noshow:yes;
527        mso-style-priority:99;
528        mso-style-link:"Balloon Text Char";
529        margin:0in;
530        margin-bottom:.0001pt;
531        mso-pagination:widow-orphan;
532        font-size:8.0pt;
533        font-family:"Tahoma","sans-serif";
534        mso-fareast-font-family:"Times New Roman";
535        mso-fareast-theme-font:minor-fareast;}
536span.MsoPlaceholderText
537        {mso-style-noshow:yes;
538        mso-style-priority:99;
539        mso-style-unhide:no;
540        color:gray;}
541p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
542        {mso-style-noshow:yes;
543        mso-style-priority:1;
544        mso-style-unhide:no;
545        mso-style-qformat:yes;
546        margin:0in;
547        margin-bottom:.0001pt;
548        mso-pagination:widow-orphan;
549        font-size:12.0pt;
550        font-family:"Times New Roman","serif";
551        mso-fareast-font-family:"Times New Roman";
552        mso-fareast-theme-font:minor-fareast;}
553p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
554        {mso-style-noshow:yes;
555        mso-style-priority:34;
556        mso-style-unhide:no;
557        mso-style-qformat:yes;
558        margin-top:0in;
559        margin-right:0in;
560        margin-bottom:0in;
561        margin-left:.5in;
562        margin-bottom:.0001pt;
563        mso-pagination:widow-orphan;
564        font-size:12.0pt;
565        font-family:"Times New Roman","serif";
566        mso-fareast-font-family:"Times New Roman";
567        mso-fareast-theme-font:minor-fareast;}
568span.MsoIntenseReference
569        {mso-style-priority:32;
570        mso-style-unhide:no;
571        mso-style-qformat:yes;
572        font-variant:small-caps;
573        color:#C0504D;
574        letter-spacing:.25pt;
575        font-weight:bold;
576        text-decoration:underline;
577        text-underline:single;}
578span.Heading1Char
579        {mso-style-name:"Heading 1 Char";
580        mso-style-priority:9;
581        mso-style-unhide:no;
582        mso-style-locked:yes;
583        mso-style-link:"Heading 1";
584        font-family:"Times New Roman","serif";
585        mso-ascii-font-family:"Times New Roman";
586        mso-hansi-font-family:"Times New Roman";
587        mso-bidi-font-family:"Times New Roman";
588        font-weight:bold;}
589span.Heading2Char
590        {mso-style-name:"Heading 2 Char";
591        mso-style-noshow:yes;
592        mso-style-priority:9;
593        mso-style-unhide:no;
594        mso-style-locked:yes;
595        mso-style-link:"Heading 2";
596        font-family:"Times New Roman","serif";
597        mso-ascii-font-family:"Times New Roman";
598        mso-hansi-font-family:"Times New Roman";
599        mso-bidi-font-family:"Times New Roman";
600        font-weight:bold;}
601span.Heading3Char
602        {mso-style-name:"Heading 3 Char";
603        mso-style-noshow:yes;
604        mso-style-priority:9;
605        mso-style-unhide:no;
606        mso-style-locked:yes;
607        mso-style-link:"Heading 3";
608        font-family:"Times New Roman","serif";
609        mso-ascii-font-family:"Times New Roman";
610        mso-hansi-font-family:"Times New Roman";
611        mso-bidi-font-family:"Times New Roman";
612        font-weight:bold;}
613span.Heading4Char
614        {mso-style-name:"Heading 4 Char";
615        mso-style-noshow:yes;
616        mso-style-priority:9;
617        mso-style-unhide:no;
618        mso-style-locked:yes;
619        mso-style-link:"Heading 4";
620        font-family:"Cambria","serif";
621        mso-ascii-font-family:Cambria;
622        mso-hansi-font-family:Cambria;
623        color:#4F81BD;
624        font-weight:bold;
625        font-style:italic;}
626span.Heading5Char
627        {mso-style-name:"Heading 5 Char";
628        mso-style-noshow:yes;
629        mso-style-priority:9;
630        mso-style-unhide:no;
631        mso-style-locked:yes;
632        mso-style-link:"Heading 5";
633        font-family:"Times New Roman","serif";
634        mso-ascii-font-family:"Times New Roman";
635        mso-hansi-font-family:"Times New Roman";
636        mso-bidi-font-family:"Times New Roman";
637        color:#4F4FFF;
638        font-weight:bold;}
639span.HTMLPreformattedChar
640        {mso-style-name:"HTML Preformatted Char";
641        mso-style-noshow:yes;
642        mso-style-priority:99;
643        mso-style-unhide:no;
644        mso-style-locked:yes;
645        mso-style-link:"HTML Preformatted";
646        font-family:"Courier New";
647        mso-ascii-font-family:"Courier New";
648        mso-hansi-font-family:"Courier New";
649        mso-bidi-font-family:"Courier New";}
650span.TitleChar
651        {mso-style-name:"Title Char";
652        mso-style-priority:10;
653        mso-style-unhide:no;
654        mso-style-locked:yes;
655        mso-style-link:Title;
656        font-family:"Cambria","serif";
657        mso-ascii-font-family:Cambria;
658        mso-hansi-font-family:Cambria;
659        color:#17365D;
660        letter-spacing:.25pt;}
661span.DocumentMapChar
662        {mso-style-name:"Document Map Char";
663        mso-style-noshow:yes;
664        mso-style-priority:99;
665        mso-style-unhide:no;
666        mso-style-locked:yes;
667        mso-style-link:"Document Map";
668        font-family:"Tahoma","sans-serif";
669        mso-ascii-font-family:Tahoma;
670        mso-hansi-font-family:Tahoma;
671        mso-bidi-font-family:Tahoma;}
672span.BalloonTextChar
673        {mso-style-name:"Balloon Text Char";
674        mso-style-noshow:yes;
675        mso-style-priority:99;
676        mso-style-unhide:no;
677        mso-style-locked:yes;
678        mso-style-link:"Balloon Text";
679        font-family:"Tahoma","sans-serif";
680        mso-ascii-font-family:Tahoma;
681        mso-hansi-font-family:Tahoma;
682        mso-bidi-font-family:Tahoma;}
683p.msotitlecxspfirst, li.msotitlecxspfirst, div.msotitlecxspfirst
684        {mso-style-name:msotitlecxspfirst;
685        mso-style-noshow:yes;
686        mso-style-priority:99;
687        mso-style-unhide:no;
688        margin:0in;
689        margin-bottom:.0001pt;
690        mso-pagination:widow-orphan;
691        font-size:26.0pt;
692        font-family:"Cambria","serif";
693        mso-fareast-font-family:"Times New Roman";
694        mso-fareast-theme-font:minor-fareast;
695        mso-bidi-font-family:"Times New Roman";
696        color:#17365D;
697        letter-spacing:.25pt;}
698p.msotitlecxspmiddle, li.msotitlecxspmiddle, div.msotitlecxspmiddle
699        {mso-style-name:msotitlecxspmiddle;
700        mso-style-noshow:yes;
701        mso-style-priority:99;
702        mso-style-unhide:no;
703        margin:0in;
704        margin-bottom:.0001pt;
705        mso-pagination:widow-orphan;
706        font-size:26.0pt;
707        font-family:"Cambria","serif";
708        mso-fareast-font-family:"Times New Roman";
709        mso-fareast-theme-font:minor-fareast;
710        mso-bidi-font-family:"Times New Roman";
711        color:#17365D;
712        letter-spacing:.25pt;}
713p.msotitlecxsplast, li.msotitlecxsplast, div.msotitlecxsplast
