source: Tutorials/CFsucrose/Charge Flipping - sucrose.htm @ 1705

Last change on this file since 1705 was 1705, checked in by toby, 7 years ago

load the tutorial web pages

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385        font-family:"Times New Roman","serif";
386        mso-fareast-font-family:"Times New Roman";
387        mso-fareast-theme-font:minor-fareast;}
388h2
389        {mso-style-noshow:yes;
390        mso-style-priority:9;
391        mso-style-qformat:yes;
392        mso-style-link:"Heading 2 Char";
393        mso-margin-top-alt:auto;
394        margin-right:0in;
395        mso-margin-bottom-alt:auto;
396        margin-left:0in;
397        mso-pagination:widow-orphan;
398        mso-outline-level:2;
399        font-size:18.0pt;
400        font-family:"Times New Roman","serif";
401        mso-fareast-font-family:"Times New Roman";
402        mso-fareast-theme-font:minor-fareast;}
403a:link, span.MsoHyperlink
404        {mso-style-noshow:yes;
405        mso-style-priority:99;
406        color:blue;
407        text-decoration:underline;
408        text-underline:single;}
409a:visited, span.MsoHyperlinkFollowed
410        {mso-style-noshow:yes;
411        mso-style-priority:99;
412        color:purple;
413        mso-themecolor:followedhyperlink;
414        text-decoration:underline;
415        text-underline:single;}
416p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
417        {mso-style-noshow:yes;
418        mso-style-priority:99;
419        mso-style-link:"Balloon Text Char";
420        margin:0in;
421        margin-bottom:.0001pt;
422        mso-pagination:widow-orphan;
423        font-size:8.0pt;
424        font-family:"Tahoma","sans-serif";
425        mso-fareast-font-family:"Times New Roman";
426        mso-fareast-theme-font:minor-fareast;}
427p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
428        {mso-style-priority:34;
429        mso-style-unhide:no;
430        mso-style-qformat:yes;
431        margin-top:0in;
432        margin-right:0in;
433        margin-bottom:0in;
434        margin-left:.5in;
435        margin-bottom:.0001pt;
436        mso-pagination:widow-orphan;
437        font-size:12.0pt;
438        font-family:"Times New Roman","serif";
439        mso-fareast-font-family:"Times New Roman";
440        mso-fareast-theme-font:minor-fareast;}
441span.Heading1Char
442        {mso-style-name:"Heading 1 Char";
443        mso-style-priority:9;
444        mso-style-unhide:no;
445        mso-style-locked:yes;
446        mso-style-link:"Heading 1";
447        mso-ansi-font-size:24.0pt;
448        mso-bidi-font-size:24.0pt;
449        font-family:"Times New Roman","serif";
450        mso-ascii-font-family:"Times New Roman";
451        mso-fareast-font-family:"Times New Roman";
452        mso-fareast-theme-font:minor-fareast;
453        mso-hansi-font-family:"Times New Roman";
454        mso-bidi-font-family:"Times New Roman";
455        mso-font-kerning:18.0pt;
456        font-weight:bold;}
457span.Heading2Char
458        {mso-style-name:"Heading 2 Char";
459        mso-style-noshow:yes;
460        mso-style-priority:9;
461        mso-style-unhide:no;
462        mso-style-locked:yes;
463        mso-style-link:"Heading 2";
464        mso-ansi-font-size:18.0pt;
465        mso-bidi-font-size:18.0pt;
466        font-family:"Times New Roman","serif";
467        mso-ascii-font-family:"Times New Roman";
468        mso-fareast-font-family:"Times New Roman";
469        mso-fareast-theme-font:minor-fareast;
470        mso-hansi-font-family:"Times New Roman";
471        mso-bidi-font-family:"Times New Roman";
472        font-weight:bold;}
473span.BalloonTextChar
474        {mso-style-name:"Balloon Text Char";
475        mso-style-noshow:yes;
476        mso-style-priority:99;
477        mso-style-unhide:no;
478        mso-style-locked:yes;
479        mso-style-link:"Balloon Text";
480        mso-ansi-font-size:8.0pt;
481        mso-bidi-font-size:8.0pt;
482        font-family:"Tahoma","sans-serif";
483        mso-ascii-font-family:Tahoma;
484        mso-fareast-font-family:"Times New Roman";
485        mso-fareast-theme-font:minor-fareast;
486        mso-hansi-font-family:Tahoma;
487        mso-bidi-font-family:Tahoma;}
488span.SpellE
489        {mso-style-name:"";
490        mso-spl-e:yes;}
491span.GramE
492        {mso-style-name:"";
493        mso-gram-e:yes;}
494.MsoChpDefault
495        {mso-style-type:export-only;
496        mso-default-props:yes;
497        font-size:12.0pt;
498        mso-ansi-font-size:12.0pt;
499        mso-bidi-font-size:12.0pt;
500        mso-fareast-font-family:Calibri;
501        mso-fareast-theme-font:minor-latin;
502        mso-bidi-font-family:"Times New Roman";
503        mso-bidi-theme-font:minor-bidi;}
504@page WordSection1
505        {size:8.5in 11.0in;
506        margin:1.0in 1.0in 1.0in 1.0in;
507        mso-header-margin:.5in;
508        mso-footer-margin:.5in;
509        mso-paper-source:0;}
510div.WordSection1
511        {page:WordSection1;}
512 /* List Definitions */
513 @list l0
514        {mso-list-id:15232614;
515        mso-list-type:hybrid;
516        mso-list-template-ids:1768441438 -647724540 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
517@list l0:level1
518        {mso-level-tab-stop:none;
519        mso-level-number-position:left;
520        margin-left:.75in;
521        text-indent:-.25in;}
522@list l0:level2
523        {mso-level-number-format:alpha-lower;
524        mso-level-tab-stop:none;
525        mso-level-number-position:left;
526        margin-left:1.25in;
527        text-indent:-.25in;}
528@list l0:level3
529        {mso-level-number-format:roman-lower;
530        mso-level-tab-stop:none;
531        mso-level-number-position:right;
532        margin-left:1.75in;
533        text-indent:-9.0pt;}
534@list l0:level4
535        {mso-level-tab-stop:none;
536        mso-level-number-position:left;
537        margin-left:2.25in;
538        text-indent:-.25in;}
539@list l0:level5
540        {mso-level-number-format:alpha-lower;
541        mso-level-tab-stop:none;
542        mso-level-number-position:left;
543        margin-left:2.75in;
544        text-indent:-.25in;}
545@list l0:level6
546        {mso-level-number-format:roman-lower;
547        mso-level-tab-stop:none;
548        mso-level-number-position:right;
549        margin-left:3.25in;
550        text-indent:-9.0pt;}
551@list l0:level7
552        {mso-level-tab-stop:none;
553        mso-level-number-position:left;
554        margin-left:3.75in;
555        text-indent:-.25in;}
556@list l0:level8
557        {mso-level-number-format:alpha-lower;
558        mso-level-tab-stop:none;
559        mso-level-number-position:left;
560        margin-left:4.25in;
561        text-indent:-.25in;}
562@list l0:level9
563        {mso-level-number-format:roman-lower;
564        mso-level-tab-stop:none;
565        mso-level-number-position:right;
566        margin-left:4.75in;
567        text-indent:-9.0pt;}
568@list l1
569        {mso-list-id:82917343;
570        mso-list-type:hybrid;
571        mso-list-template-ids:-1527319822 -2100533712 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
572@list l1:level1
573        {mso-level-tab-stop:none;
574        mso-level-number-position:left;
575        margin-left:.75in;
576        text-indent:-.25in;}
577@list l1:level2
578        {mso-level-number-format:alpha-lower;
579        mso-level-tab-stop:none;
580        mso-level-number-position:left;
581        margin-left:1.25in;
582        text-indent:-.25in;}
583@list l1:level3
584        {mso-level-number-format:roman-lower;
585        mso-level-tab-stop:none;
586        mso-level-number-position:right;
587        margin-left:1.75in;
588        text-indent:-9.0pt;}
589@list l1:level4
590        {mso-level-tab-stop:none;
591        mso-level-number-position:left;
592        margin-left:2.25in;
593        text-indent:-.25in;}
594@list l1:level5
595        {mso-level-number-format:alpha-lower;
596        mso-level-tab-stop:none;
597        mso-level-number-position:left;
598        margin-left:2.75in;
599        text-indent:-.25in;}
600@list l1:level6
601        {mso-level-number-format:roman-lower;
602        mso-level-tab-stop:none;
603        mso-level-number-position:right;
604        margin-left:3.25in;
605        text-indent:-9.0pt;}
606@list l1:level7
607        {mso-level-tab-stop:none;
608        mso-level-number-position:left;
609        margin-left:3.75in;
610        text-indent:-.25in;}
611@list l1:level8
612        {mso-level-number-format:alpha-lower;
613        mso-level-tab-stop:none;
614        mso-level-number-position:left;
615        margin-left:4.25in;
616        text-indent:-.25in;}
617@list l1:level9
618        {mso-level-number-format:roman-lower;
