source: trunk/help/Charge Flipping - sucrose.htm @ 870

Last change on this file since 870 was 870, checked in by vondreele, 9 years ago

fix plot

File size: 136.1 KB
Line 
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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><span class=GramE>Step 1.</span> 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>. It is an area relatively
972clear of peaks and makes a good place to end the calculations with a reflection
973set of ~1Å resolution as needed for charge flipping. Enter <b style='mso-bidi-font-weight:
974normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
975minor-latin;mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span
976class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
977"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
978minor-latin'>Tmax</span></b></span> as the upper limit and make a note of the
979exact d-spacing (1.0125Å) using the mouse cursor on the plot.</p>
980
981<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
982style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
983style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
984<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
985mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
986Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
987style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
988mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
989style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
990mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
991profile</span></b> to recover the default values. The peak fitting done earlier
992is over a much more limited range of 2<span style='font-family:Symbol;
993mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
994mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
995symbol;mso-symbol-font-family:Symbol'>Q</span></span> giving values that might
996not extrapolate well over the wider range to be used in the Pawley refinement.
997We will refine them again later.</p>
998
999<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1000style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1001style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1002<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1003mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1004Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1005normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1006minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.
1007While you are here set <b style='mso-bidi-font-weight:normal'><span
1008style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1009mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> to <b
1010style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1011mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>.</p>
1012
1013<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1014style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1015style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1016to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1017mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1018to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1019"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1020minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1021normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1022minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
1023box and enter the d-spacing (1.0125) into the <b style='mso-bidi-font-weight:
1024normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1025minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
1026box.</p>
1027
1028<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1029style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1030mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1031
1032<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1033 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1034 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1035 <v:stroke joinstyle="miter"/>
1036 <v:formulas>
1037  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1038  <v:f eqn="sum @0 1 0"/>
1039  <v:f eqn="sum 0 0 @1"/>
1040  <v:f eqn="prod @2 1 2"/>
1041  <v:f eqn="prod @3 21600 pixelWidth"/>
1042  <v:f eqn="prod @3 21600 pixelHeight"/>
1043  <v:f eqn="sum @0 0 1"/>
1044  <v:f eqn="prod @6 1 2"/>
1045  <v:f eqn="prod @7 21600 pixelWidth"/>
1046  <v:f eqn="sum @8 21600 0"/>
1047  <v:f eqn="prod @7 21600 pixelHeight"/>
1048  <v:f eqn="sum @10 21600 0"/>
1049 </v:formulas>
1050 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1051 <o:lock v:ext="edit" aspectratio="t"/>
1052</v:shapetype><v:shape id="Picture_x0020_25" o:spid="_x0000_i1064" type="#_x0000_t75"
1053 style='width:545.25pt;height:303.75pt;visibility:visible;mso-wrap-style:square'>
1054 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image001.png" o:title=""/>
1055</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
1056src="Charge%20Flipping%20-%20sucrose_files/image001.png" v:shapes="Picture_x0020_25"><![endif]></span></p>
1057
1058<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1059style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1060mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1061for a single line of text. Do <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'>Edit/Add powder histograms</span></b>; a
1064dialog box will appear</p>
1065
1066<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1067 id="Picture_x0020_2" o:spid="_x0000_i1063" type="#_x0000_t75" style='width:259.5pt;
1068 height:252pt;visibility:visible;mso-wrap-style:square'>
1069 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image002.png" o:title=""/>
1070</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1071src="Charge%20Flipping%20-%20sucrose_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1072
1073<p class=MsoNormal>Select either choice; the desired data set will be added to
1074this phase for analysis. The data tab now shows the new data set; check the <b
1075style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1076mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
1077button to see the full information</p>
1078
1079<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1080 id="Picture_x0020_3" o:spid="_x0000_i1062" type="#_x0000_t75" style='width:480pt;
1081 height:393pt;visibility:visible;mso-wrap-style:square'>
1082 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image003.png" o:title=""/>
1083</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=524
1084src="Charge%20Flipping%20-%20sucrose_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
1085
1086<p class=MsoNormal>I’ve stretched the window slightly to see the entire
1087contents. This is the location for all the phase dependent parameters for this
1088histogram. Notice that it includes phase fraction, size &amp; <span
1089class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1090and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1091intended for protein work where a significant region of the structure is
1092disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1093surfaces</p>
1094
1095<p class=MsoNormal><span class=GramE>and</span> preferred orientation
1096correction curves.</p>
1097
1098<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1099style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1100mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1101empty except for column headings. <span class=GramE>Do</span> <b
1102style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1103mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley
1104create</span></b>; this makes the reflection set over the range covered by
1105setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1106mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1107class=SpellE>dmin</span></span></b>. The table should list reflections 0-781.