714        {mso-style-name:msotitlecxsplast;
715        mso-style-noshow:yes;
716        mso-style-priority:99;
717        mso-style-unhide:no;
718        margin-top:0in;
719        margin-right:0in;
720        margin-bottom:15.0pt;
721        margin-left:0in;
722        mso-pagination:widow-orphan;
723        font-size:26.0pt;
724        font-family:"Cambria","serif";
725        mso-fareast-font-family:"Times New Roman";
726        mso-fareast-theme-font:minor-fareast;
727        mso-bidi-font-family:"Times New Roman";
728        color:#17365D;
729        letter-spacing:.25pt;}
730p.msolistparagraphcxspfirst, li.msolistparagraphcxspfirst, div.msolistparagraphcxspfirst
731        {mso-style-name:msolistparagraphcxspfirst;
732        mso-style-noshow:yes;
733        mso-style-priority:99;
734        mso-style-unhide:no;
735        margin-top:0in;
736        margin-right:0in;
737        margin-bottom:0in;
738        margin-left:.5in;
739        margin-bottom:.0001pt;
740        mso-pagination:widow-orphan;
741        font-size:12.0pt;
742        font-family:"Times New Roman","serif";
743        mso-fareast-font-family:"Times New Roman";
744        mso-fareast-theme-font:minor-fareast;}
745p.msolistparagraphcxspmiddle, li.msolistparagraphcxspmiddle, div.msolistparagraphcxspmiddle
746        {mso-style-name:msolistparagraphcxspmiddle;
747        mso-style-noshow:yes;
748        mso-style-priority:99;
749        mso-style-unhide:no;
750        margin-top:0in;
751        margin-right:0in;
752        margin-bottom:0in;
753        margin-left:.5in;
754        margin-bottom:.0001pt;
755        mso-pagination:widow-orphan;
756        font-size:12.0pt;
757        font-family:"Times New Roman","serif";
758        mso-fareast-font-family:"Times New Roman";
759        mso-fareast-theme-font:minor-fareast;}
760p.msolistparagraphcxsplast, li.msolistparagraphcxsplast, div.msolistparagraphcxsplast
761        {mso-style-name:msolistparagraphcxsplast;
762        mso-style-noshow:yes;
763        mso-style-priority:99;
764        mso-style-unhide:no;
765        margin-top:0in;
766        margin-right:0in;
767        margin-bottom:0in;
768        margin-left:.5in;
769        margin-bottom:.0001pt;
770        mso-pagination:widow-orphan;
771        font-size:12.0pt;
772        font-family:"Times New Roman","serif";
773        mso-fareast-font-family:"Times New Roman";
774        mso-fareast-theme-font:minor-fareast;}
775p.msochpdefault, li.msochpdefault, div.msochpdefault
776        {mso-style-name:msochpdefault;
777        mso-style-noshow:yes;
778        mso-style-priority:99;
779        mso-style-unhide:no;
780        mso-margin-top-alt:auto;
781        margin-right:0in;
782        mso-margin-bottom-alt:auto;
783        margin-left:0in;
784        mso-pagination:widow-orphan;
785        font-size:10.0pt;
786        font-family:"Calibri","sans-serif";
787        mso-fareast-font-family:"Times New Roman";
788        mso-fareast-theme-font:minor-fareast;
789        mso-bidi-font-family:Calibri;}
790span.SpellE
791        {mso-style-name:"";
792        mso-spl-e:yes;}
793span.GramE
794        {mso-style-name:"";
795        mso-gram-e:yes;}
796.MsoChpDefault
797        {mso-style-type:export-only;
798        mso-default-props:yes;
799        font-size:10.0pt;
800        mso-ansi-font-size:10.0pt;
801        mso-bidi-font-size:10.0pt;
802        font-family:"Calibri","sans-serif";
803        mso-ascii-font-family:Calibri;
804        mso-hansi-font-family:Calibri;
805        mso-bidi-font-family:Calibri;}
806@page WordSection1
807        {size:8.5in 11.0in;
808        margin:1.0in 1.0in 1.0in 1.0in;
809        mso-header-margin:.5in;
810        mso-footer-margin:.5in;
811        mso-paper-source:0;}
812div.WordSection1
813        {page:WordSection1;}
814 /* List Definitions */
815 @list l0
816        {mso-list-id:608973138;
817        mso-list-type:hybrid;
818        mso-list-template-ids:-1449999034 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
819@list l0:level1
820        {mso-level-tab-stop:none;
821        mso-level-number-position:left;
822        text-indent:-.25in;}
823@list l0:level2
824        {mso-level-number-format:alpha-lower;
825        mso-level-tab-stop:none;
826        mso-level-number-position:left;
827        text-indent:-.25in;}
828@list l0:level3
829        {mso-level-number-format:roman-lower;
830        mso-level-tab-stop:none;
831        mso-level-number-position:right;
832        text-indent:-9.0pt;}
833@list l0:level4
834        {mso-level-tab-stop:none;
835        mso-level-number-position:left;
836        text-indent:-.25in;}
837@list l0:level5
838        {mso-level-number-format:alpha-lower;
839        mso-level-tab-stop:none;
840        mso-level-number-position:left;
841        text-indent:-.25in;}
842@list l0:level6
843        {mso-level-number-format:roman-lower;
844        mso-level-tab-stop:none;
845        mso-level-number-position:right;
846        text-indent:-9.0pt;}
847@list l0:level7
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946
947<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
948
949<div class=WordSection1>
950
951<h1><span style='mso-fareast-font-family:"Times New Roman"'>MC/SA in GSAS-II<o:p></o:p></span></h1>
952
953<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction: <o:p></o:p></span></h2>
954
955<p class=MsoNormal>In these exercises you will use GSAS-II to solve the
956structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
957diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
958were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
959and were originally collected on NSLS beam line X3b1. The MC/SA technique is
960needed in these cases because as you will see the data does not extend very far
961in 2&#920; so one cannot use charge flipping to solve them. The steps for each
962begin with peak selection and fitting, then indexing to identify the lattice
963parameters. A Pawley refinement is used to obtain a set of structure factors
964needed for the MC/SA runs. We will use previously developed models for the two
965molecules; I used the freeware program Avogadro (<a
966href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
967to create them.</p>
968
969<p class=MsoNormal>If you have not done so already, <a
970href="Starting%20GSAS.htm">start GSAS-II</a>.</p>
971
972<h2><span class=GramE>Step 1.</span> Import powder data for 3-aminoquinoline</h2>
973
974<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
975style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
976style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
977the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
978mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
979Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder
980data file</span></b> menu item to read the data file into the current GSAS-II
981project. Change the file directory to <b style='mso-bidi-font-weight:normal'><span
982style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
983mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
984minor-latin'>Exercises/MCSA</span></b><span style='font-family:"Calibri","sans-serif";
985mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
986Calibri;mso-bidi-theme-font:minor-latin'> to find the file; you may need to
987change the file type to <b style='mso-bidi-font-weight:normal'>All files (*.*)</b>
988to find the desired file.</span></p>
989
990<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
991style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
992style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
993the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
994style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
995mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
996minor-latin'>Quinoli.gda</span></b></span><span style='font-family:"Calibri","sans-serif";
997mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
998Calibri;mso-bidi-theme-font:minor-latin'> data</span> file in the first dialog
999and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1000mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1001Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
1002Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1003style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1004mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1005minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
1006style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1007mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1008minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
1009style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1010mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1011Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
1012proceed.</p>
1013
1014<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1015style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1016style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1017the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1018mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1019Calibri;mso-bidi-theme-font:minor-latin'>BNL-<span class=SpellE>I.instprm</span></span></b>
1020instrument parameter file in the second dialog and press <b style='mso-bidi-font-weight:
1021normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1022minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1023mso-bidi-theme-font:minor-latin'>Open</span></b>. You’ll have to change the
1024file type to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1025"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1026minor-latin'>*.<span class=SpellE>instprm</span></span></b> (GSAS-II instrument
1027parameter file). The powder pattern will immediately appear.</p>
1028
1029<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
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1054
1055<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1056
1057<p class=MsoListParagraph>Notice that the pattern extends only to a minimum
1058d-spacing of ~1.81Å; this is not far enough to use charge flipping which needs
10591Å or better. </p>
1060
1061<h2><span class=GramE>Step 2.</span> Peak picking &amp; fitting</h2>
1062
1063<p class=MsoNormal>Next you need to select limits so that ~20 peaks are
1064selected for indexing; go to <b style='mso-bidi-font-weight:normal'><span
1065style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1066mso-hansi-theme-font:minor-latin'>Limits</span></b> and choose <b
1067style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1068mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>9-25</span></b>°
10692&#920;. Next go to <b style='mso-bidi-font-weight:normal'><span
1070style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1071mso-hansi-theme-font:minor-latin'>Peak List</span></b> and pick all the peaks
1072you can see between the limits. This is most easily done by hand as the <b
1073style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1074mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Auto search</span></b>
1075routine gives a lot of spurious peaks for this rather noisy and weak data; I
1076picked 21 peaks, skipping a few very weak ones. Then use <b style='mso-bidi-font-weight:
1077normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1078minor-latin;mso-hansi-theme-font:minor-latin'>Peak fitting/LSQ <span
1079class=SpellE>PeakFit</span> </span></b>to fit them. You will need to vary at
1080least <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1081mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
1082&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1083mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
1084in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1085mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1086Parameters</span></b> along with <span class=SpellE><b style='mso-bidi-font-weight:
1087normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1088minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span> &amp; <span
1089class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1090"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1091minor-latin'>int</span></b></span> in the <b style='mso-bidi-font-weight:normal'><span
1092style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1093mso-hansi-theme-font:minor-latin'>Peak List</span></b> to get a reasonable fit
1094suitable for indexing.</p>
1095
1096<h2><span class=GramE>Step 3.</span> Indexing</h2>
1097
1098<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
1099style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1100mso-hansi-theme-font:minor-latin'>Index Peak List</span></b> and do <b
1101style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1102mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1103to set up the peaks for indexing. Then go to <b style='mso-bidi-font-weight:
1104normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1105minor-latin;mso-hansi-theme-font:minor-latin'>Unit Cells List</span></b> for
1106indexing. The most likely <span class=SpellE>Bravais</span> lattice for these
1107small organic molecules is either Orthorhombic-P or Monoclinic-P; you can try
1108both and see what comes out (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
1109style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1110mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>). The correct unit
1111cell should almost immediately appear with an M20 ~330 with a=7.748, b=7.651,
1112c=12.736, <span class=SpellE>Vol</span>=755.01. Do <b style='mso-bidi-font-weight:
1113normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1114minor-latin;mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Copy Cell</span></b>;
1115you can then try various space groups. Press the <b style='mso-bidi-font-weight:
1116normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1117minor-latin;mso-hansi-theme-font:minor-latin'>Show HKL positions</span></b> to
1118see the lines with extinctions (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
1119style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1120mso-hansi-theme-font:minor-latin'>P 2<sub>1</sub> 2<sub>1</sub> 2<sub>1</sub></span></b>).