619        mso-level-tab-stop:none;
620        mso-level-number-position:right;
621        margin-left:4.75in;
622        text-indent:-9.0pt;}
623@list l2
624        {mso-list-id:236667377;
625        mso-list-type:hybrid;
626        mso-list-template-ids:-513138304 1385070818 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
627@list l2:level1
628        {mso-level-tab-stop:none;
629        mso-level-number-position:left;
630        margin-left:.75in;
631        text-indent:-.25in;}
632@list l2:level2
633        {mso-level-number-format:alpha-lower;
634        mso-level-tab-stop:none;
635        mso-level-number-position:left;
636        margin-left:1.25in;
637        text-indent:-.25in;}
638@list l2:level3
639        {mso-level-number-format:roman-lower;
640        mso-level-tab-stop:none;
641        mso-level-number-position:right;
642        margin-left:1.75in;
643        text-indent:-9.0pt;}
644@list l2:level4
645        {mso-level-tab-stop:none;
646        mso-level-number-position:left;
647        margin-left:2.25in;
648        text-indent:-.25in;}
649@list l2:level5
650        {mso-level-number-format:alpha-lower;
651        mso-level-tab-stop:none;
652        mso-level-number-position:left;
653        margin-left:2.75in;
654        text-indent:-.25in;}
655@list l2:level6
656        {mso-level-number-format:roman-lower;
657        mso-level-tab-stop:none;
658        mso-level-number-position:right;
659        margin-left:3.25in;
660        text-indent:-9.0pt;}
661@list l2:level7
662        {mso-level-tab-stop:none;
663        mso-level-number-position:left;
664        margin-left:3.75in;
665        text-indent:-.25in;}
666@list l2:level8
667        {mso-level-number-format:alpha-lower;
668        mso-level-tab-stop:none;
669        mso-level-number-position:left;
670        margin-left:4.25in;
671        text-indent:-.25in;}
672@list l2:level9
673        {mso-level-number-format:roman-lower;
674        mso-level-tab-stop:none;
675        mso-level-number-position:right;
676        margin-left:4.75in;
677        text-indent:-9.0pt;}
678@list l3
679        {mso-list-id:533275380;
680        mso-list-type:hybrid;
681        mso-list-template-ids:-1319630076 -1606007952 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
682@list l3:level1
683        {mso-level-tab-stop:none;
684        mso-level-number-position:left;
685        margin-left:.75in;
686        text-indent:-.25in;}
687@list l3:level2
688        {mso-level-number-format:alpha-lower;
689        mso-level-tab-stop:none;
690        mso-level-number-position:left;
691        margin-left:1.25in;
692        text-indent:-.25in;}
693@list l3:level3
694        {mso-level-number-format:roman-lower;
695        mso-level-tab-stop:none;
696        mso-level-number-position:right;
697        margin-left:1.75in;
698        text-indent:-9.0pt;}
699@list l3:level4
700        {mso-level-tab-stop:none;
701        mso-level-number-position:left;
702        margin-left:2.25in;
703        text-indent:-.25in;}
704@list l3:level5
705        {mso-level-number-format:alpha-lower;
706        mso-level-tab-stop:none;
707        mso-level-number-position:left;
708        margin-left:2.75in;
709        text-indent:-.25in;}
710@list l3:level6
711        {mso-level-number-format:roman-lower;
712        mso-level-tab-stop:none;
713        mso-level-number-position:right;
714        margin-left:3.25in;
715        text-indent:-9.0pt;}
716@list l3:level7
717        {mso-level-tab-stop:none;
718        mso-level-number-position:left;
719        margin-left:3.75in;
720        text-indent:-.25in;}
721@list l3:level8
722        {mso-level-number-format:alpha-lower;
723        mso-level-tab-stop:none;
724        mso-level-number-position:left;
725        margin-left:4.25in;
726        text-indent:-.25in;}
727@list l3:level9
728        {mso-level-number-format:roman-lower;
729        mso-level-tab-stop:none;
730        mso-level-number-position:right;
731        margin-left:4.75in;
732        text-indent:-9.0pt;}
733@list l4
734        {mso-list-id:588542776;
735        mso-list-type:hybrid;
736        mso-list-template-ids:477805396 -2056748102 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
737@list l4:level1
738        {mso-level-tab-stop:none;
739        mso-level-number-position:left;
740        margin-left:.75in;
741        text-indent:-.25in;}
742@list l4:level2
743        {mso-level-number-format:alpha-lower;
744        mso-level-tab-stop:none;
745        mso-level-number-position:left;
746        margin-left:1.25in;
747        text-indent:-.25in;}
748@list l4:level3
749        {mso-level-number-format:roman-lower;
750        mso-level-tab-stop:none;
751        mso-level-number-position:right;
752        margin-left:1.75in;
753        text-indent:-9.0pt;}
754@list l4:level4
755        {mso-level-tab-stop:none;
756        mso-level-number-position:left;
757        margin-left:2.25in;
758        text-indent:-.25in;}
759@list l4:level5
760        {mso-level-number-format:alpha-lower;
761        mso-level-tab-stop:none;
762        mso-level-number-position:left;
763        margin-left:2.75in;
764        text-indent:-.25in;}
765@list l4:level6
766        {mso-level-number-format:roman-lower;
767        mso-level-tab-stop:none;
768        mso-level-number-position:right;
769        margin-left:3.25in;
770        text-indent:-9.0pt;}
771@list l4:level7
772        {mso-level-tab-stop:none;
773        mso-level-number-position:left;
774        margin-left:3.75in;
775        text-indent:-.25in;}
776@list l4:level8
777        {mso-level-number-format:alpha-lower;
778        mso-level-tab-stop:none;
779        mso-level-number-position:left;
780        margin-left:4.25in;
781        text-indent:-.25in;}
782@list l4:level9
783        {mso-level-number-format:roman-lower;
784        mso-level-tab-stop:none;
785        mso-level-number-position:right;
786        margin-left:4.75in;
787        text-indent:-9.0pt;}
788@list l5
789        {mso-list-id:854225785;
790        mso-list-type:hybrid;
791        mso-list-template-ids:-2071413312 1417604178 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
792@list l5:level1
793        {mso-level-tab-stop:none;
794        mso-level-number-position:left;
795        margin-left:.75in;
796        text-indent:-.25in;}
797@list l5:level2
798        {mso-level-number-format:alpha-lower;
799        mso-level-tab-stop:none;
800        mso-level-number-position:left;
801        margin-left:1.25in;
802        text-indent:-.25in;}
803@list l5:level3
804        {mso-level-number-format:roman-lower;
805        mso-level-tab-stop:none;
806        mso-level-number-position:right;
807        margin-left:1.75in;
808        text-indent:-9.0pt;}
809@list l5:level4
810        {mso-level-tab-stop:none;
811        mso-level-number-position:left;
812        margin-left:2.25in;
813        text-indent:-.25in;}
814@list l5:level5
815        {mso-level-number-format:alpha-lower;
816        mso-level-tab-stop:none;
817        mso-level-number-position:left;
818        margin-left:2.75in;
819        text-indent:-.25in;}
820@list l5:level6
821        {mso-level-number-format:roman-lower;
822        mso-level-tab-stop:none;
823        mso-level-number-position:right;
824        margin-left:3.25in;
825        text-indent:-9.0pt;}
826@list l5:level7
827        {mso-level-tab-stop:none;
828        mso-level-number-position:left;
829        margin-left:3.75in;
830        text-indent:-.25in;}
831@list l5:level8
832        {mso-level-number-format:alpha-lower;
833        mso-level-tab-stop:none;
834        mso-level-number-position:left;
835        margin-left:4.25in;
836        text-indent:-.25in;}
837@list l5:level9
838        {mso-level-number-format:roman-lower;
839        mso-level-tab-stop:none;
840        mso-level-number-position:right;
841        margin-left:4.75in;
842        text-indent:-9.0pt;}
843@list l6
844        {mso-list-id:1022125565;
845        mso-list-type:hybrid;
846        mso-list-template-ids:-482838388 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
847@list l6:level1
848        {mso-level-tab-stop:none;
849        mso-level-number-position:left;
850        margin-left:1.0in;
851        text-indent:-.25in;}
852@list l6:level2
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929</head>
930
931<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
932
933<div class=WordSection1>
934
935<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in
936GSAS-II - sucrose<o:p></o:p></span></h1>
937
938<h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1>
939
940<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
941of sucrose from powder diffraction data via charge flipping. This structure was
942originally solved from single crystal data in the space group P2<sub>1</sub>.
