source: trunk/help/Charge Flipping - sucrose.htm @ 872

Last change on this file since 872 was 872, checked in by vondreele, 9 years ago

cleanup tutorial

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384        font-size:24.0pt;
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
853        {mso-level-number-format:alpha-lower;
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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 needed
974for 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>
1053 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
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:366pt;
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=488 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. This makes all the negative intensities
1273positive. Next in the <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'>General</span></b> tab set the <b
1276style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1277mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley neg.
1278wt.</span></b> to <b style='mso-bidi-font-weight:normal'><span
1279style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1280mso-hansi-theme-font:minor-latin'>0.01</span></b>; this will suppress the
1281negative Pawley intensities. Do <b style='mso-bidi-font-weight:normal'><span
1282style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1283mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>. After
1284refinement, mine converged to ~5.7% and the plot looked like</p>
1285
1286<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1287 id="Picture_x0020_29" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:507pt;
1288 height:434.25pt;visibility:visible;mso-wrap-style:square'>
1289 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image009.png" o:title=""/>
1290</v:shape><![endif]--><![if !vml]><img border=0 width=676 height=579
1291src="Charge%20Flipping%20-%20sucrose_files/image009.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
1292
1293<p class=MsoNormal>Let’s see if this is good enough for charge flipping.</p>
1294
1295<h2>Step 3: Charge flipping</h2>
1296
1297<p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
1298Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1299mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1300and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1301"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1302minor-latin'>Charge flip controls</span></b> in the middle of the <b
1303style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1304mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1305tab.</p>
1306
1307<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1308mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1309"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1310</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
1311style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1312mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b
1313style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1314mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
131511bmb_8716.fxye Bank 1</span></b> (the only choice!). This makes the reflection
1316set to be used those in <b style='mso-bidi-font-weight:normal'><span
1317style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1318mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
1319data set; these should match the <b style='mso-bidi-font-weight:normal'><span
1320style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1321mso-hansi-theme-font:minor-latin'>Pawley reflection</span></b> set.</p>
1322
1323<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1324mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1325"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1326</span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span
1327style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1328mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b
1329style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1330mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map
1331controls</span></b>) to <b style='mso-bidi-font-weight:normal'><span
1332style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1333mso-hansi-theme-font:minor-latin'>20%</span></b>. This controls the map search
1334routine.</p>
1335
1336<p class=MsoNormal>For powder data it is not usually advisable to select a <b
1337style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1338mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing
1339element</span></b>; if selected a periodic table appears – select an element or
1340‘<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'>None’</span></b>.
1342The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1343mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1344defines the map spacing and thus the extent of the reflection set; the observed
1345reflection set is zero filled to this limit for charge flipping. The <b
1346style='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-factor</span></b>
1348and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1349mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b>
1350determine the lower threshold and upper limit for charge flipping,
1351respectively. The latter is used to avoid “Uranium solutions” in the result.
1352Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1353"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1354minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
1355ones. For sucrose set it to <b style='mso-bidi-font-weight:normal'><span
1356style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1357mso-hansi-theme-font:minor-latin'>12.</span></b> When ready select <b
1358style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1359mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1360flipping</span></b>; a progress bar dialog will appear that tracks the residual
1361found in each charge flipping cycle. It will quickly drop to some level
1362(42-44%) and then for a successful charge flipping run perhaps drop again into
1363the 20-25% range after a considerable length of time. You should save the
1364project if you get an apparently good solution. Many times it will not drop
1365below ~40%; just try <b style='mso-bidi-font-weight:normal'><span
1366style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1367mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b> again. If
1368several tries fail to yield a solution, go back to the last step of the Pawley
1369refinement and just repeat it (that is do <b style='mso-bidi-font-weight:normal'><span
1370style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1371mso-hansi-theme-font:minor-latin'>Pawley update</span></b> and <b
1372style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1373mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>).