1121You can then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1122"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1123minor-latin'>Cell Index/Refine/Refine Cell</span></b> to improve the lattice
1124parameters with M20 ~380. Finally do <b style='mso-bidi-font-weight:normal'><span
1125style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1126mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Make new phase</span></b>
1127to create the phase; I named it <b style='mso-bidi-font-weight:normal'><span
1128style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1129mso-hansi-theme-font:minor-latin'>3-aminoquinoline</span></b>.</p>
1130
1131<h2><span class=GramE>Step 4.</span> Setup for Pawley refinement</h2>
1132
1133<p class=MsoNormal>There are a number of steps that must be done in preparation
1134for a Pawley refinement after having completed the unit cell indexing and new
1135phase creation. These cover two things: one is to prepare the powder pattern
1136(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1137
1138<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1139style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1140style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1141<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1142mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
1143in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1144region at the end of the data is readily seen. This is ~37deg 2<span
1145style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
1146"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
1147style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>;
1148there is a zero point at the end that needs to be excluded. Use the right mouse
1149button and pick a point just inside the end avoiding the zero. Make a note of
1150the exact d-spacing (for me 1.8133) using the mouse cursor on the plot.</p>
1151
1152<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1153style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1154style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1155<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1156mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1157Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1158style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1159mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1160style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1161mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1162profile</span></b> to recover the default values. The peak fitting done earlier
1163is over a more limited range of 2<span style='font-family:Symbol;mso-ascii-font-family:
1164"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
1165mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
1166Symbol'>Q</span></span> giving values that will not extrapolate well over the
1167wider range to be used in the Pawley refinement. We may refine them again
1168later.</p>
1169
1170<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1171style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1172style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1173<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1174mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b>
1175and uncheck refinement of <b style='mso-bidi-font-weight:normal'><span
1176style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1177mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
1178
1179<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1180style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1181style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1182to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1183mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b>
1184to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1185"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1186minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1187normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1188minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
1189box and enter the d-spacing (1.8133) into the <b style='mso-bidi-font-weight:
1190normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1191minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
1192box.</p>
1193
1194<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1195style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1196mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1197
1198<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1199 id="Picture_x0020_2" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:465.75pt;
1200 height:375pt;visibility:visible;mso-wrap-style:square'>
1201 <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/>
1202</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=500
1203src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
1204
1205<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1206
1207<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1208style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1209mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1210for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
1211style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1212mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
1213dialog box will appear</p>
1214
1215<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1216 id="Picture_x0020_3" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:259.5pt;
1217 height:252pt;visibility:visible;mso-wrap-style:square'>
1218 <v:imagedata src="MCSA%20in%20GSAS_files/image005.png" o:title=""/>
1219</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1220src="MCSA%20in%20GSAS_files/image033.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
1221
1222<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1223
1224<p class=MsoNormal>Select either choice; the desired data set will be added to
1225this phase for analysis. The data tab now shows the new data set; check the <b
1226style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1227mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
1228button to see the full information</p>
1229
1230<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1231 id="Picture_x0020_28" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:359.25pt;
1232 height:375pt;visibility:visible;mso-wrap-style:square'>
1233 <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/>
1234</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500
1235src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
1236
1237<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1238
1239<p class=MsoNormal>This is the location for all the phase dependent parameters
1240for this histogram. Notice that it includes phase fraction, size &amp; <span
1241class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1242and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1243intended for protein work where a significant region of the structure is
1244disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1245surfaces and preferred orientation correction curves.</p>
1246
1247<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1248style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1249mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1250empty except for column headings. <span class=GramE>Do</span> <b
1251style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1252mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley
1253create</span></b>; this makes the reflection set over the range covered by
1254setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1255mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1256class=SpellE>dmin</span></span></b>. The table should list reflections 0-91.
1257Select and check the <b style='mso-bidi-font-weight:normal'><span
1258style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1259mso-hansi-theme-font:minor-latin'>refine</span></b> column using the same
1260technique you used for the peak list. </p>
1261
1262<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1263 id="Picture_x0020_5" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;
1264 height:225pt;visibility:visible;mso-wrap-style:square'>
1265 <v:imagedata src="MCSA%20in%20GSAS_files/image009.png" o:title=""/>
1266</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
1267src="MCSA%20in%20GSAS_files/image035.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
1268
1269<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1270
1271<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1272you didn’t skip a step as it might not work correctly if you did.</p>
1273
1274<h2><span class=GramE>Step 5.</span> Pawley refinement</h2>
1275
1276<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1277normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1278minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1279the main GSAS-II data tree window. Before it begins a backup of the project
1280file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
1281style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1282mso-hansi-theme-font:minor-latin'>aminoquinoline.bck0.gpx</span></b>. It can be
1283used to recover from a bad refinement. A progress dialog box will appear
1284showing the residual as the refinement proceeds. My refinement completed with <span