943It is a difficult exercise to complete as the charge flipping does not always
944yield a solution and to even have a chance the Pawley refinement must be done
945with particular care. We have given a route that sometimes works.</p>
946
947<p class=MsoNormal>If you have not done so already, <a
948href="Starting%20GSAS.htm">start GSAS-II</a> and open the GSAS-II project file
949(I called it <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
950style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
951mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b></span>) you saved from
952the third part of the <a href="Fit%20Peaks.htm#sucrose_peak_fit">peak
953fitting-indexing exercise</a>. If you didn’t do that exercise, do it now.</p>
954
955<h2>Step 1: Setup for Pawley refinement</h2>
956
957<p class=MsoNormal>There are a number of steps that must be done in preparation
958for a Pawley refinement after having completed the unit cell indexing and new
959phase creation. These cover two things: one is to prepare the powder pattern
960(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
961
962<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
963style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
964style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
965<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
966mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
967in the GSAS-II data tree for the PWDR data set and expand the plot so that the
968region near d=1.0Å is readily seen. This is ~24deg 2<span style='font-family:
969Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
970mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
971symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
972relatively clear of peaks that makes a good place to end the calculations with
973a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution
974needed for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span
975style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
976mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span class=SpellE><b
977style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
978mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b></span>
979as the upper limit and make a note of the exact d-spacing (1.0125Å) using the
980mouse cursor on the plot.</p>
981
982<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
983style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
984style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
985<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
986mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
987Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
988style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
989mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
990style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
991mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
992profile</span></b> to recover the default values. The peak fitting done earlier
993is over a much more limited range of 2<span style='font-family:Symbol;
994mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
995mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
996symbol;mso-symbol-font-family:Symbol'>Q</span></span> giving values that might
997not extrapolate well over the wider range to be used in the Pawley refinement.
998We will refine them again later.</p>
999
1000<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1001style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1002style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1003<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1004mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1005Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1006normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1007minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.
1008While you are here set <b style='mso-bidi-font-weight:normal'><span
1009style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1010mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> to <b
1011style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1012mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>.</p>
1013
1014<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1015style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1016style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1017to <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'>Phases/sucrose</span></b>
1019to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1020"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1021minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1022normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1023minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
1024box and enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
1025style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1026mso-hansi-theme-font:minor-latin'>1.0125</span></b>) into the <b
1027style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1028mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1029class=SpellE>dmin</span></span></b> box.</p>
1030
1031<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1032style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1033mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1034
1035<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1036 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1037 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1038 <v:stroke joinstyle="miter"/>
1039 <v:formulas>
1040  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1041  <v:f eqn="sum @0 1 0"/>
1042  <v:f eqn="sum 0 0 @1"/>
1043  <v:f eqn="prod @2 1 2"/>
1044  <v:f eqn="prod @3 21600 pixelWidth"/>
1045  <v:f eqn="prod @3 21600 pixelHeight"/>
1046  <v:f eqn="sum @0 0 1"/>
1047  <v:f eqn="prod @6 1 2"/>
1048  <v:f eqn="prod @7 21600 pixelWidth"/>
1049  <v:f eqn="sum @8 21600 0"/>
1050  <v:f eqn="prod @7 21600 pixelHeight"/>
1051  <v:f eqn="sum @10 21600 0"/>
1052 </v:formulas>
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1054 <o:lock v:ext="edit" aspectratio="t"/>
1055</v:shapetype><v:shape id="Picture_x0020_25" o:spid="_x0000_i1064" type="#_x0000_t75"
1056 style='width:545.25pt;height:303.75pt;visibility:visible;mso-wrap-style:square'>
1057 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image001.png" o:title=""/>
1058</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
1059src="Charge%20Flipping%20-%20sucrose_files/image001.png" v:shapes="Picture_x0020_25"><![endif]></span></p>
1060
1061<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1062style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1063mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1064for a single line of text. Do <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'>Edit/Add powder histograms</span></b>; a
1067dialog box will appear</p>
1068
1069<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1070 id="Picture_x0020_2" o:spid="_x0000_i1063" type="#_x0000_t75" style='width:259.5pt;
1071 height:252pt;visibility:visible;mso-wrap-style:square'>
1072 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image002.png" o:title=""/>
1073</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1074src="Charge%20Flipping%20-%20sucrose_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1075
1076<p class=MsoNormal>Select either choice; the desired data set will be added to
1077this phase for analysis. The data tab now shows the new data set; check the <b
1078style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1079mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
1080button to see the full information</p>
1081
1082<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1083 id="Picture_x0020_3" o:spid="_x0000_i1062" type="#_x0000_t75" style='width:480pt;
1084 height:393pt;visibility:visible;mso-wrap-style:square'>
1085 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image003.png" o:title=""/>
1086</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=524
1087src="Charge%20Flipping%20-%20sucrose_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
1088
1089<p class=MsoNormal>I’ve stretched the window slightly to see the entire
1090contents. This is the location for all the phase dependent parameters for this
1091histogram. Notice that it includes phase fraction, size &amp; <span
1092class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1093and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1094intended for protein work where a significant region of the structure is
1095disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1096surfaces</p>
1097
1098<p class=MsoNormal><span class=GramE>as</span> well as preferred orientation
1099correction curves.</p>
1100
1101<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1102style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1103mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1104empty except for column headings. <span class=GramE>Do</span> <b
1105style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1106mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley
1107create</span></b>; this makes the reflection set over the range covered by
1108setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1109mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1110class=SpellE>dmin</span></span></b>. The table should list reflections 0-781.