1374This will generate a different set of intensities for the highly overlapped
1375part of the powder pattern; perhaps they will give a successful charge flip
1376solution. Unless otherwise interrupted, GSAS-II will try 10000 times for a
1377charge flip solution (for sucrose this takes 5-10min on my laptop). Press <b
1378style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1379mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b>
1380to stop the charge flipping; a peak list and a drawing of the solution will
1381appear. One of my runs gave</p>
1382
1383<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1384 id="Picture_x0020_30" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:337.5pt;
1385 height:225pt;visibility:visible;mso-wrap-style:square'>
1386 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image010.png" o:title=""/>
1387</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
1388src="Charge%20Flipping%20-%20sucrose_files/image010.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1389
1390<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1391
1392<p class=MsoNormal><!--[if gte vml 1]><v:group id="Group_x0020_39" o:spid="_x0000_s1026"
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1491position:absolute;z-index:251662336;margin-left:315px;margin-top:308px;
1492width:16px;height:35px'><img width=16 height=35
1493src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
1494style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
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1496 visibility:visible;mso-wrap-style:square'>
1497 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image012.png" o:title=""
1498  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
1499</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=575
1500src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
1501
1502<p class=MsoNormal>The result looks very promising! Charge flipping operates
1503without regard to symmetry and GSAS-II attempts to locate the map with respect
1504to the symmetry elements from the computed reflection phases. (NB: charge
1505flipping also will give a solution without regard to handedness; this solution
1506may be either the correct one for sucrose or its inverse.) Errors in these
1507phases can disrupt this process so that the map and peak positions are offset
1508from their true positions. To discover this and fix it, rotate the drawing
1509around to check that atom positions are related via the 2<sub>1</sub> screw
1510axis (through the multicolored cross in the center of the cell and parallel to
1511the y-axis – the green cell edge). Avoid motions with the right mouse button
1512pressed, this moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:
1513normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1514minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the
1515cross to the cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my
1516drawing above to show where I think it should be. If you find an offset to the
1517map, orient it so the offset is horizontal or vertical and then press the <b
1518style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1519mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</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'>R</span></b>,
1522<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'>U</span></b>
1524or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1525mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
1526keys to shift the map and peaks as needed. The shift is in resolution units
1527(0.5Å) so the fix can only be approximate. Repeat as needed. Notice that the
1528peak positions in the table are updated as the offset is changed. In this case,
1529I needed just a few steps to correct the map offset. NB: you can use these keys
1530to move the result anywhere you wish, e.g. to select a different origin for the
1531structure but pay attention to the location of symmetry elements. After
1532adjustment, my solution looked like</p>
1533
1534<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1535 id="Picture_x0020_12" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:500.25pt;
1536 height:424.5pt;visibility:visible;mso-wrap-style:square'>
1537 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image014.png" o:title=""
1538  croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/>
1539</v:shape><![endif]--><![if !vml]><img border=0 width=667 height=566
1540src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
1541
1542<h2>Step 4: Obtain solution from charge flip result</h2>
1543
1544<p class=MsoNormal>The next step is to extract the unique peak positions from
1545the map and make atoms out of them. The map peak list is initially sorted by
1546peak magnitude; you can change the sorting to be along any of the column
1547headings in the table by a single click on the desired heading. The <span
1548class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1549"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1550minor-latin'>dzero</span></b></span> column gives the distance of each peak from
1551the origin. The menu items under Map peaks give you several tools to aid in the
1552peak selection process; we will just use a couple in this example. I have
1553chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:normal'><span
1554style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1555mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and then finding
1556the unique ones. </p>
1557
1558<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1559mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1560"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1561</span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight:
1562normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1563minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> column heading. This
1564will sort the peaks in increasing z-axis coordinate.</p>
1565
1566<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1567mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1568"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1569</span></span></span><![endif]>Do a single click on the upper left (empty) box
1570of the table. All entries will be colored grey indicating their selection.</p>
1571
1572<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1573mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1574"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1575</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1576style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1577mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That should
1578select (grey) 23 out of 46 peak positions in the table and all should be near
1579the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
1580that would be all the C &amp; O atoms! They will be colored green in the plot.
1581If more are selected then check the map offset – it may need a slight
1582correction.</p>
1583
1584<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1585 id="Picture_x0020_13" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:337.5pt;
1586 height:411.75pt;visibility:visible;mso-wrap-style:square'>
1587 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image016.png" o:title=""/>
1588</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=549
1589src="Charge%20Flipping%20-%20sucrose_files/image016.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1590
1591<p class=MsoNormal>The drawing shows the selected atoms in green.</p>
1592
1593<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1594 id="Picture_x0020_14" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:7in;
1595 height:429pt;visibility:visible;mso-wrap-style:square'>
1596 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image017.png" o:title=""
1597  croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/>
1598</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=572
1599src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
1600
1601<p class=MsoNormal>Notice that in my case one atom is in a neighboring
1602molecule, one can deselect it and then pick the desired equivalent. Hold the <b
1603style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1604mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1605key down and use the right mouse button to pick/unpick atoms in the drawing.