1108Select and check the refine column using the same technique you used for the
1109peak list. </p>
1110
1111<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1112 id="Picture_x0020_4" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:375pt;
1113 height:225pt;visibility:visible;mso-wrap-style:square'>
1114 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image004.png" o:title=""/>
1115</v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300
1116src="Charge%20Flipping%20-%20sucrose_files/image004.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
1117
1118<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1119you didn’t skip a step as it might not work correctly if you did.</p>
1120
1121<h2>Step 2 Pawley refinement</h2>
1122
1123<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1124normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1125minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1126the main GSAS-II data tree window. Before it begins a backup of the project
1127file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
1128style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1129mso-hansi-theme-font:minor-latin'>sucrose.bck0.gpx</span></b>. It can be used
1130to recover from a bad refinement. A progress dialog box will appear showing the
1131residual as the refinement proceeds. Notice that there was a singular matrix
1132warning on the console window and the last reflection (781) was removed from
1133the refinement because it was off the end of the used part of the pattern. This
1134is the GSAS-II singular matrix recovery mechanism; you can go to the <b
1135style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1136mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1137reflections</span></b> tab and uncheck the last reflection. Then repeat <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'>Calculate/Refine</span></b>
1140to make sure it has essentially minimized. My refinement completed with <span
1141class=SpellE>Rwp</span> ~26.3%; a dialog box appears asking if you wish to load
1142the result. Press <b style='mso-bidi-font-weight:normal'><span
1143style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1144mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
1145PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
1146
1147<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1148 id="Picture_x0020_5" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:503.25pt;
1149 height:431.25pt;visibility:visible;mso-wrap-style:square'>
1150 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image005.png" o:title=""/>
1151</v:shape><![endif]--><![if !vml]><img border=0 width=671 height=575
1152src="Charge%20Flipping%20-%20sucrose_files/image005.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
1153
1154<p class=MsoNormal>It is evident from examining the plot that some improvement
1155can be had by refining the lattice and profile parameters and perhaps the
1156sample X position. Go to <b style='mso-bidi-font-weight:normal'><span
1157style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1158mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> in the GSAS-II data
1159tree and check the <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'>Refine unit cell</span></b> box. Now select <b
1162style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1163mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1164parameters</span></b> for the PWDR data set in the GSAS-II data tree and check <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'>U</span></b>,
1167<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1168mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>,
1169<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1170mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,<b
1171style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1172mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
1173class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
1174style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1175mso-hansi-theme-font:minor-latin'> Y</span></b>. The go to <b style='mso-bidi-font-weight:
1176normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1177minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and
1178check <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1179mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1180class=SpellE>displ</span></span></b>.; make the <b style='mso-bidi-font-weight:
1181normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1182minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> <b
1183style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1184mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1185if you didn’t do this earlier. Repeat <b style='mso-bidi-font-weight:normal'><span
1186style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1187mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged;
1188I obtained an improved residual of ~9.05% with a much better fit at the high
1189angle part of the pattern but still not fit well for the lower part.</p>
1190
1191<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1192 id="Picture_x0020_26" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:504.75pt;
1193 height:432.75pt;visibility:visible;mso-wrap-style:square'>
1194 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image006.png" o:title=""/>
1195</v:shape><![endif]--><![if !vml]><img border=0 width=673 height=577
1196src="Charge%20Flipping%20-%20sucrose_files/image006.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
1197
1198<p class=MsoNormal>What you see is that the background has a substantial
1199diffuse scattering feature at ~5deg as well as some peak shape issues (which
1200may be a consequence of the poor background fit). Also notice the negative <b
1201style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1202mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
1203value in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1204mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1205parameters</span></b>; the problem is that the default <span class=SpellE>mustrain</span>
1206value (1000.0) is much too high for this material and we’d like the fit to be
1207better before trying charge flipping. First select <span class=GramE><b
1208style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1209mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>,</span>
1210set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1211mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peaks in
1212background: No. peaks</span></b> to <b style='mso-bidi-font-weight:normal'><span
1213style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1214mso-hansi-theme-font:minor-latin'>1</span></b> from the pull down box; the
1215window changes to </p>
1216
1217<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1218 id="Picture_x0020_27" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:366pt;
1219 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1220 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image007.png" o:title=""/>
1221</v:shape><![endif]--><![if !vml]><img border=0 width=488 height=263
1222src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span><span
1223style='mso-spacerun:yes'> </span></p>
1224
1225<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
1226style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1227mso-hansi-theme-font:minor-latin'>5.0</span></b> for <span class=SpellE><b
1228style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1229mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span>,
1230<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1231mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
1232for <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1233style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1234mso-hansi-theme-font:minor-latin'>int</span></b></span> and <b
1235style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1236mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1237for <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'>sig</span></b>
1239(as appropriate for broad diffuse peaks) and then check all three refine boxes.