1285class=SpellE>Rwp</span> ~12.9%; a dialog box appears asking if you wish to load
1286the result. Press <b style='mso-bidi-font-weight:normal'><span
1287style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1288mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
1289PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
1290
1291<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1292 id="Picture_x0020_6" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
1293 height:450pt;visibility:visible;mso-wrap-style:square'>
1294 <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/>
1295</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1296src="MCSA%20in%20GSAS_files/image036.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
1297
1298<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1299
1300<p class=MsoNormal>I’ve expanded the vertical scale to show the fit; it is
1301evident from examining the plot that improvement can be had by improving the
1302background model. One easy way to fit that broad hump is to add a peak to the
1303background. Go to <b style='mso-bidi-font-weight:normal'><span
1304style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1305mso-hansi-theme-font:minor-latin'>Background</span></b> and set <b
1306style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1307mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. peaks</span></b>
1308to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1309mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>,
1310then change <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1311style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1312mso-hansi-theme-font:minor-latin'>pos</span></b></span> to <b style='mso-bidi-font-weight:
1313normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1314minor-latin;mso-hansi-theme-font:minor-latin'>19</span></b>, <span
1315class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1316"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1317minor-latin'>int</span></b></span> to <b style='mso-bidi-font-weight:normal'><span
1318style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1319mso-hansi-theme-font:minor-latin'>100000</span></b> and <b style='mso-bidi-font-weight:
1320normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1321minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> to <b
1322style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1323mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>;
1324for the peak only refine <b style='mso-bidi-font-weight:normal'><span
1325style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1326mso-hansi-theme-font:minor-latin'>int</span></b>. I also set <b
1327style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1328mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
1329class=SpellE>coeff</span>.</span></b> <span class=GramE>to</span> <b
1330style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1331mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>;
1332the window shows</p>
1333
1334<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1335 id="Picture_x0020_7" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:402pt;
1336 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1337 <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/>
1338</v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
1339src="MCSA%20in%20GSAS_files/image037.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
1340
1341<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1342
1343<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
1344style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1345mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
1346class=SpellE>Rwp</span> fell to ~8.5%. In <b style='mso-bidi-font-weight:normal'><span
1347style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1348mso-hansi-theme-font:minor-latin'>Background</span></b> select <span
1349class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1350"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1351minor-latin'>pos</span></b></span> &amp; <b style='mso-bidi-font-weight:normal'><span
1352style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1353mso-hansi-theme-font:minor-latin'>sig</span></b> for refinement and in <b
1354style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1355mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1356Parameters</span></b> select <b style='mso-bidi-font-weight:normal'><span
1357style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1358mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
1359normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1360minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> for refinement; then
1361do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1362style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1363mso-hansi-theme-font:minor-latin'>Calculate</span></b></span><b
1364style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1365mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> /Refine</span></b>
1366again. I got Rwp~7.5% at convergence and the fit looked like</p>
1367
1368<p class=MsoNormal><span style='mso-no-proof:yes'>c<!--[if gte vml 1]><v:shape
1369 id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:525pt;
1370 height:450pt;visibility:visible;mso-wrap-style:square'>
1371 <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/>
1372</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1373src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
1374
1375<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1376
1377<p class=MsoNormal>This may be good enough to try Monte Carlo/Simulated
1378Annealing.</p>
1379
1380<h2><span class=GramE>Step 6.</span> Setup for Monte Carlo/Simulated Annealing</h2>
1381
1382<p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic rings
1383with one N-substituted position and an amino side group</p>
1384
1385<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1386 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:142.5pt;
1387 height:93.75pt;visibility:visible;mso-wrap-style:square'>
1388 <v:imagedata src="MCSA%20in%20GSAS_files/image017.png" o:title="" croptop="20629f"
1389  cropbottom="17428f" cropleft="9893f" cropright="13874f"/>
1390</v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125
1391src="MCSA%20in%20GSAS_files/image039.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
1392
1393<p class=MsoNormal>MC/SA structure solution consists of optimizing the position
1394and orientation of this object in the unit cell; it has no internal degrees of
1395freedom. Thus we need to determine essentially six parameters. To do this in
1396GSAS-II we need to put a model of this molecule in as a rigid body. One must
1397create the model outside of GSAS-<span class=GramE>II,</span> it has no
1398facilities for model building. I used the Avogadro (<a
1399href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
1400package for this and created a simple xyz Cartesian coordinate file for it (if
1401you have Avogadro or something equivalent you can try this for yourself). To
1402start go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1403"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1404minor-latin'>Rigid bodies</span></b> in the main GSAS-II data tree. You will
1405see a window with two tabs; select <b style='mso-bidi-font-weight:normal'><span
1406style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1407mso-hansi-theme-font:minor-latin'>Residue rigid bodies</span></b> and then do <b
1408style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1409mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Import
1410XYZ</span></b>. Change the file type to <b style='mso-bidi-font-weight:normal'><span
1411style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1412mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and select <span
1413class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1414"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1415minor-latin'>aminoquinoline.xyz</span></b></span>. The <b style='mso-bidi-font-weight:
1416normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1417minor-latin;mso-hansi-theme-font:minor-latin'>Rigid <span class=GramE>bodies</span></span></b>
1418window will show</p>
1419
1420<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1421 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:300pt;
1422 height:320.25pt;visibility:visible;mso-wrap-style:square'>
1423 <v:imagedata src="MCSA%20in%20GSAS_files/image019.png" o:title=""/>
1424</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=427
1425src="MCSA%20in%20GSAS_files/image040.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
1426
1427<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1428
1429<p class=MsoNormal><span class=GramE>If you select the <b style='mso-bidi-font-weight:
1430normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1431minor-latin;mso-hansi-theme-font:minor-latin'>Plot?</span></b></span> <span
1432class=GramE>box</span> a drawing will appear</p>
1433
1434<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1435 id="Picture_x0020_1" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:286.5pt;
1436 height:234pt;visibility:visible;mso-wrap-style:square'>
1437 <v:imagedata src="MCSA%20in%20GSAS_files/image021.png" o:title="" croptop="13685f"