1606NB: the left mouse button will clear all the selections. The other two “lone”
1607atoms belong to molecules in neighboring unit cells; we’ll deal with them
1608later.</p>
1609
1610<p class=MsoNormal>These are now ready to turn into atoms. Do <b
1611style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1612mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1613peaks/Move peaks</span></b>. The drawing will show white balls for each of the
1614selected positions and the <b style='mso-bidi-font-weight:normal'><span
1615style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1616mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 23 new H
1617atoms. </p>
1618
1619<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1620 id="Picture_x0020_15" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:7in;
1621 height:433.5pt;visibility:visible;mso-wrap-style:square'>
1622 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image019.png" o:title=""
1623  croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/>
1624</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=578
1625src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
1626
1627<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1628 id="Picture_x0020_44" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
1629 height:414.75pt;visibility:visible;mso-wrap-style:square'>
1630 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image021.png" o:title=""/>
1631</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=553
1632src="Charge%20Flipping%20-%20sucrose_files/image021.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
1633
1634<p class=MsoNormal>The atom names indicate the peak magnitude to aid
1635identification (M100 for the largest in the <b style='mso-bidi-font-weight:
1636normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1637minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
1638may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
1639style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1640mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
1641them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
1642style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1643mso-hansi-theme-font:minor-latin'>Alt</span></b> key down and then selecting a
1644position in the table with the <b style='mso-bidi-font-weight:normal'><span
1645style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1646mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. After sorting
1647by magnitude, my list is now </p>
1648
1649<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1650 id="Picture_x0020_17" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:525pt;
1651 height:417pt;visibility:visible;mso-wrap-style:square'>
1652 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image022.png" o:title=""/>
1653</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=556
1654src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1655
1656<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out
1657into two groups with a clear gap between M79 and M64. The higher ones are
1658likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit
1659of ambiguity in the middle, but just assign the top 11 as O and the rest as C
1660and see what happens. You can do this by selecting a block of atoms, go to <b
1661style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1662mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1663atom parameters</span></b> and select <b style='mso-bidi-font-weight:normal'><span
1664style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1665mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a
1666periodic table will appear. Select the desired element and they will be changed
1667in the list and drawing.</p>
1668
1669<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1670 id="Picture_x0020_18" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:7in;
1671 height:405.75pt;visibility:visible;mso-wrap-style:square'>
1672 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image023.png" o:title=""
1673  croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/>
1674</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=541
1675src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
1676
1677<p class=MsoNormal>The original charge flipping solution is still visible and
1678the atoms are now identified, I’ve changed the drawing to show balls and sticks
1679and labeled the atoms with their names, this is done in the <b
1680style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1681mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b>
1682tab. Double click the appropriate column heading and make the selection from
1683the dialog box.<span style='mso-spacerun:yes'>  </span></p>
1684
1685<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1686 id="Picture_x0020_19" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:450pt;
1687 height:415.5pt;visibility:visible;mso-wrap-style:square'>
1688 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image025.png" o:title=""/>
1689</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=554
1690src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
1691
1692<p class=MsoNormal>Now one can safely remove the map peaks (do <b
1693style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1694mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1695peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span
1696style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1697mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
1698charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1699style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1700mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
1701normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1702minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
1703style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1704mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1705tab). The atom positions I obtained have two atoms (O3 &amp; O4) not connected
1706to the sucrose molecule because they belong to neighboring molecules. We need to
1707discover the equivalent ones that belong to this molecule. Follow the steps:</p>
1708
1709<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1710mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1711"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1712</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1713style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1714mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> tab and select them
1715(hold the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1716mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ctrl</span></b>
1717key down and select the appropriate rows). </p>
1718
1719<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1720mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1721"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1722</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1723style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1724mso-hansi-theme-font:minor-latin'>Edit/Fill unit cell</span></b>; new atoms
1725will appear at end of list and in the drawing. </p>
1726
1727<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1728mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1729"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1730</span></span></span><![endif]>Select all the atoms in the <b style='mso-bidi-font-weight:
1731normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1732minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table by a
1733double click on upper left corner box of the table.</p>
1734
1735<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1736mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1737"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1738</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1739style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1740mso-hansi-theme-font:minor-latin'>Edit/Fill CN-sphere</span></b>; new atoms