1240Also set <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'>No. <span
1242class=SpellE>coeff</span>.</span></b> <span class=SpellE><span class=GramE>pulldown</span></span>
1243to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1244mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>
1245for the <span class=SpellE>chebyschev</span> part of the background. The window
1246should look like</p>
1247
1248<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1249 id="Picture_x0020_28" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:402pt;
1250 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1251 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image008.png" o:title=""/>
1252</v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
1253src="Charge%20Flipping%20-%20sucrose_files/image008.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1254
1255<p class=MsoNormal>Go to the <b style='mso-bidi-font-weight:normal'><span
1256style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1257mso-hansi-theme-font:minor-latin'>Controls</span></b> item in the GSAS-II data
1258tree and set the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1259"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1260minor-latin'>Max cycles</span></b> to <b style='mso-bidi-font-weight:normal'><span
1261style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1262mso-hansi-theme-font:minor-latin'>5</span></b>. Now do <b style='mso-bidi-font-weight:
1263normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1264minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until
1265the refinement converges. After a set of refinement cycles go to the Pawley reflections
1266tab and check the intensities. If there are many negatives amongst the highest
1267angle reflections do <b style='mso-bidi-font-weight:normal'><span
1268style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1269mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this replaces all
1270the values with those in the extracted from the profile and listed in the <b
1271style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1272mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1273list</span></b> for the PWDR data set. Next in the <b style='mso-bidi-font-weight:
1274normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1275minor-latin;mso-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 Pawley reflection set.</p>
1320
1321<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1322mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1323"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1324</span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span
1325style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1326mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b
1327style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1328mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map
1329controls</span></b>) to <b style='mso-bidi-font-weight:normal'><span
1330style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1331mso-hansi-theme-font:minor-latin'>20%</span></b>. This controls the map search
1332routine.</p>
1333
1334<p class=MsoNormal>For powder data it is not usually advisable to select a <b
1335style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1336mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing
1337element</span></b>; if selected a periodic table appears – select an element or
1338‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1339mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None’</span></b>.
1340The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1341mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1342defines the map spacing and thus the extent of the reflection set; the observed
1343reflection set is zero filled to this limit for charge flipping. The <b
1344style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1345mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b>
1346and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1347mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b>
1348determine the lower threshold and upper limit for charge flipping,
1349respectively. The latter is used to avoid “Uranium solutions” in the result.
1350Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1351"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1352minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
1353ones. <span class=GramE>For sucrose, set this to <b style='mso-bidi-font-weight:
1354normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1355minor-latin;mso-hansi-theme-font:minor-latin'>12.</span></b></span> When ready
1356select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1357mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1358flipping</span></b>; a progress bar dialog will appear that tracks the residual
1359found in each charge flipping cycle. It will quickly drop to some level
1360(42-44%) and then perhaps drop again into the 20-25% range after a considerable
1361length of time for a successful charge flipping run. You should save the
1362project if you get an apparently good solution. Many times it will not drop
1363below ~40%; just try <b style='mso-bidi-font-weight:normal'><span
1364style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1365mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b> again. If
1366several tries fail to yield a solution, go back to the last step of the Pawley
1367refinement and just repeat it (that is do <b style='mso-bidi-font-weight:normal'><span
1368style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1369mso-hansi-theme-font:minor-latin'>Pawley update</span></b> and <b
1370style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1371mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>).