1438  cropbottom="15961f" cropleft="36898f" cropright="13504f"/>
1439</v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312
1440src="MCSA%20in%20GSAS_files/image041.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
1441
1442<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1443
1444<p class=MsoNormal>The orientation is determined by rotation and translation
1445about a coordinate system centered on C1 and defined by the vectors C1-C2 and
1446C1-C3; you can change these via the pull downs (you can’t pick the same atom
1447for two of these so pick them appropriately; I chose C2, C3 &amp; C6). My new
1448model is</p>
1449
1450<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1451 id="Picture_x0020_36" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:4in;
1452 height:234.75pt;visibility:visible;mso-wrap-style:square'>
1453 <v:imagedata src="MCSA%20in%20GSAS_files/image023.png" o:title="" croptop="13609f"
1454  cropbottom="16027f" cropleft="37724f" cropright="12673f"/>
1455</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=313
1456src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
1457
1458<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1459
1460<p class=MsoNormal>Notice that the model includes H-atoms; they are not really
1461needed for MC/SA and will just make computation times a bit longer than
1462necessary. You should change the <b style='mso-bidi-font-weight:normal'><span
1463style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1464mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something meaningful,
1465I used <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1466mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
1467
1468<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
1469style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1470mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b> and select
1471the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1472mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA</span></b>
1473tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1474"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1475minor-latin'>MC/SA/Add rigid body</span></b>; select the only choice (<b
1476style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1477mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>)
1478from the popup selection box. The MC/SA window shows</p>
1479
1480<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1481 id="Picture_x0020_37" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:448.5pt;
1482 height:251.25pt;visibility:visible;mso-wrap-style:square'>
1483 <v:imagedata src="MCSA%20in%20GSAS_files/image025.png" o:title=""/>
1484</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=335
1485src="MCSA%20in%20GSAS_files/image043.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
1486
1487<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1488
1489<p class=MsoNormal>And the plot shows the arbitrarily positioned molecules.</p>
1490
1491<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1492 id="Picture_x0020_14" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:4in;
1493 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1494 <v:imagedata src="MCSA%20in%20GSAS_files/image044.png" o:title="" croptop="17592f"
1495  cropbottom="12829f" cropleft="38911f" cropright="11642f"/>
1496</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=310
1497src="MCSA%20in%20GSAS_files/image045.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
1498
1499<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1500
1501<p class=MsoNormal>You see the four equivalent molecules for space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>
1502whose centers fall within the unit cell; the reference one is that in the lower
1503left corner with C1 at the origin. You can enter values in the <span
1504class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1505"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1506minor-latin'>x<span class=GramE>,y,z</span></span></b></span> boxes and see how
1507the structure changes. Similarly, you can enter an angle in <span class=SpellE><b
1508style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1509mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>
1510or a vector in the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1511style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1512mso-hansi-theme-font:minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><span
1513style='mso-spacerun:yes'>  </span>box to see the effects of rotating the
1514molecule. Each of these parameters has a defined range for the MC/SA
1515optimization run we are about to do; they define the multidimensional search
1516volume. Within that volume will be a number of correct solutions to the
1517structure problem all related by translational and space group symmetry. One
1518can limit this volume by choosing more limited ranges, but here we’ll just go
1519with the default. We want to optimize the position and orientation of this
1520molecule; check the <b style='mso-bidi-font-weight:normal'><span
1521style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1522mso-hansi-theme-font:minor-latin'>x</span></b>, <b style='mso-bidi-font-weight:
1523normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1524minor-latin;mso-hansi-theme-font:minor-latin'>y</span></b> &amp; <b
1525style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1526mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>
1527boxes and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1528"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1529minor-latin'>AV</span></b> from the <span class=SpellE><b style='mso-bidi-font-weight:
1530normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1531minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>, <span
1532class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1533"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1534minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><b
1535style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1536mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Vary?</span></b>
1537<span class=SpellE><span class=GramE>pulldown</span></span>. The MC/SA window
1538should look like</p>
1539
1540<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1541 id="Picture_x0020_39" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:448.5pt;
1542 height:193.5pt;visibility:visible;mso-wrap-style:square'>
1543 <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/>
1544</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258
1545src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
1546style='mso-spacerun:yes'> </span></p>
1547
1548<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1549
1550<p class=MsoNormal>This completes the set up for MC/SA processing. </p>
1551
1552<h2><span class=GramE>Step 7.</span> Monte Carlo/Simulated Annealing</h2>
1553
1554<p class=MsoNormal>Now go to the <b style='mso-bidi-font-weight:normal'><span
1555style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1556mso-hansi-theme-font:minor-latin'>General</span></b> tab; the MC/SA controls
1557are at the bottom of the window. To begin the setup of these controls, select a
1558source of the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1559"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1560minor-latin'>Reflection set</span></b> to be used in the MC/SA runs. The choice
1561is to use either the Pawley reflections or the Reflection List for the PWDR
1562data set. If you choose <b style='mso-bidi-font-weight:normal'><span
1563style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1564mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> then the
1565structure factors will be Pawley model values, <span class=SpellE><span
1566class=GramE>Fsq</span></span><span class=GramE>(</span><span class=SpellE>hkl</span>)
1567in Pawley table, and the covariance matrix developed from the refinement will
1568be used for peak overlap effects in the MC/SA calculations. Alternatively, if
1569you choose <b style='mso-bidi-font-weight:normal'><span style='font-family:
1570"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1571minor-latin'>PWDR <span class=SpellE>Quinoli.gda</span> Bank 1 </span></b>then
1572the structure factors will be those, <span class=SpellE>Fosq</span> in
1573Reflection table, extracted during the Pawley refinement and the peak FWHMs
1574will be used for peak overlap effects in the MC/SA calculations. Notice that
1575the Pawley <span class=SpellE><span class=GramE>Fsq</span></span><span
1576class=GramE>(</span><span class=SpellE>hkl</span>) values are the same as the <span
1577class=SpellE>Fcsq</span> Reflection List values. Here I chose <b
1578style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1579mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1580reflections</span></b> for the <b style='mso-bidi-font-weight:normal'><span
1581style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1582mso-hansi-theme-font:minor-latin'>Reflection set</span></b> as it give slightly
1583better performance in MC/SA.</p>
1584
1585<p class=MsoNormal>Next, you need to set the minimum d-spacing (<b
1586style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1587mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>d-min</span></b>).