1741will appear that are bonded to the molecule.</p>
1742
1743<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1744mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1745"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1746</span></span></span><![endif]>Select these new atoms that are in the molecule;
1747they will probably be outside the unit cell box. Do this on the drawing with <b
1748style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1749mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift left</span></b>
1750for the first one &amp; <b style='mso-bidi-font-weight:normal'><span
1751style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1752mso-hansi-theme-font:minor-latin'>Shift right</span></b> for <span
1753class=SpellE>the</span> rest, they will show in green. </p>
1754
1755<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1756mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1757"Times New Roman"'><span style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1758</span></span></span><![endif]>Look at the <b style='mso-bidi-font-weight:normal'><span
1759style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1760mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the
1761selections and make note of the <span class=SpellE><b style='mso-bidi-font-weight:
1762normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1763minor-latin;mso-hansi-theme-font:minor-latin'>Sym</span></b></span><b
1764style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1765mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Op</span></b>
1766for each one. In my case they were “<b style='mso-bidi-font-weight:normal'><span
1767style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1768mso-hansi-theme-font:minor-latin'>2+1<span class=GramE>,0,0</span></span></b>”
1769for O(4) and “<b style='mso-bidi-font-weight:normal'><span style='font-family:
1770"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1771minor-latin'>2+2,-1,1</span></b>” for O(3). The first number is the symmetry
1772operator number and the 3 numbers after the ‘<b style='mso-bidi-font-weight:
1773normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1774minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’ are unit cell
1775translations.</p>
1776
1777<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1778mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1779"Times New Roman"'><span style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1780</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1781style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1782mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab.</p>
1783
1784<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1785mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1786"Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1787</span></span></span><![endif]>Select an atom in turn that needs to be moved,
1788e.g. in my case <span class=GramE>O(</span>3) or O(4). </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'>9.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1793</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1794style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1795mso-hansi-theme-font:minor-latin'>Edit/Transform <span class=GramE>atoms<span
1796style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
1797select the operator and unit cell translations, then press <b style='mso-bidi-font-weight:
1798normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1799minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom
1800coordinates will be transformed.</p>
1801
1802<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1803mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1804"Times New Roman"'><span style='mso-list:Ignore'>10.<span style='font:7.0pt "Times New Roman"'>&nbsp;
1805</span></span></span><![endif]>Repeat 8 &amp; 9 for any other atoms to be
1806moved.</p>
1807
1808<p class=MsoNormal style='margin-left:.5in'>This will complete the molecule
1809with the extra atoms. <span class=GramE>Do</span> <b style='mso-bidi-font-weight:
1810normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1811minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>
1812to see the completed molecule. I’ve made it a balls &amp; sticks with names as
1813labels.</p>
1814
1815<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1816 id="Picture_x0020_20" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:7in;
1817 height:6in;visibility:visible;mso-wrap-style:square'>
1818 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image026.png" o:title=""
1819  cropbottom="28348f" cropleft="41090f" cropright="9483f"/>
1820</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=576
1821src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
1822
1823<p class=MsoNormal>Save the project file; the next step is to complete the
1824structure by finding H-atoms and then do the final Rietveld refinements.</p>
1825
1826<h2>Step 5: Complete the structure</h2>
1827
1828<p class=MsoNormal>To complete the structure you will need to perform a
1829preliminary Rietveld refinement. This will make the atom positions more
1830accurate and prepare a set of calculated structure factors needed to generate a
1831difference Fourier map good enough to maybe reveal the H atoms. There are a
1832number of steps needed to set all the controls from the previous Pawley
1833refinement to get a successful start for the Rietveld refinement.</p>
1834
1835<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1836mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1837"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1838</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1839style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1840mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the
1841GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span
1842style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1843mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You don’t want to
1844start with these when the scale factor is unknown.</p>
1845
1846<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1847mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1848"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1849</span></span></span><![endif]>Go to <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'>Sample Parameters</span></b> and check the <b
1852style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1853mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
1854scale factor</span></b> box. This is the scale factor for the data set. Uncheck
1855the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1856mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1857class=SpellE>displ</span></span></b>.</p>
1858
1859<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1860mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1861"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1862</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
1863style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1864mso-hansi-theme-font:minor-latin'>Phases/sucrose General</span></b> tab and
1865uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1866mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
1867cell</span></b> and <b style='mso-bidi-font-weight:normal'><span
1868style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1869mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The
1870latter is most important; if you forget you will just get another Pawley
1871refinement!</p>
1872
1873<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1874style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1875mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
1876GSAS-II data tree menu; only scale and background are refined. I got <span