1372This will generate a different set of intensities for the highly overlapped
1373part of the powder pattern; perhaps they will give a successful charge flip
1374solution. Unless otherwise interrupted, GSAS-II will try 10000 times for a
1375charge flip solution (for sucrose this takes 5-10min on my laptop). Press <b
1376style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1377mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b>
1378to stop the charge flipping; a peak list and a drawing of the solution will
1379appear. One of my runs gave</p>
1380
1381<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1382 id="Picture_x0020_30" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:337.5pt;
1383 height:225pt;visibility:visible;mso-wrap-style:square'>
1384 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image010.png" o:title=""/>
1385</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
1386src="Charge%20Flipping%20-%20sucrose_files/image010.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1387
1388<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1389
1390<p class=MsoNormal><!--[if gte vml 1]><v:group id="Group_x0020_39" o:spid="_x0000_s1026"
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1488 </v:shape></v:group><![endif]--><![if !vml]><span style='mso-ignore:vglayout;
1489position:absolute;z-index:251662336;margin-left:315px;margin-top:308px;
1490width:16px;height:35px'><img width=16 height=35
1491src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
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1494 visibility:visible;mso-wrap-style:square'>
1495 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image012.png" o:title=""
1496  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
1497</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=575
1498src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
1499
1500<p class=MsoNormal>The result looks very promising! Charge flipping operates
1501without regard to symmetry and GSAS-II attempts to locate the map with respect
1502to the symmetry elements from the computed reflection phases. NB: charge
1503flipping also will give a solution without regard to handedness. This solution
1504may be either the correct one for sucrose or its reverse. Errors in these
1505phases can disrupt this process so that the map and peak positions are offset
1506from their true positions. To discover this and fix it, rotate the drawing
1507around to check that atom positions are related via the 2<sub>1</sub> screw
1508axis (through the multicolored cross in the center of the cell and parallel to
1509the y-axis – the green cell edge). Avoid motions with the right mouse button
1510pressed, this moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:
1511normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1512minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the
1513cross to the cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my
1514drawing above to show where I think it should be. If you find an offset to the
1515map, orient it so the offset is horizontal or vertical and then press the <b
1516style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1517mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>,
1518<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1519mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>,
1520<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1521mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
1522or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1523mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
1524keys to shift the map and peaks as needed. The shift is in resolution units
1525(0.5Å) so the fix can only be approximate. Repeat as needed. Notice that the
1526peak positions in the table are updated as the offset is changed. In this case,
1527I needed just a few steps to correct the map offset. NB: you can use these keys
1528to move the result anywhere you wish, e.g. to select a different origin for the
1529structure but pay attention to the location of symmetry elements. After
1530adjustment, my solution looked like</p>
1531
1532<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1533 id="Picture_x0020_12" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:500.25pt;
1534 height:424.5pt;visibility:visible;mso-wrap-style:square'>
1535 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image014.png" o:title=""
1536  croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/>
1537</v:shape><![endif]--><![if !vml]><img border=0 width=667 height=566
1538src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
1539
1540<h2>Step 4 Obtain solution from charge flip result</h2>
1541
1542<p class=MsoNormal>The next step is to extract the unique peak positions from
1543the map and make atoms out of them. The map peak list is sorted with the
1544highest peak first; you can change the sorting to be along any of the column
1545headings in the table by a single click on the desired heading. The <span
1546class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1547"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1548minor-latin'>dzero</span></b></span> column gives the distance of each peak from
1549the origin. The menu items under Map peaks give you several tools to aid in the
1550peak selection process; we will just use a couple in this example. I have
1551chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:normal'><span
1552style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1553mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and then finding
1554the unique ones. </p>
1555
1556<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1557mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1558"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1559</span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight:
1560normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1561minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> column heading. This
1562will sort the peaks in increasing z-axis coordinate.</p>
1563
1564<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1565mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1566"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1567</span></span></span><![endif]>Do a single click on the upper left (empty) box
1568of the table. All entries will be colored grey indicating their selection.</p>
1569
1570<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1571mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1572"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1573</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1574style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1575mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That should
1576select (grey) 23 out of 46 peak positions in the table and all should be near
1577the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
1578that would be all the C &amp; O atoms! They will be colored green in the plot.
1579If more are selected then check the map offset – it may need a slight
1580correction.</p>
1581
1582<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1583 id="Picture_x0020_13" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:337.5pt;
1584 height:411.75pt;visibility:visible;mso-wrap-style:square'>
1585 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image016.png" o:title=""/>
1586</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=549
1587src="Charge%20Flipping%20-%20sucrose_files/image016.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1588
1589<p class=MsoNormal>The drawing shows the selected atoms in green.</p>
1590
1591<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1592 id="Picture_x0020_14" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:7in;
1593 height:429pt;visibility:visible;mso-wrap-style:square'>
1594 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image017.png" o:title=""
1595  croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/>
1596</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=572
1597src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
1598
1599<p class=MsoNormal>Notice that in my case one atom is in a neighboring
1600molecule, one can deselect it and then pick the desired equivalent. Hold the <b
1601style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1602mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1603key down and use the right mouse button to pick/unpick atoms in the drawing.