1111Select and check the refine column using the same technique you used for the
1112peak list. </p>
1113
1114<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1115 id="Picture_x0020_4" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:375pt;
1116 height:225pt;visibility:visible;mso-wrap-style:square'>
1117 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image004.png" o:title=""/>
1118</v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300
1119src="Charge%20Flipping%20-%20sucrose_files/image004.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
1120
1121<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1122you didn’t skip a step as it might not work correctly if you did.</p>
1123
1124<h2>Step 2: Pawley refinement</h2>
1125
1126<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1127normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1128minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1129the main GSAS-II data tree window. Before it begins a backup of the project
1130file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
1131style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1132mso-hansi-theme-font:minor-latin'>sucrose.bck0.gpx</span></b>. It can be used
1133to recover from a bad refinement. A progress dialog box will appear showing the
1134residual as the refinement proceeds. Notice that there was a singular matrix
1135warning on the console window and the last reflection (781) was removed from
1136the refinement because it was off the end of the used part of the pattern. This
1137is the GSAS-II singular matrix recovery mechanism; you can go to the <b
1138style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1139mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1140reflections</span></b> tab and uncheck the last reflection. Then repeat <b
1141style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1142mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1143to make sure it has essentially minimized. My refinement completed with <span
1144class=SpellE>Rwp</span> ~26.3%; a dialog box appears asking if you wish to load
1145the result. Press <b style='mso-bidi-font-weight:normal'><span
1146style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1147mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
1148PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
1149
1150<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1151 id="Picture_x0020_5" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:503.25pt;
1152 height:431.25pt;visibility:visible;mso-wrap-style:square'>
1153 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image005.png" o:title=""/>
1154</v:shape><![endif]--><![if !vml]><img border=0 width=671 height=575
1155src="Charge%20Flipping%20-%20sucrose_files/image005.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
1156
1157<p class=MsoNormal>It is evident from examining the plot that some improvement
1158can be had by refining the lattice and profile parameters and perhaps the
1159sample X position. Go to <b style='mso-bidi-font-weight:normal'><span
1160style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1161mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> in the GSAS-II data
1162tree and check the <b style='mso-bidi-font-weight:normal'><span
1163style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1164mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> box. Now select <b
1165style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1166mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1167parameters</span></b> for the PWDR data set in the GSAS-II data tree and check <b
1168style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1169mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>,
1170<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1171mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>,
1172<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1173mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,<b
1174style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1175mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
1176class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
1177style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1178mso-hansi-theme-font:minor-latin'> Y</span></b>. The go to <b style='mso-bidi-font-weight:
1179normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1180minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and
1181check <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1182mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1183class=SpellE>displ</span></span></b>.; make the <b style='mso-bidi-font-weight:
1184normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1185minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> <b
1186style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1187mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1188if you didn’t do this earlier. Repeat <b style='mso-bidi-font-weight:normal'><span
1189style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1190mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged;
1191I obtained an improved residual of ~9.05% with a much better fit at the high
1192angle part of the pattern but still not fit well for the lower part.</p>
1193
1194<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1195 id="Picture_x0020_26" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:504.75pt;
1196 height:432.75pt;visibility:visible;mso-wrap-style:square'>
1197 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image006.png" o:title=""/>
1198</v:shape><![endif]--><![if !vml]><img border=0 width=673 height=577
1199src="Charge%20Flipping%20-%20sucrose_files/image006.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
1200
1201<p class=MsoNormal>What you see is that the background has a substantial
1202diffuse scattering feature at ~5deg and there are some peak shape issues (which
1203may be a consequence of the poor background fit). We’d like the fit to be
1204better before trying charge flipping. First select <span class=GramE><b
1205style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1206mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>,</span>
1207set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1208mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peaks in
1209background: No. peaks</span></b> to <b style='mso-bidi-font-weight:normal'><span
1210style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1211mso-hansi-theme-font:minor-latin'>1</span></b> from the pull down box; the
1212window changes to </p>
1213
1214<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1215 id="Picture_x0020_27" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:366.75pt;
1216 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1217 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image007.png" o:title=""/>
1218</v:shape><![endif]--><![if !vml]><img border=0 width=489 height=263
1219src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span><span
1220style='mso-spacerun:yes'> </span></p>
1221
1222<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
1223style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1224mso-hansi-theme-font:minor-latin'>5.0</span></b> for <span class=SpellE><b
1225style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1226mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span>,
1227<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1228mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
1229for <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1230style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1231mso-hansi-theme-font:minor-latin'>int</span></b></span> and <b
1232style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1233mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1234for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1235mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
1236(as appropriate for broad diffuse peaks) and then check all three refine boxes.
1237Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1238mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
1239class=SpellE>coeff</span>.</span></b> <span class=SpellE><span class=GramE>pulldown</span></span>
1240to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1241mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>
1242for the <span class=SpellE>chebyschev</span> part of the background. The window
1243should look like</p>
1244
1245<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1246 id="Picture_x0020_28" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:402pt;
1247 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1248 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image008.png" o:title=""/>
1249</v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
1250src="Charge%20Flipping%20-%20sucrose_files/image008.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1251
1252<p class=MsoNormal>Go to the <b style='mso-bidi-font-weight:normal'><span
1253style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1254mso-hansi-theme-font:minor-latin'>Controls</span></b> item in the GSAS-II data
1255tree and set the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1256"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1257minor-latin'>Max cycles</span></b> to <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'>5</span></b>. Now do <b style='mso-bidi-font-weight:
1260normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1261minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until
1262the refinement converges. After a set of refinement cycles go to the <b
1263style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1264mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b>
1265tab and check the intensities. If there are many negatives amongst the highest
1266angle reflections do <b style='mso-bidi-font-weight:normal'><span
1267style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1268mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this replaces all
1269the values with those in the extracted from the profile as listed in the <b
1270style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1271mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1272list</span></b> for the PWDR data set each multiplied by 0.5. Additionally
1273their refinement flags are turned off. Do <b style='mso-bidi-font-weight:normal'><span
1274style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1275mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b><span
1276style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1277mso-hansi-theme-font:minor-latin'>; this will adjust all the reflections in the
1278vicinity of the reset ones</span>. You may repeat this process to suppress any
1279new negatives that may appear. Then set all the Pawley refinement flags back on
1280(excluding any that lead to a singular matrix) and repeat the refinement. After
1281refinement, mine converged to ~5.7% with very few negatives and <span
1282class=SpellE>and</span> the plot looked like</p>
1283
1284<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1285 id="Picture_x0020_29" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:507pt;
1286 height:434.25pt;visibility:visible;mso-wrap-style:square'>
1287 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image009.png" o:title=""/>
1288</v:shape><![endif]--><![if !vml]><img border=0 width=676 height=579
1289src="Charge%20Flipping%20-%20sucrose_files/image009.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
1290
1291<p class=MsoNormal>Let’s see if this is good enough for charge flipping.</p>
1292
1293<h2>Step 3: Charge flipping</h2>
1294
1295<p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
1296Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1297mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1298and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1299"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1300minor-latin'>Charge flip controls</span></b> in the middle of the <b
1301style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1302mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1303tab.</p>
1304
1305<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1306mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1307"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1308</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
1309style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1310mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b
1311style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1312mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
131311bmb_8716.fxye Bank 1</span></b> (the only choice!). This makes the reflection
1314set to be used those in <b style='mso-bidi-font-weight:normal'><span
1315style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1316mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
1317data set; these should match the <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'>Pawley reflection</span></b> set.</p>
1320
1321<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1322mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1323"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1324</span></span></span><![endif]>Set the <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'>Peak cutoff</span></b> (in <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'>Fourier map
1329controls</span></b>) to <b style='mso-bidi-font-weight:normal'><span
1330style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1331mso-hansi-theme-font:minor-latin'>20%</span></b>. This controls the map search
1332routine.</p>
1333
1334<p class=MsoNormal>For powder data it is not usually advisable to select a <b
1335style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1336mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing
1337element</span></b>; if selected a periodic table appears – select an element or
1338‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1339mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None’</span></b>.
1340The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1341mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1342defines the map spacing and thus the extent of the reflection set; the observed
1343reflection set is zero filled to this limit for charge flipping. The <b
1344style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1345mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b>
1346and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1347mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b>
1348determine the lower threshold and upper limit for charge flipping,
1349respectively. The latter is used to avoid “Uranium solutions” in the result.
1350Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1351"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1352minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
1353ones. For sucrose set it to <b style='mso-bidi-font-weight:normal'><span
1354style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1355mso-hansi-theme-font:minor-latin'>12.</span></b> When ready select <b
1356style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1357mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1358flipping</span></b>; a progress bar dialog will appear that tracks the residual
1359found in each charge flipping cycle. It will quickly drop to some level
1360(42-44%) and then for a successful charge flipping run perhaps drop again into
1361the 20-25% range after a considerable length of time. You should save the
1362project if you get an apparently good solution. Many times it will not drop
1363below ~40%; just try <b style='mso-bidi-font-weight:normal'><span
1364style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1365mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b> again. If
1366several tries fail to yield a solution, go back to the last step of the Pawley
1367refinement and just repeat it (that is do <b style='mso-bidi-font-weight:normal'><span
1368style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1369mso-hansi-theme-font:minor-latin'>Pawley update</span></b> and <b
1370style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1371mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>).