1877class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear
1878intensity differences; the atom positions obviously need refinement.</p>
1879
1880<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1881 id="Picture_x0020_21" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:502.5pt;
1882 height:430.5pt;visibility:visible;mso-wrap-style:square'>
1883 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/>
1884</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=574
1885src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
1886
1887<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
1888obvious.</p>
1889
1890<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
1891style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1892mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and select the <b
1893style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1894mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1895tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub>
1896has an arbitrary location along the y-axis. Then double click the <b
1897style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1898mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1899column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight:
1900normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1901minor-latin;mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and
1902press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1903mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1904The atoms table will show the refinement controls</p>
1905
1906<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1907 id="Picture_x0020_22" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
1908 height:225pt;visibility:visible;mso-wrap-style:square'>
1909 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/>
1910</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
1911src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
1912
1913<p class=MsoNormal>To deal with the warning we need to set a “Hold” on one atom
1914y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span
1915style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1916mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II
1917data tree.</p>
1918
1919<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1920 id="Picture_x0020_23" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:225pt;
1921 height:187.5pt;visibility:visible;mso-wrap-style:square'>
1922 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image030.png" o:title=""/>
1923</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
1924src="Charge%20Flipping%20-%20sucrose_files/image030.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
1925
1926<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
1927style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1928mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
1929style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1930mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
1931class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will
1932fix the shift along y for the <span class=GramE>O(</span>1) atom.</p>
1933
1934<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1935 id="Picture_x0020_53" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:259.5pt;
1936 height:271.5pt;visibility:visible;mso-wrap-style:square'>
1937 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/>
1938</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=362
1939src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
1940
1941<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1942style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1943mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will
1944show the hold</p>
1945
1946<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1947 id="Picture_x0020_54" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:225pt;
1948 height:187.5pt;visibility:visible;mso-wrap-style:square'>
1949 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image032.png" o:title=""/>
1950</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
1951src="Charge%20Flipping%20-%20sucrose_files/image032.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
1952
1953<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
1954style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1955mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
1956class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice
1957parameters (in the <b style='mso-bidi-font-weight:normal'><span
1958style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1959mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
1960style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1961mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>),
1962the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1963mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1964parameters</span></b> <b style='mso-bidi-font-weight:normal'><span
1965style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1966mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
1967normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1968minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b
1969style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1970mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
1971<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1972mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
1973&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1974mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
1975and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1976mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1977class=SpellE>displ</span></span></b>. You can also include refinement of atom
1978thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
1979refinement improved slightly to Rwp~10.0%. Let’s see if a difference Fourier
1980map will show anything.<br>
1981Go to the <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'>Phases/sucrose
1983General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
1984style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1985mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway
1986down the window.</p>
1987
1988<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1989mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
1990"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1991</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
1992normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1993minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
1994style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1995mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
1996for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1997mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
1998
1999<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2000mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2001"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2002</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
2003style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2004mso-hansi-theme-font:minor-latin'>PWDR 11bmb_8716.fxye Bank 1</span></b> for
2005the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2006mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
2007set from</span></b> item (the only choice). The Fourier calculation will use
2008the structure factors shown in the <b style='mso-bidi-font-weight:normal'><span
2009style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2010mso-hansi-theme-font:minor-latin'>Reflection list</span></b> item for this PWDR
2011data set.</p>
2012
2013<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2014mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2015"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2016</span></span></span><![endif]>Do <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'>Compute/Fourier map</span></b> from the <b