1604NB: the left mouse button will clear all the selections. The other two “lone”
1605atoms belong to molecules in neighboring unit cells; we’ll deal with them
1606later.</p>
1607
1608<p class=MsoNormal>These are now ready to turn into atoms. Do <b
1609style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1610mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1611peaks/Move peaks</span></b>. The drawing will show white balls for each of the
1612selected positions and the <b style='mso-bidi-font-weight:normal'><span
1613style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1614mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 23 new H
1615atoms. </p>
1616
1617<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1618 id="Picture_x0020_15" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:7in;
1619 height:433.5pt;visibility:visible;mso-wrap-style:square'>
1620 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image019.png" o:title=""
1621  croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/>
1622</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=578
1623src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
1624
1625<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1626 id="Picture_x0020_44" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
1627 height:414.75pt;visibility:visible;mso-wrap-style:square'>
1628 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image021.png" o:title=""/>
1629</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=553
1630src="Charge%20Flipping%20-%20sucrose_files/image021.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
1631
1632<p class=MsoNormal>The atom names indicate the peak magnitude to aid
1633identification (M100 for the largest in the <b style='mso-bidi-font-weight:
1634normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1635minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
1636may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
1637style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1638mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
1639them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
1640style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1641mso-hansi-theme-font:minor-latin'>Alt</span></b> key down and then selecting a
1642position in the table with the <b style='mso-bidi-font-weight:normal'><span
1643style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1644mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. After sorting
1645by magnitude, my list is now </p>
1646
1647<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1648 id="Picture_x0020_17" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:525pt;
1649 height:417pt;visibility:visible;mso-wrap-style:square'>
1650 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image022.png" o:title=""/>
1651</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=556
1652src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1653
1654<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out into
1655two groups with a clear gap between M79 and M64. The higher ones are likely to
1656be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of
1657ambiguity in the middle, but just assign the top 11 as O and the rest as C and
1658see what happens. You can do this by selecting a block of atoms, go to <b
1659style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1660mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1661atom parameters</span></b> and select <b style='mso-bidi-font-weight:normal'><span
1662style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1663mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a
1664periodic table will appear. Select the desired element and they will be changed
1665in the list and drawing.</p>
1666
1667<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1668 id="Picture_x0020_18" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:7in;
1669 height:405.75pt;visibility:visible;mso-wrap-style:square'>
1670 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image023.png" o:title=""
1671  croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/>
1672</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=541
1673src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
1674
1675<p class=MsoNormal>The original charge flipping solution is still visible and
1676the atoms are now identified, I’ve changed the drawing to show balls and sticks
1677and labeled the atoms with their names, this is done in the <b
1678style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1679mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b>
1680tab. Pick the appropriate column and make the selection from the dialog
1681box.<span style='mso-spacerun:yes'>  </span></p>
1682
1683<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1684 id="Picture_x0020_19" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:450pt;
1685 height:415.5pt;visibility:visible;mso-wrap-style:square'>
1686 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image025.png" o:title=""/>
1687</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=554
1688src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
1689
1690<p class=MsoNormal>Interestingly the atoms identified exactly matched with the
1691magnitudes of the charge flip map peaks with O at the top and C at the bottom.</p>
1692
1693<p class=MsoNormal>Now one can safely remove the map peaks (do <b
1694style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1695mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1696peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span
1697style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1698mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
1699charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1700style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1701mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
1702normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1703minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
1704style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1705mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1706tab). The atom positions I obtained have two atoms (O3 &amp; O4) not connected
1707to the sucrose molecule because they belong to neighboring molecules. We need to
1708discover the equivalent ones that belong to this molecule. Follow the steps:</p>
1709
1710<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1711mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1712"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1713</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1714style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1715mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> tab and select them
1716(hold the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1717mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ctrl</span></b>
1718key down and select the appropriate rows). </p>
1719
1720<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1721mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1722"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1723</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1724style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1725mso-hansi-theme-font:minor-latin'>Edit/Fill unit cell</span></b>; new atoms
1726will appear at end of list and in the drawing. </p>
1727
1728<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1729mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1730"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1731</span></span></span><![endif]>Select all the atoms in the <b style='mso-bidi-font-weight:
1732normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1733minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table by a