1372This will generate a different set of intensities for the highly overlapped
1373part of the powder pattern; perhaps they will give a successful charge flip
1374solution. Unless otherwise interrupted, GSAS-II will try 10000 times for a
1375charge flip solution (for sucrose this takes 5-10min on my laptop). Press <b
1376style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1377mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b>
1378to stop the charge flipping; a peak list and a drawing of the solution will
1379appear. One of my runs gave</p>
1380
1381<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1382 id="Picture_x0020_30" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:337.5pt;
1383 height:225pt;visibility:visible;mso-wrap-style:square'>
1384 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image010.png" o:title=""/>
1385</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
1386src="Charge%20Flipping%20-%20sucrose_files/image010.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1387
1388<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1389
1390<p class=MsoNormal><!--[if gte vml 1]><v:group id="Group_x0020_39" o:spid="_x0000_s1026"
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1488 </v:shape></v:group><![endif]--><![if !vml]><span style='mso-ignore:vglayout;
1489position:absolute;z-index:251662336;margin-left:315px;margin-top:308px;
1490width:16px;height:35px'><img width=16 height=35
1491src="Charge%20Flipping%20-%20sucrose_files/image052.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
1492style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
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1494 visibility:visible;mso-wrap-style:square'>
1495 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image012.png" o:title=""
1496  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
1497</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=575
1498src="Charge%20Flipping%20-%20sucrose_files/image053.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
1499
1500<p class=MsoNormal>The result looks very promising! Charge flipping operates
1501without regard to symmetry and GSAS-II attempts to locate the map with respect
1502to the symmetry elements from the computed reflection phases. (NB: charge
1503flipping also will give a solution without regard to handedness; this solution
1504may be either the correct one for sucrose or its inverse.) Errors in these
1505phases can disrupt this process so that the map and peak positions are offset
1506from their true positions. To discover this and fix it, rotate the drawing
1507around to check that atom positions are related via the 2<sub>1</sub> screw
1508axis (through the multicolored cross in the center of the cell and parallel to
1509the y-axis – the green cell edge). Avoid motions with the right mouse button
1510pressed, this moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:
1511normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1512minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the
1513cross to the cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my
1514drawing above to show where I think it should be. If you find an offset to the
1515map, orient it so the offset is horizontal or vertical and then press the <b
1516style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1517mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>,
1518<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1519mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>,
1520<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1521mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
1522or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1523mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
1524keys to shift the map and peaks as needed. The shift is in resolution units
1525(0.5Å) so the fix can only be approximate. Repeat as needed. Notice that the
1526peak positions in the table are updated as the offset is changed. In this case,
1527I needed just a few steps to correct the map offset. NB: you can use these keys
1528to move the result anywhere you wish, e.g. to select a different origin for the
1529structure but pay attention to the location of symmetry elements. After
1530adjustment, my solution looked like</p>
1531
1532<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1533 id="Picture_x0020_12" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:500.25pt;
1534 height:424.5pt;visibility:visible;mso-wrap-style:square'>
1535 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image014.png" o:title=""
1536  croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/>
1537</v:shape><![endif]--><![if !vml]><img border=0 width=667 height=566
1538src="Charge%20Flipping%20-%20sucrose_files/image054.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
1539
1540<h2>Step 4: Obtain solution from charge flip result</h2>
1541
1542<p class=MsoNormal>The next step is to extract the unique peak positions from
1543the map and make atoms out of them. The map peak list is initially sorted by
1544peak magnitude; you can change the sorting to be along any of the column
1545headings in the table by a single click on the desired heading. The <span
1546class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1547"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1548minor-latin'>dzero</span></b></span> column gives the distance of each peak from
1549the origin. The menu items under Map peaks give you several tools to aid in the
1550peak selection process; we will just use a couple in this example. I have
1551chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:normal'><span
1552style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1553mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and then finding
1554the unique ones. </p>
1555
1556<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1557mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1558"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1559</span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight:
1560normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1561minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> column heading. This
1562will sort the peaks in increasing z-axis coordinate.</p>
1563
1564<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1565mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1566"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1567</span></span></span><![endif]>Do a single click on the upper left (empty) box
1568of the table. All entries will be colored grey indicating their selection.</p>
1569
1570<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1571mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1572"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1573</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1574style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1575mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That should
1576select (grey) 23 out of 46 peak positions in the table and all should be near
1577the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
1578that would be all the C &amp; O atoms! They will be colored green in the plot.
1579If more are selected then check the map offset – it may need a slight
1580correction.</p>
1581
1582<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1583 id="Picture_x0020_13" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:337.5pt;
1584 height:411.75pt;visibility:visible;mso-wrap-style:square'>
1585 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image016.png" o:title=""/>
1586</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=549
1587src="Charge%20Flipping%20-%20sucrose_files/image016.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1588
1589<p class=MsoNormal>The drawing shows the selected atoms in green.</p>
1590
1591<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1592 id="Picture_x0020_14" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:7in;
1593 height:429pt;visibility:visible;mso-wrap-style:square'>
1594 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image017.png" o:title=""
1595  croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/>
1596</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=572
1597src="Charge%20Flipping%20-%20sucrose_files/image055.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
1598
1599<p class=MsoNormal>Notice that in my case one atom is in a neighboring
1600molecule, one can deselect it and then pick the desired equivalent. Hold the <b
1601style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1602mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1603key down and use the right mouse button to pick/unpick atoms in the drawing.