1588Smaller values gives minima in the MC/SA minimization surface that are more
1589sharply defined (thus harder to locate), while larger values yield insufficient
1590numbers of reflections to give sufficient redundancy in the calculations. One
1591should have 5-8 reflections for each MC/SA parameter; in this case 35-50
1592reflections are needed. If you examine the reflection list (either <b
1593style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1594mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley</span></b>
1595or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1596mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1597List</span></b>) you’ll see that a <b style='mso-bidi-font-weight:normal'><span
1598style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1599mso-hansi-theme-font:minor-latin'>d-min</span></b> of <b style='mso-bidi-font-weight:
1600normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1601minor-latin;mso-hansi-theme-font:minor-latin'>2.5</span></b> will give
1602sufficient reflections.</p>
1603
1604<p class=MsoNormal>Lastly, you need to set the run controls. I used <b
1605style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1606mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>500</span></b>
1607for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1608mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. trials</span></b>;
1609this is the number of random tries at each “temperature” in the annealing
1610schedule. When done the <b style='mso-bidi-font-weight:normal'><span
1611style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1612mso-hansi-theme-font:minor-latin'>General</span></b> window should look like</p>
1613
1614<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1615 id="Picture_x0020_16" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:7in;
1616 height:375pt;visibility:visible;mso-wrap-style:square'>
1617 <v:imagedata src="MCSA%20in%20GSAS_files/image030.png" o:title=""/>
1618</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500
1619src="MCSA%20in%20GSAS_files/image058.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
1620
1621<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1622
1623<p class=MsoNormal>When ready, you can start the MC/SA calculation by doing <b
1624style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1625mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>
1626from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1627mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1628window menu. A progress bar will appear that shows the MC/SA residual (an
1629R-factor) as the calculation progresses through the annealing schedule as well
1630as indicating which MC/SA run is being done. When it finishes, control is
1631shifted to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1632"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1633minor-latin'>MC/SA</span></b> window which gives a list of the solutions it
1634found at the bottom of the window (scroll down to see them).</p>
1635
1636<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1637 id="Picture_x0020_19" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:560.25pt;
1638 height:273.75pt;visibility:visible;mso-wrap-style:square'>
1639 <v:imagedata src="MCSA%20in%20GSAS_files/image048.png" o:title=""/>
1640</v:shape><![endif]--><![if !vml]><img border=0 width=747 height=365
1641src="MCSA%20in%20GSAS_files/image059.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
1642
1643<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1644
1645<p class=MsoNormal>The one with the lowest residual is already chosen and the
1646corresponding structure is drawn</p>
1647
1648<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1649 id="Picture_x0020_20" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:279.75pt;
1650 height:243.75pt;visibility:visible;mso-wrap-style:square'>
1651 <v:imagedata src="MCSA%20in%20GSAS_files/image050.png" o:title="" croptop="11773f"
1652  cropbottom="16530f" cropleft="37715f" cropright="13079f"/>
1653</v:shape><![endif]--><![if !vml]><img border=0 width=373 height=325
1654src="MCSA%20in%20GSAS_files/image060.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
1655
1656<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1657
1658<p class=MsoNormal>If you are lucky (like I was!) then the result is clearly a
1659good solution with a very low Residual (~4.8%). This problem typically gives
1660suitable solutions with Residuals of 4-5%. If no good solution appears (e.g.
1661molecules clashing), then you should just rerun MC/SA perhaps using more runs
1662or more trials. Be sure to set the <b style='mso-bidi-font-weight:normal'><span
1663style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1664mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any solutions you
1665want to retain; the others will be cleared before the next MC/SA run starts.
1666When you think you have a good one, <span class=GramE><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'>Select</span></b></span> it; the
1669parameters will be copied to the appropriate boxes in the upper part of the
1670MC/SA window and the structure is drawn again. Next we want to refine this
1671solution so go back to the <b style='mso-bidi-font-weight:normal'><span
1672style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1673mso-hansi-theme-font:minor-latin'>General</span></b> tab.</p>
1674
1675<p class=MsoNormal>MC/SA refinement is achieved by narrowing the search ranges
1676and rerunning the MC/SA calculations. This is done by checking the <b
1677style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1678mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA Refine</span></b>
1679box. Using 10% of the ranges reduces the search volume in this case by ~6
1680orders of magnitude so that the true minimum is much easier to find. Now rerun <b
1681style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1682mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>;
1683be sure to select the best one before starting. The residual should drop to a
1684much lower level. This refinement can be repeated with tighter restriction on
1685the ranges; I used 5% for a final run and got</p>
1686
1687<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1688 id="Picture_x0020_22" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:569.25pt;
1689 height:285pt;visibility:visible;mso-wrap-style:square'>
1690 <v:imagedata src="MCSA%20in%20GSAS_files/image052.png" o:title=""/>
1691</v:shape><![endif]--><![if !vml]><img border=0 width=759 height=380
1692src="MCSA%20in%20GSAS_files/image061.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
1693
1694<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1695
1696<p class=MsoNormal>This is clearly a good result (R ~ <span class=GramE>0.4%</span>!)
1697and the structure</p>
1698
1699<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1700 id="Picture_x0020_23" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:288.75pt;
1701 height:248.25pt;visibility:visible;mso-wrap-style:square'>
1702 <v:imagedata src="MCSA%20in%20GSAS_files/image054.png" o:title="" croptop="11555f"
1703  cropbottom="16469f" cropleft="37988f" cropright="12498f"/>
1704</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=331
1705src="MCSA%20in%20GSAS_files/image062.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
1706
1707<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1708
1709<p class=MsoNormal><span class=GramE>is</span> identical to the published one</p>
1710
1711<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1712 id="Picture_x0020_24" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:288.75pt;
1713 height:225.75pt;visibility:visible;mso-wrap-style:square'>
1714 <v:imagedata src="MCSA%20in%20GSAS_files/image056.png" o:title="" croptop="14378f"
1715  cropbottom="21852f" cropleft="3509f" cropright="49103f"/>
1716</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301
1717src="MCSA%20in%20GSAS_files/image063.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
1718
1719<p class=MsoNormal><span class=GramE>as</span> drawn by the Mercury program </p>
1720
1721<p class=MsoNormal>(<a
1722href="https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx">https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx</a>).