2019style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2020mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2021tab window. The map will be computed via fast Fourier techniques and is very
2022fast. A few lines summarizing the map is printed on the console, the structure
2023plot may show a single green dot somewhere (it could be hidden beneath an
2024atom!), this is the highest point in the map.</p>
2025
2026<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2027mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2028"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2029</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2030style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2031mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b
2032style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2033mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
2034level</span></b> slider until something appears on the map. You can also reduce
2035the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2036mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
2037to help clarify the view.</p>
2038
2039<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2040 id="Picture_x0020_35" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:502.5pt;
2041 height:435.75pt;visibility:visible;mso-wrap-style:square'>
2042 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title=""
2043  croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/>
2044</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=581
2045src="Charge%20Flipping%20-%20sucrose_files/image034.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
2046
2047<p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots
2048whose size are proportional to the electron density. There are peaks that might
2049be H-atom positions as well as features that suggest C &amp; O-atoms out of
2050position. Recall that the refinement was just done without any H-atoms; it will
2051make the best fit compensating for the missing H-atoms by displacing the C
2052&amp; O atoms in the direction of the missing H-atoms. </p>
2053
2054<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2055mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2056"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2057</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2058style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2059mso-hansi-theme-font:minor-latin'>Phases/<span class=GramE>sucrose<span
2060style='mso-spacerun:yes'>  </span>Draw</span> Atoms</span></b> tab.</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'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2065</span></span></span><![endif]>Select a C or O atom with possible H-atom
2066density nearby. It will appear green. Do <b style='mso-bidi-font-weight:normal'><span
2067style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2068mso-hansi-theme-font:minor-latin'>Edit/View point</span></b>; this will
2069position the cross on the selected atom.</p>
2070
2071<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2072mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2073"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2074</span></span></span><![endif]>Using the mouse, position the multicolored cross
2075directly in the center of the nearby H atom peak. Rotate the drawing around
2076with the left mouse button and shift the cross with the right mouse button. You
2077can zoom in using the roll wheel on the mouse (or else use the <b
2078style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2079mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Camera
2080distance</span></b> slider in the <b style='mso-bidi-font-weight:normal'><span
2081style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2082mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab if your mouse
2083lacks a wheel).</p>
2084
2085<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2086 id="Picture_x0020_36" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:7in;
2087 height:435.75pt;visibility:visible;mso-wrap-style:square'>
2088 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""
2089  croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/>
2090</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=581
2091src="Charge%20Flipping%20-%20sucrose_files/image036.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
2092
2093<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2094mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2095"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2096</span></span></span><![endif]>Go to the Atoms tab and do <b style='mso-bidi-font-weight:
2097normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2098minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>,
2099a white ball will appear at the selected position and an H-atom (name = <b
2100style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2101mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>)
2102will be appended to the end of the atom list. Repeat steps 1-4 for as many
2103recognizable H-atom positions you can find; the goal is to find all 22 of them
2104(you probably will find less than that, but you could guess many of the rest).
2105I easily found all but 5 of them.</p>
2106
2107<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2108 id="Picture_x0020_38" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:7in;
2109 height:427.5pt;visibility:visible;mso-wrap-style:square'>
2110 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image037.png" o:title=""
2111  croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/>
2112</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=570
2113src="Charge%20Flipping%20-%20sucrose_files/image038.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
2114
2115<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2116mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2117"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2118</span></span></span><![endif]>Change their <b style='mso-bidi-font-weight:
2119normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2120minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> to <b
2121style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2122mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>,
2123they will be renamed and make then all ball &amp; stick. Do a <b
2124style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2125mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
2126there should be a drop in <span class=SpellE>Rwp</span>. Then repeat the <b
2127style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2128mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier
2129map</span></b> in the <b style='mso-bidi-font-weight:normal'><span
2130style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2131mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust the <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'>Contour
2134level</span></b> and <b style='mso-bidi-font-weight:normal'><span
2135style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2136mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for
2137the remaining H-atoms; you may have to guess positions for some of them using
2138known stereochemistry rules. My model looked like</p>
2139
2140<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2141 id="Picture_x0020_39" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:502.5pt;
2142 height:421.5pt;visibility:visible;mso-wrap-style:square'>
2143 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image039.png" o:title=""
2144  croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/>
2145</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=562
2146src="Charge%20Flipping%20-%20sucrose_files/image040.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
2147