1604NB: the left mouse button will clear all the selections. The other two “lone”
1605atoms belong to molecules in neighboring unit cells; we’ll deal with them
1606later.</p>
1607
1608<p class=MsoNormal>These are now ready to turn into atoms. Do <b
1609style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1610mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1611peaks/Move peaks</span></b>. The drawing will show white balls for each of the
1612selected positions and the <b style='mso-bidi-font-weight:normal'><span
1613style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1614mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 23 new H
1615atoms. </p>
1616
1617<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1618 id="Picture_x0020_15" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:7in;
1619 height:433.5pt;visibility:visible;mso-wrap-style:square'>
1620 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image019.png" o:title=""
1621  croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/>
1622</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=578
1623src="Charge%20Flipping%20-%20sucrose_files/image056.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
1624
1625<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1626 id="Picture_x0020_44" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
1627 height:414.75pt;visibility:visible;mso-wrap-style:square'>
1628 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image021.png" o:title=""/>
1629</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=553
1630src="Charge%20Flipping%20-%20sucrose_files/image021.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
1631
1632<p class=MsoNormal>The atom names indicate the peak magnitude to aid
1633identification (M100 for the largest in the <b style='mso-bidi-font-weight:
1634normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1635minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
1636may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
1637style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1638mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
1639them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
1640style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1641mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
1642normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1643minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
1644and then selecting a position in the table with the <b style='mso-bidi-font-weight:
1645normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1646minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
1647Linux machines the <b style='mso-bidi-font-weight:normal'><span
1648style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1649mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by
1650the operating system; use <b style='mso-bidi-font-weight:normal'><span
1651style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1652mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms. After
1653sorting by magnitude, my list is now </p>
1654
1655<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1656 id="Picture_x0020_17" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:525pt;
1657 height:417pt;visibility:visible;mso-wrap-style:square'>
1658 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image022.png" o:title=""/>
1659</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=556
1660src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1661
1662<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out
1663into two groups with a clear gap between M79 and M64. The higher ones are
1664likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit
1665of ambiguity in the middle, but just assign the top 11 as O and the rest as C
1666and see what happens. You can do this by selecting a block of atoms, go to <b
1667style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1668mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1669atom parameters</span></b> and select <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'>Type</span></b> from the dialog box; a
1672periodic table will appear. Select the desired element and they will be changed
1673in the list and drawing.</p>
1674
1675<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1676 id="Picture_x0020_18" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:7in;
1677 height:405.75pt;visibility:visible;mso-wrap-style:square'>
1678 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image023.png" o:title=""
1679  croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/>
1680</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=541
1681src="Charge%20Flipping%20-%20sucrose_files/image057.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
1682
1683<p class=MsoNormal>The original charge flipping solution is still visible and
1684the atoms are now identified, I’ve changed the drawing to show balls and sticks
1685and labeled the atoms with their names, this is done in the <b
1686style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1687mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b>
1688tab. Double click the appropriate column heading and make the selection from
1689the dialog box.<span style='mso-spacerun:yes'>  </span></p>
1690
1691<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1692 id="Picture_x0020_19" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:450pt;
1693 height:415.5pt;visibility:visible;mso-wrap-style:square'>
1694 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image025.png" o:title=""/>
1695</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=554
1696src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
1697
1698<p class=MsoNormal>Now one can safely remove the map peaks (do <b
1699style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1700mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1701peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span
1702style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1703mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
1704charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1705style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1706mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
1707normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1708minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
1709style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1710mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1711tab). The atom positions I obtained have two atoms (O3 &amp; O4) not connected
1712to the sucrose molecule because they belong to neighboring molecules. We need
1713to discover the equivalent ones that belong to this molecule. Follow the steps:</p>
1714
1715<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1716mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1717"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1718</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1719style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1720mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> tab and select them
1721(hold the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1722mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ctrl</span></b>
1723key down and select the appropriate rows). </p>
1724
1725<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1726mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1727"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1728</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1729style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1730mso-hansi-theme-font:minor-latin'>Edit/Fill unit cell</span></b>; new atoms
1731will appear at end of list and in the drawing. </p>
1732
1733<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1734mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1735"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1736</span></span></span><![endif]>Select all the atoms in the <b style='mso-bidi-font-weight:
1737normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1738minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table by a
1739double click on upper left corner box of the table.</p>
1740
1741<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1742mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1743"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1744</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1745style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1746mso-hansi-theme-font:minor-latin'>Edit/Fill CN-sphere</span></b>; new atoms
1747will appear that are bonded to the molecule.</p>
1748
1749<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1750mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1751"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1752</span></span></span><![endif]>Select these new atoms that are in the molecule;
1753they will probably be outside the unit cell box. Do this on the drawing with <b
1754style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1755mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift left</span></b>
1756for the first one &amp; <b style='mso-bidi-font-weight:normal'><span
1757style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1758mso-hansi-theme-font:minor-latin'>Shift right</span></b> for the rest, they
1759will show in green. </p>
1760
1761<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1762mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1763"Times New Roman"'><span style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1764</span></span></span><![endif]>Look at the <b style='mso-bidi-font-weight:normal'><span
1765style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1766mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the
1767selections and make note of the <span class=SpellE><b style='mso-bidi-font-weight:
1768normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1769minor-latin;mso-hansi-theme-font:minor-latin'>Sym</span></b></span><b
1770style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1771mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Op</span></b>
1772for each one. In my case they were “<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'>2+1<span class=GramE>,0,0</span></span></b>”
1775for O(4) and “<b style='mso-bidi-font-weight:normal'><span style='font-family:
1776"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1777minor-latin'>2+2,-1,1</span></b>” for O(3). The first number is the symmetry
1778operator number and the 3 numbers after the ‘<b style='mso-bidi-font-weight:
1779normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1780minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’ are unit cell
1781translations.</p>
1782
1783<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1784mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1785"Times New Roman"'><span style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1786</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1787style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1788mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab.</p>
1789
1790<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1791mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1792"Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1793</span></span></span><![endif]>Select an atom in turn that needs to be moved,
1794e.g. in my case <span class=GramE>O(</span>3) or O(4). </p>
1795
1796<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1797mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1798"Times New Roman"'><span style='mso-list:Ignore'>9.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1799</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1800style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1801mso-hansi-theme-font:minor-latin'>Edit/Transform <span class=GramE>atoms<span
1802style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
1803select the operator and unit cell translations, then press <b style='mso-bidi-font-weight:
1804normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1805minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom
1806coordinates will be transformed.</p>
1807
1808<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1809mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1810"Times New Roman"'><span style='mso-list:Ignore'>10.<span style='font:7.0pt "Times New Roman"'>&nbsp;
1811</span></span></span><![endif]>Repeat 8 &amp; 9 for any other atoms to be
1812moved.</p>
1813
1814<p class=MsoNormal style='margin-left:.5in'>This will complete the molecule
1815with the extra atoms. <span class=GramE>Do</span> <b style='mso-bidi-font-weight:
1816normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1817minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>
1818to see the completed molecule. I’ve made it a balls &amp; sticks with names as
1819labels.</p>
1820
1821<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1822 id="Picture_x0020_20" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:7in;
1823 height:6in;visibility:visible;mso-wrap-style:square'>
1824 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image026.png" o:title=""
1825  cropbottom="28348f" cropleft="41090f" cropright="9483f"/>
1826</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=576
1827src="Charge%20Flipping%20-%20sucrose_files/image058.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
1828
1829<p class=MsoNormal>Save the project file; the next step is to complete the
1830structure by finding H-atoms and then do the final <span class=SpellE>Rietveld</span>
1831refinements.</p>
1832
1833<h2>Step 5: Complete the structure</h2>
1834
1835<p class=MsoNormal>To complete the structure you will need to perform a
1836preliminary <span class=SpellE>Rietveld</span> refinement. This will make the
1837atom positions more accurate and prepare a set of calculated structure factors
1838needed to generate a difference Fourier map good enough to maybe reveal the H
1839atoms. There are a number of steps needed to set all the controls from the
1840previous Pawley refinement to get a successful start for the <span
1841class=SpellE>Rietveld</span> refinement.</p>
1842
1843<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1844mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1845"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1846</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1847style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1848mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the
1849GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span
1850style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1851mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You don’t want to
1852start with these when the scale factor is unknown.</p>
1853
1854<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1855mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1856"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1857</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
1858style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1859mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b
1860style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1861mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
1862scale factor</span></b> box. This is the scale factor for the data set. Uncheck
1863the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1864mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1865class=SpellE>displ</span></span></b>.</p>
1866
1867<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1868mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1869"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1870</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
1871style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1872mso-hansi-theme-font:minor-latin'>Phases/sucrose General</span></b> tab and
1873uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1874mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
1875cell</span></b> and <b style='mso-bidi-font-weight:normal'><span
1876style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1877mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The
1878latter is most important; if you forget you will just get another Pawley
1879refinement!</p>
1880
1881<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1882style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1883mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
1884GSAS-II data tree menu; only scale and background are refined. I got <span
1885class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear
1886intensity differences; the atom positions obviously need refinement.</p>
1887
1888<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1889 id="Picture_x0020_21" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:502.5pt;
1890 height:430.5pt;visibility:visible;mso-wrap-style:square'>
1891 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/>
1892</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=574
1893src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
1894
1895<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
1896obvious.</p>
1897
1898<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
1899style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1900mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and select the <b
1901style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1902mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1903tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub>
1904has an arbitrary location along the y-axis. Then double click the <b
1905style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1906mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1907column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight:
1908normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1909minor-latin;mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and
1910press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1911mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1912The atoms table will show the refinement controls</p>
1913
1914<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1915 id="Picture_x0020_22" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
1916 height:225pt;visibility:visible;mso-wrap-style:square'>
1917 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/>
1918</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
1919src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
1920
1921<p class=MsoNormal>To deal with the warning we need to set a “Hold” on one atom
1922y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span
1923style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1924mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II
1925data tree.</p>
1926
1927<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1928 id="Picture_x0020_23" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:225pt;
1929 height:187.5pt;visibility:visible;mso-wrap-style:square'>
1930 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image030.png" o:title=""/>