1723To save this solution to the <b style='mso-bidi-font-weight:normal'><span
1724style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1725mso-hansi-theme-font:minor-latin'>Atoms</span></b> list do <b style='mso-bidi-font-weight:
1726normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1727minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA/Move MC/SA solution</span></b>;
1728the drawing will show the new atom positions</p>
1729
1730<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1731 id="Picture_x0020_25" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:4in;
1732 height:243.75pt;visibility:visible;mso-wrap-style:square'>
1733 <v:imagedata src="MCSA%20in%20GSAS_files/image064.png" o:title="" croptop="12581f"
1734  cropbottom="15938f" cropleft="37111f" cropright="13377f"/>
1735</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=325
1736src="MCSA%20in%20GSAS_files/image065.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
1737
1738<p class=MsoNormal>And they will be listed in the Atoms table.</p>
1739
1740<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1741 id="Picture_x0020_26" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
1742 height:225pt;visibility:visible;mso-wrap-style:square'>
1743 <v:imagedata src="MCSA%20in%20GSAS_files/image066.png" o:title=""/>
1744</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
1745src="MCSA%20in%20GSAS_files/image067.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
1746
1747<p class=MsoNormal>It is now ready for <span class=SpellE>Rietveld</span>
1748refinement; this needs to use the rigid body as the data will not support
1749independent atom position refinement.</p>
1750
1751<h2><span class=GramE>Step 8.</span> Initial <span class=SpellE>Rietveld</span>
1752refinement</h2>
1753
1754<p class=MsoNormal>After a few simple steps the 3-aminoquinoline structure will
1755be ready for the first <span class=SpellE>Rietveld</span> refinement: 1) On the
1756<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1757mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1758tab uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1759"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1760minor-latin'>Do Pawley refinement?</span></b> box, 2) check the <b
1761style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1762mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
1763scale factor</span></b> box in <b style='mso-bidi-font-weight:normal'><span
1764style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1765mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and 3) zero both
1766<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1767mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
1768&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1769mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
1770and uncheck their refine boxes in <b style='mso-bidi-font-weight:normal'><span
1771style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1772mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>. Then do <b
1773style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1774mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1775from the main GSAS-II data tree window; my <span class=SpellE>R<sub>wp</sub></span>
1776was ~9%. Next check the <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'>Refine unit cell</span></b> in the <b
1779style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1780mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1781window and in the <b style='mso-bidi-font-weight:normal'><span
1782style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1783mso-hansi-theme-font:minor-latin'>Data</span></b> window, using the <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'>uniaxial</span></b>
1786model for <span class=SpellE>mustrain</span>, check both <span class=SpellE><b
1787style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1788mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b
1789style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1790mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span
1791class=GramE>size</span></span></b> &amp; <span class=SpellE><b
1792style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1793mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b></span>
1794boxes and do another <b style='mso-bidi-font-weight:normal'><span
1795style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1796mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I got an <span
1797class=SpellE>R<sub>wp</sub></span> ~8.5% for this. We’ve not refined atom
1798positions or thermal parameters; to do this we need to describe the structure
1799as a rigid body.</p>
1800
1801<h2><span class=GramE>Step 9.</span> Rigid body model</h2>
1802
1803<p class=MsoNormal>The rigid body itself has already been defined; it was used
1804for the MC/SA structure solution. Now we have to place it in the unit cell
1805matching the atom positions obtained from the MC/SA runs. First go to the <b
1806style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1807mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
1808tab and change the <b style='mso-bidi-font-weight:normal'><span
1809style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1810mso-hansi-theme-font:minor-latin'>Style</span></b> to <b style='mso-bidi-font-weight:
1811normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1812minor-latin;mso-hansi-theme-font:minor-latin'>balls &amp; sticks</span></b> and
1813the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1814mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Label</span></b>
1815to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1816mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>name</span></b>.
1817Double click on the column headings and select the item from the popup control.
1818Next go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1819"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1820minor-latin'>RB Models</span></b> tab; it will be empty. Do <b
1821style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1822mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assign
1823atoms to rigid body</span></b>; then select <b style='mso-bidi-font-weight:
1824normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1825minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b> in the <b
1826style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1827mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select rigid
1828body model</span></b> pull down (the only choice). The <b style='mso-bidi-font-weight:
1829normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1830minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window will
1831show</p>
1832
1833<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1834 id="Picture_x0020_27" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:337.5pt;
1835 height:218.25pt;visibility:visible;mso-wrap-style:square'>
1836 <v:imagedata src="MCSA%20in%20GSAS_files/image068.png" o:title=""/>
1837</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=291
1838src="MCSA%20in%20GSAS_files/image069.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
1839
1840<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1841
1842<p class=MsoNormal>You will orient the rigid body against the atoms by matching
1843up the 3 reference atoms in the rigid body (C1, C2 &amp; C5) to the
1844corresponding atoms in the structure (C(2), C(3) &amp; C(6)). Do <span
1845class=GramE>these in order</span>; the drawing will show the shift of molecular
1846origin and then its reorientation as the three atoms are selected. Press <span
1847class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1848"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1849minor-latin'>Ready</span></b></span> when done; the structure will be drawn
1850with yellow bonds indicating that it is now a rigid body and not independent
1851atoms. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
1852"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1853minor-latin'>RB Models</span></b> window shows the new rigid body</p>
1854
1855<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1856 id="Picture_x0020_29" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:474.75pt;
1857 height:210pt;visibility:visible;mso-wrap-style:square'>
1858 <v:imagedata src="MCSA%20in%20GSAS_files/image070.png" o:title=""/>
1859</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=280
1860src="MCSA%20in%20GSAS_files/image071.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
1861
1862<p class=MsoNormal>To refine the rigid body parameters check the <b
1863style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1864mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
1865<span class=GramE>box</span>, select <b style='mso-bidi-font-weight:normal'><span
1866style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1867mso-hansi-theme-font:minor-latin'>AV</span></b> from the pull down, choose <span
1868class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1869"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1870minor-latin'>Uiso</span></b></span> from the thermal parameter model and check
1871its <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1872mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
1873<span class=GramE>box</span>. Then do <b style='mso-bidi-font-weight:normal'><span
1874style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1875mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; after a couple
1876of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span> ~7.9% and
1877the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1878style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1879mso-hansi-theme-font:minor-latin'>RBModels</span></b></span> window shows the
1880new parameters</p>
1881
1882<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1883 id="Picture_x0020_32" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:474.75pt;
1884 height:225.75pt;visibility:visible;mso-wrap-style:square'>
1885 <v:imagedata src="MCSA%20in%20GSAS_files/image073.png" o:title=""/>
1886</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=301
1887src="MCSA%20in%20GSAS_files/image075.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
1888
1889<p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
1890
1891<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1892 id="Picture_x0020_31" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
1893 height:450pt;visibility:visible;mso-wrap-style:square'>
1894 <v:imagedata src="MCSA%20in%20GSAS_files/image074.png" o:title=""/>
1895</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1896src="MCSA%20in%20GSAS_files/image081.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
1897
1898<p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.
1899Next is a more complex case involving some internal degrees of freedom in the
1900molecule of a-d-<span class=GramE>lactose.</span></p>
1901
1902</div>
1903
1904</body>
1905
1906</html>
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