2148<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2149style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2150mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> to finish this
2151stage in the structure analysis. My <span class=SpellE>Rwp</span> was ~8.02%
2152with all the H-atoms included (but not refined). The fit looks pretty good</p>
2153
2154<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2155 id="Picture_x0020_40" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
2156 height:450pt;visibility:visible;mso-wrap-style:square'>
2157 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image041.png" o:title=""/>
2158</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2159src="Charge%20Flipping%20-%20sucrose_files/image041.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
2160
2161<h2>Step 6: Final refinement</h2>
2162
2163<p class=MsoNormal>Looking at the fit, there may be room for improvement and
2164we’d like to refine the H-atom positions. First we need to change the profile
2165model to include crystallite size and <span class=SpellE>mustrain</span>
2166broadening. Go to <b style='mso-bidi-font-weight:normal'><span
2167style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2168mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>, set <b
2169style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2170mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2171and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2172mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2173to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2174mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>zero</span></b>
2175and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2176"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2177minor-latin'>Refine</span></b> flags for them.</p>
2178
2179<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
2180style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2181mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and look at the <b
2182style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2183mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
2184tab; make sure the <b style='mso-bidi-font-weight:normal'><span
2185style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2186mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the
2187boxes for both <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2188style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2189mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b style='mso-bidi-font-weight:
2190normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2191minor-latin;mso-hansi-theme-font:minor-latin'>. <span class=GramE>size</span></span></b>
2192and <span class=SpellE><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'>microstrain</span></b></span>.</p>
2195
2196<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2197 id="Picture_x0020_41" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:480pt;
2198 height:339pt;visibility:visible;mso-wrap-style:square'>
2199 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/>
2200</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=452
2201src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
2202
2203<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2204style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2205mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2206class=SpellE>Rwp</span> will start out high but should converge to where it was
2207before this change. I got 8.08% and the <b style='mso-bidi-font-weight:normal'><span
2208style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2209mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>
2210
2211<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2212 id="Picture_x0020_42" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:480pt;
2213 height:334.5pt;visibility:visible;mso-wrap-style:square'>
2214 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image043.png" o:title=""/>
2215</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=446
2216src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
2217
2218<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
2219style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2220mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span
2221class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2222"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2223minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span
2224style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2225mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
2226phenomenological model for <span class=SpellE>microstrain</span> which has 9
2227terms for monoclinic structures. Check all the boxes for it.</p>
2228
2229<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2230 id="Picture_x0020_43" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:480pt;
2231 height:303.75pt;visibility:visible;mso-wrap-style:square'>
2232 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image044.png" o:title=""/>
2233</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=405
2234src="Charge%20Flipping%20-%20sucrose_files/image044.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
2235
2236<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2237style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2238mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2239class=SpellE>Rwp</span> will start out high but should converge lower than
2240where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight:
2241normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2242minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like.
2243If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2244style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2245mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b
2246style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2247mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot
2248type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span>
2249surface plot for ground sucrose.</p>
2250
2251<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2252 id="Picture_x0020_45" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:480pt;
2253 height:305.25pt;visibility:visible;mso-wrap-style:square'>
2254 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image045.png" o:title=""/>
2255</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=407
2256src="Charge%20Flipping%20-%20sucrose_files/image045.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
2257
2258<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2259style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2260mso-hansi-theme-font:minor-latin;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2261 id="Picture_x0020_47" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
2262 height:450pt;visibility:visible;mso-wrap-style:square'>
2263 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image046.png" o:title=""/>
2264</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2265src="Charge%20Flipping%20-%20sucrose_files/image046.png" v:shapes="Picture_x0020_47"><![endif]></span></b></p>
2266
2267<p class=MsoNormal>Before refining H-atom positions it would be wise to create
2268restraints on their bond distances and angles. Locate <b style='mso-bidi-font-weight:
2269normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2270minor-latin;mso-hansi-theme-font:minor-latin'>Restraints</span></b> in the main
2271GSAS-II data tree; there will be an almost blank window telling you there are
2272no bond restraints for sucrose. Do <b style='mso-bidi-font-weight:normal'><span
2273style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2274mso-hansi-theme-font:minor-latin'>Edit/Add <span class=GramE>restraints<span
2275style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
2276a dialog box will appear asking for the origin atom for the bond. </p>
2277