1931</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
1932src="Charge%20Flipping%20-%20sucrose_files/image030.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
1933
1934<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
1935style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1936mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
1937style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1938mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
1939class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will
1940fix the shift along y for the <span class=GramE>O(</span>1) atom.</p>
1941
1942<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1943 id="Picture_x0020_53" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:259.5pt;
1944 height:271.5pt;visibility:visible;mso-wrap-style:square'>
1945 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/>
1946</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=362
1947src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
1948
1949<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1950style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1951mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will
1952show the hold</p>
1953
1954<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1955 id="Picture_x0020_54" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:225pt;
1956 height:187.5pt;visibility:visible;mso-wrap-style:square'>
1957 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image032.png" o:title=""/>
1958</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
1959src="Charge%20Flipping%20-%20sucrose_files/image032.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
1960
1961<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
1962style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1963mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
1964class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice
1965parameters (in the <b style='mso-bidi-font-weight:normal'><span
1966style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1967mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
1968style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1969mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>),
1970the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1971mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1972parameters</span></b> <b style='mso-bidi-font-weight:normal'><span
1973style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1974mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
1975normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1976minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b
1977style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1978mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
1979<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1980mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
1981&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1982mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
1983and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1984mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1985class=SpellE>displ</span></span></b>. You can also include refinement of atom
1986thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
1987refinement improved slightly to Rwp~10.0%. Let’s see if a difference Fourier
1988map will show anything.<br>
1989Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1990mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose
1991General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
1992style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1993mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway
1994down the window.</p>
1995
1996<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1997mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
1998"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1999</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
2000normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2001minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
2002style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2003mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
2004for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2005mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
2006
2007<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2008mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2009"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2010</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
2011style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2012mso-hansi-theme-font:minor-latin'>PWDR 11bmb_8716.fxye Bank 1</span></b> for
2013the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2014mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
2015set from</span></b> item (the only choice). The Fourier calculation will use
2016the structure factors shown in the <b style='mso-bidi-font-weight:normal'><span
2017style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2018mso-hansi-theme-font:minor-latin'>Reflection list</span></b> item for this PWDR
2019data set.</p>
2020
2021<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2022mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2023"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2024</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2025style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2026mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b
2027style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2028mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2029tab window. The map will be computed via fast Fourier techniques and is very
2030fast. A few lines summarizing the map is printed on the console, the structure
2031plot may show a single green dot somewhere (it could be hidden beneath an
2032atom!), this is the highest point in the map.</p>
2033
2034<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2035mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2036"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2037</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2038style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2039mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b
2040style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2041mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
2042level</span></b> slider until something appears on the map. You can also reduce
2043the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2044mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
2045to help clarify the view.</p>
2046
2047<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2048 id="Picture_x0020_35" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:502.5pt;
2049 height:435.75pt;visibility:visible;mso-wrap-style:square'>
2050 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title=""
2051  croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/>
2052</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=581
2053src="Charge%20Flipping%20-%20sucrose_files/image059.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
2054
2055<p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots
2056whose size are proportional to the electron density. There are peaks that might
2057be H-atom positions as well as features that suggest C &amp; O-atoms out of
2058position. Recall that the refinement was just done without any H-atoms; it will
2059make the best fit compensating for the missing H-atoms by displacing the C
2060&amp; O atoms in the direction of the missing H-atoms. </p>
2061
2062<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2063mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2064"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2065</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2066style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2067mso-hansi-theme-font:minor-latin'>Phases/<span class=GramE>sucrose<span
2068style='mso-spacerun:yes'>  </span>Draw</span> Atoms</span></b> tab.</p>
2069
2070<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2071mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2072"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2073</span></span></span><![endif]>Select a C or O atom with possible H-atom
2074density nearby. It will appear green. Do <b style='mso-bidi-font-weight:normal'><span
2075style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2076mso-hansi-theme-font:minor-latin'>Edit/View point</span></b>; this will
2077position the cross on the selected atom.</p>
2078
2079<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2080mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2081"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2082</span></span></span><![endif]>Using the mouse, position the multicolored cross
2083directly in the center of the nearby H atom peak. Rotate the drawing around
2084with the left mouse button and shift the cross with the right mouse button. You
2085can zoom in using the roll wheel on the mouse (or else use the <b
2086style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2087mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Camera
2088distance</span></b> slider in the <b style='mso-bidi-font-weight:normal'><span
2089style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2090mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab if your mouse
2091lacks a wheel).</p>
2092
2093<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2094 id="Picture_x0020_36" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:7in;
2095 height:435.75pt;visibility:visible;mso-wrap-style:square'>
2096 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""
2097  croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/>
2098</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=581
2099src="Charge%20Flipping%20-%20sucrose_files/image060.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
2100
2101<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2102mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2103"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2104</span></span></span><![endif]>Go to the Atoms tab and do <b style='mso-bidi-font-weight:
2105normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2106minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>,
2107a white ball will appear at the selected position and an H-atom (name = <b
2108style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2109mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>)
2110will be appended to the end of the atom list. Repeat steps 1-4 for as many
2111recognizable H-atom positions you can find; the goal is to find all 22 of them
2112(you probably will find less than that, but you could guess many of the rest).
2113I easily found all but 5 of them.</p>
2114
2115<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2116 id="Picture_x0020_38" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:7in;
2117 height:427.5pt;visibility:visible;mso-wrap-style:square'>
2118 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image037.png" o:title=""
2119  croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/>
2120</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=570
2121src="Charge%20Flipping%20-%20sucrose_files/image061.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
2122
2123<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2124mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2125"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2126</span></span></span><![endif]>Change their <b style='mso-bidi-font-weight:
2127normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2128minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> to <b
2129style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2130mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>,
2131they will be renamed and make then all ball &amp; stick. Do a <b
2132style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2133mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
2134there should be a drop in <span class=SpellE>Rwp</span>. Then repeat the <b
2135style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2136mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier
2137map</span></b> in the <b style='mso-bidi-font-weight:normal'><span
2138style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2139mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust the <b
2140style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2141mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
2142level</span></b> and <b style='mso-bidi-font-weight:normal'><span
2143style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2144mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for
2145the remaining H-atoms; you may have to guess positions for some of them using
2146known stereochemistry rules. My model looked like</p>
2147
2148<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2149 id="Picture_x0020_39" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:502.5pt;
2150 height:421.5pt;visibility:visible;mso-wrap-style:square'>
2151 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image039.png" o:title=""
2152  croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/>
2153</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=562
2154src="Charge%20Flipping%20-%20sucrose_files/image062.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
2155
2156<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2157style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2158mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> to finish this
2159stage in the structure analysis. My <span class=SpellE>Rwp</span> was ~8.02%
2160with all the H-atoms included (but not refined). The fit looks pretty good</p>
2161
2162<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2163 id="Picture_x0020_40" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
2164 height:450pt;visibility:visible;mso-wrap-style:square'>
2165 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image041.png" o:title=""/>
2166</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2167src="Charge%20Flipping%20-%20sucrose_files/image041.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
2168
2169<h2>Step 6: Final refinement</h2>
2170
2171<p class=MsoNormal>Looking at the fit, there may be room for improvement and
2172we’d like to refine the H-atom positions. First we need to change the profile
2173model to include crystallite size and <span class=SpellE>mustrain</span>
2174broadening. Go to <b style='mso-bidi-font-weight:normal'><span
2175style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2176mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>, set <b
2177style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2178mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2179and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2180mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2181to <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'>zero</span></b>
2183and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2184"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2185minor-latin'>Refine</span></b> flags for them.</p>
2186
2187<p class=MsoNormal>Next go to <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'>Phases/sucrose</span></b> and look at the <b
2190style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2191mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
2192tab; make sure the <b style='mso-bidi-font-weight:normal'><span
2193style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2194mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the
2195boxes for both <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2196style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2197mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b style='mso-bidi-font-weight:
2198normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2199minor-latin;mso-hansi-theme-font:minor-latin'>. <span class=GramE>size</span></span></b>
2200and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2201style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2202mso-hansi-theme-font:minor-latin'>microstrain</span></b></span>.</p>
2203
2204<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2205 id="Picture_x0020_41" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:480pt;
2206 height:339pt;visibility:visible;mso-wrap-style:square'>
2207 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/>
2208</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=452
2209src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
2210
2211<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2212style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2213mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2214class=SpellE>Rwp</span> will start out high but should converge to where it was
2215before this change. I got 8.08% and the <b style='mso-bidi-font-weight:normal'><span
2216style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2217mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>
2218
2219<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2220 id="Picture_x0020_42" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:480pt;
2221 height:334.5pt;visibility:visible;mso-wrap-style:square'>
2222 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image043.png" o:title=""/>
2223</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=446
2224src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
2225
2226<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
2227style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2228mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span
2229class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2230"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2231minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span
2232style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2233mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
2234phenomenological model for <span class=SpellE>microstrain</span> which has 9
2235terms for monoclinic structures. Check all the boxes for it.</p>
2236
2237<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2238 id="Picture_x0020_43" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:480pt;
2239 height:303.75pt;visibility:visible;mso-wrap-style:square'>
2240 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image044.png" o:title=""/>
2241</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=405
2242src="Charge%20Flipping%20-%20sucrose_files/image044.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
2243
2244<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2245style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2246mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2247class=SpellE>Rwp</span> will start out high but should converge lower than
2248where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight:
2249normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2250minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like.
2251If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2252style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2253mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b
2254style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2255mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot
2256type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span>
2257surface plot for ground sucrose.</p>
2258
2259<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2260 id="Picture_x0020_45" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:480pt;
2261 height:305.25pt;visibility:visible;mso-wrap-style:square'>
2262 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image045.png" o:title=""/>
2263</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=407
2264src="Charge%20Flipping%20-%20sucrose_files/image045.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
2265
2266<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2267style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2268mso-hansi-theme-font:minor-latin;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2269 id="Picture_x0020_47" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
2270 height:450pt;visibility:visible;mso-wrap-style:square'>
2271 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image046.png" o:title=""/>
2272</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2273src="Charge%20Flipping%20-%20sucrose_files/image046.png" v:shapes="Picture_x0020_47"><![endif]></span></b></p>
2274
2275<p class=MsoNormal>Before refining H-atom positions it would be wise to create
2276restraints on their bond distances and angles. Locate <b style='mso-bidi-font-weight:
2277normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2278minor-latin;mso-hansi-theme-font:minor-latin'>Restraints</span></b> in the main
2279GSAS-II data tree; there will be an almost blank window telling you there are
2280no bond restraints for sucrose. Do <b style='mso-bidi-font-weight:normal'><span
2281style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2282mso-hansi-theme-font:minor-latin'>Edit/Add <span class=GramE>restraints<span
2283style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
2284a dialog box will appear asking for the origin atom for the bond. </p>
2285
2286<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2287 id="Picture_x0020_48" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:259.5pt;
2288 height:252pt;visibility:visible;mso-wrap-style:square'>
2289 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image047.png" o:title=""/>
2290</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
2291src="Charge%20Flipping%20-%20sucrose_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
2292
2293<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2294style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2295mso-hansi-theme-font:minor-latin'>all H</span></b> and press <b
2296style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2297mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2298A new dialog box will appear asking for the target atoms for the bonds.</p>
2299
2300<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2301 id="Picture_x0020_49" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:259.5pt;
2302 height:252pt;visibility:visible;mso-wrap-style:square'>
2303 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image048.png" o:title=""/>
2304</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
2305src="Charge%20Flipping%20-%20sucrose_files/image048.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
2306
2307<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2308style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2309mso-hansi-theme-font:minor-latin'>all C</span></b> and <b style='mso-bidi-font-weight:
2310normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2311minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b> and a third
2312dialog box appears asking for the bond length</p>
2313
2314<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2315 id="Picture_x0020_50" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:147pt;
2316 height:78.75pt;visibility:visible;mso-wrap-style:square'>
2317 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image049.png" o:title=""/>
2318</v:shape><![endif]--><![if !vml]><img border=0 width=196 height=105
2319src="Charge%20Flipping%20-%20sucrose_files/image049.png" v:shapes="Picture_x0020_50"><![endif]></span><span
2320style='mso-spacerun:yes'> </span></p>
2321
2322<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
2323style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2324mso-hansi-theme-font:minor-latin'>1.09</span></b> and press <b
2325style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2326mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2327I got a short list of 8 H-C and H-O restraints, but I expect 22 of them. Change
2328the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2329mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Search range</span></b>
2330to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2331mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.5</span></b>
2332and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
2333"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2334minor-latin'>Edit/Add restraints</span></b>. There are now 22 restraints on H-C
2335and H-O bond lengths.</p>
2336
2337<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2338 id="Picture_x0020_51" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:450pt;
2339 height:423pt;visibility:visible;mso-wrap-style:square'>
2340 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image050.png" o:title=""/>
2341</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=564
2342src="Charge%20Flipping%20-%20sucrose_files/image050.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
2343
2344<p class=MsoNormal>Next select the <b style='mso-bidi-font-weight:normal'><span
2345style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2346mso-hansi-theme-font:minor-latin'>Angle restraints</span></b> tab and again
2347there aren’t any. Do <b style='mso-bidi-font-weight:normal'><span
2348style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2349mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
2350will appear asking for the A atom in the angle A-B-C. Select <b
2351style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2352mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all H</span></b>.
2353The next dialog asks for the B atom in the A-B-C angle, select <b
2354style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2355mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all C</span></b>
2356and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2357mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b>.
2358The third dialog asks for the angle and has a default of <b style='mso-bidi-font-weight:
2359normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2360minor-latin;mso-hansi-theme-font:minor-latin'>109.54</span></b>. This is the
2361tetrahedral angle so just press <b style='mso-bidi-font-weight:normal'><span
2362style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2363mso-hansi-theme-font:minor-latin'>OK</span></b>. 36 restraints will be listed;
2364they are listed in order of the B atom. O-atoms should have one angle apiece;
2365C-atoms will have more. </p>
2366
2367<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2368 id="Picture_x0020_52" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:450pt;
2369 height:365.25pt;visibility:visible;mso-wrap-style:square'>
2370 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image051.png" o:title=""/>
2371</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=487
2372src="Charge%20Flipping%20-%20sucrose_files/image051.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
2373
2374<p class=MsoNormal>Now go back the <b style='mso-bidi-font-weight:normal'><span
2375style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2376mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab in <b style='mso-bidi-font-weight:
2377normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2378minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>, select
2379<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2380mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>
2381from the dialog box by double clicking on the <b style='mso-bidi-font-weight:
2382normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2383minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column. Then do <b
2384style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2385mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Set
2386atom refinement flags</span></b>. Select <b style='mso-bidi-font-weight:normal'><span
2387style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2388mso-hansi-theme-font:minor-latin'>X-coordinates</span></b>; this will set those
2389for all H-atoms. Now do <b style='mso-bidi-font-weight:normal'><span
2390style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2391mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>, the console will
2392list progress on the “Penalty function” (i.e. the restraints) and the <span
2393class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase the <b
2394style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2395mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Restraint
2396weight factors</span></b> to tighten them up at some expense in <span
2397class=SpellE>Rwp</span>. In the end I chose <b style='mso-bidi-font-weight:
2398normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2399minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b> for both <b
2400style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2401mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond</span></b>
2402and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2403mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b>
2404restraints to give a final <span class=SpellE>Rwp</span> ~7.1%. NB: the H-atom
2405positions may not be correct even though the refinement apparently succeeded.
2406You should check that the OH ones all give reasonable H-bonds to neighboring
2407O-atoms. As this is powder data such changes will hardly affect the fit but
2408will be more satisfying. At present such checking is outside the scope of
2409GSAS-II.</p>
2410
2411<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2412
2413<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2414
2415</div>
2416
2417</body>
2418
2419</html>
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