2278<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2279 id="Picture_x0020_48" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:259.5pt;
2280 height:252pt;visibility:visible;mso-wrap-style:square'>
2281 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image047.png" o:title=""/>
2282</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
2283src="Charge%20Flipping%20-%20sucrose_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
2284
2285<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2286style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2287mso-hansi-theme-font:minor-latin'>all H</span></b> and press <b
2288style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2289mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2290A new dialog box will appear asking for the target atoms for the bonds.</p>
2291
2292<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2293 id="Picture_x0020_49" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:259.5pt;
2294 height:252pt;visibility:visible;mso-wrap-style:square'>
2295 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image048.png" o:title=""/>
2296</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
2297src="Charge%20Flipping%20-%20sucrose_files/image048.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
2298
2299<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2300style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2301mso-hansi-theme-font:minor-latin'>all C</span></b> and <b style='mso-bidi-font-weight:
2302normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2303minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b> and a third
2304dialog box appears asking for the bond length</p>
2305
2306<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2307 id="Picture_x0020_50" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:147pt;
2308 height:78.75pt;visibility:visible;mso-wrap-style:square'>
2309 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image049.png" o:title=""/>
2310</v:shape><![endif]--><![if !vml]><img border=0 width=196 height=105
2311src="Charge%20Flipping%20-%20sucrose_files/image049.png" v:shapes="Picture_x0020_50"><![endif]></span><span
2312style='mso-spacerun:yes'> </span></p>
2313
2314<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
2315style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2316mso-hansi-theme-font:minor-latin'>1.09</span></b> and press <b
2317style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2318mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2319I got a short list of 8 H-C and H-O restraints, but I expect 22 of them. Change
2320the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2321mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Search range</span></b>
2322to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2323mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.5</span></b>
2324and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
2325"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2326minor-latin'>Edit/Add restraints</span></b>. There are now 22 restraints on H-C
2327and H-O bond lengths.</p>
2328
2329<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2330 id="Picture_x0020_51" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:450pt;
2331 height:423pt;visibility:visible;mso-wrap-style:square'>
2332 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image050.png" o:title=""/>
2333</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=564
2334src="Charge%20Flipping%20-%20sucrose_files/image050.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
2335
2336<p class=MsoNormal>Next select the <b style='mso-bidi-font-weight:normal'><span
2337style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2338mso-hansi-theme-font:minor-latin'>Angle restraints</span></b> tab and again
2339there aren’t any. Do <b style='mso-bidi-font-weight:normal'><span
2340style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2341mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
2342will appear asking for the A atom in the angle A-B-C. Select <b
2343style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2344mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all H</span></b>.
2345The next dialog asks for the B atom in the A-B-C angle, select <b
2346style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2347mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all C</span></b>
2348and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2349mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b>.
2350The third dialog asks for the angle and has a default of <b style='mso-bidi-font-weight:
2351normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2352minor-latin;mso-hansi-theme-font:minor-latin'>109.54</span></b>. This is the
2353tetrahedral angle so just press <b style='mso-bidi-font-weight:normal'><span
2354style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2355mso-hansi-theme-font:minor-latin'>OK</span></b>. 36 restraints will be listed;
2356they are listed in order of the B atom. O-atoms should have one angle apiece;
2357C-atoms will have more. </p>
2358
2359<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2360 id="Picture_x0020_52" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:450pt;
2361 height:365.25pt;visibility:visible;mso-wrap-style:square'>
2362 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image051.png" o:title=""/>
2363</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=487
2364src="Charge%20Flipping%20-%20sucrose_files/image051.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
2365
2366<p class=MsoNormal>Now go back the <b style='mso-bidi-font-weight:normal'><span
2367style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2368mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab in <b style='mso-bidi-font-weight:
2369normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2370minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>, select
2371<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2372mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>
2373from the dialog box by double clicking on the <b style='mso-bidi-font-weight:
2374normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2375minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column. Then do <b
2376style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2377mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Set
2378atom refinement flags</span></b>. Select <b style='mso-bidi-font-weight:normal'><span
2379style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2380mso-hansi-theme-font:minor-latin'>X-coordinates</span></b>; this will set those
2381for all H-atoms. Now do <b style='mso-bidi-font-weight:normal'><span
2382style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2383mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>, the console will
2384list progress on the “Penalty function” (i.e. the restraints) and the <span
2385class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase the <b
2386style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2387mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Restraint
2388weight factors</span></b> to tighten them up at some expense in <span
2389class=SpellE>Rwp</span>. In the end I chose <b style='mso-bidi-font-weight:
2390normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2391minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b> for both <b
2392style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2393mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond</span></b>
2394and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2395mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b>
2396restraints to give a final <span class=SpellE>Rwp</span> ~7.1%.</p>
2397
2398<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2399
2400<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2401
2402</div>
2403
2404</body>
2405
2406</html>
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