1734double click on upper left corner box of the table.</p>
1735
1736<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1737mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1738"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1739</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1740style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1741mso-hansi-theme-font:minor-latin'>Edit/Fill CN-sphere</span></b>; new atoms
1742will appear that are bonded to the molecule.</p>
1743
1744<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1745mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1746"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1747</span></span></span><![endif]>Select these new atoms that are in the molecule;
1748they will probably be outside the unit cell box. Do this on the drawing with <b
1749style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1750mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1751left &amp; right mouse buttons, they will show in green. </p>
1752
1753<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1754mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1755"Times New Roman"'><span style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1756</span></span></span><![endif]>Look at the <b style='mso-bidi-font-weight:normal'><span
1757style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1758mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the
1759selections and make note of the <span class=SpellE><b style='mso-bidi-font-weight:
1760normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1761minor-latin;mso-hansi-theme-font:minor-latin'>Sym</span></b></span><b
1762style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1763mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Op</span></b>
1764for each one. In my case they were “<b style='mso-bidi-font-weight:normal'><span
1765style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1766mso-hansi-theme-font:minor-latin'>2+1<span class=GramE>,0,0</span></span></b>”
1767for O(4) and “<b style='mso-bidi-font-weight:normal'><span style='font-family:
1768"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1769minor-latin'>2+2,-1,1</span></b>” for O(3). The first number is the symmetry
1770operator number and the 3 numbers after the ‘<b style='mso-bidi-font-weight:
1771normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1772minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’ are unit cell
1773translations.</p>
1774
1775<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1776mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1777"Times New Roman"'><span style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1778</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1779style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1780mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab.</p>
1781
1782<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1783mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1784"Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1785</span></span></span><![endif]>Select an atom in turn that needs to be moved,
1786e.g. in my case <span class=GramE>O(</span>3) or O(4). </p>
1787
1788<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1789mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1790"Times New Roman"'><span style='mso-list:Ignore'>9.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1791</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1792style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1793mso-hansi-theme-font:minor-latin'>Edit/Transform <span class=GramE>atoms<span
1794style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
1795select the operator and unit cell translations, then press <b style='mso-bidi-font-weight:
1796normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1797minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom
1798coordinates will be transformed.</p>
1799
1800<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1801mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1802"Times New Roman"'><span style='mso-list:Ignore'>10.<span style='font:7.0pt "Times New Roman"'>&nbsp;
1803</span></span></span><![endif]>Repeat 8 &amp; 9 for any other atoms to be
1804moved.</p>
1805
1806<p class=MsoNormal style='margin-left:.5in'>This will complete the molecule
1807with the extra atoms. <span class=GramE>Do</span> <b style='mso-bidi-font-weight:
1808normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1809minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>
1810to see the completed molecule. I’ve made it a balls &amp; sticks with names as
1811labels.</p>
1812
1813<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1814 id="Picture_x0020_20" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:7in;
1815 height:6in;visibility:visible;mso-wrap-style:square'>
1816 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image026.png" o:title=""
1817  cropbottom="28348f" cropleft="41090f" cropright="9483f"/>
1818</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=576
1819src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
1820
1821<p class=MsoNormal>Save the project file; the next step is to <span
1822class=GramE>do<span style='mso-spacerun:yes'>  </span>the</span> Rietveld
1823refinement on the completed structure.</p>
1824
1825<h2>Step 5 Complete the structure</h2>
1826
1827<p class=MsoNormal>To complete the structure you will need to perform a
1828preliminary Rietveld refinement. This will make the atom positions more
1829accurate and prepare a set of calculated structure factors needed to generate a
1830difference Fourier map good enough to maybe reveal the H atoms. There are a
1831number of steps needed to set all the controls from the previous Pawley
1832refinement to get a successful start for the Rietveld refinement.</p>
1833
1834<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1835mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1836"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1837</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1838style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1839mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the
1840GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span
1841style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1842mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You don’t want to
1843start with these when the scale factor is unknown.</p>
1844
1845<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1846mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1847"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1848</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
1849style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1850mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b
1851style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1852mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
1853scale factor</span></b> box. This is the scale factor for the data set. Uncheck
1854the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1855mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1856class=SpellE>displ</span></span></b>.</p>
1857
1858<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1859mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1860"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1861</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
1862style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1863mso-hansi-theme-font:minor-latin'>Phases/sucrose General</span></b> tab and
1864uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1865mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
1866cell</span></b> and <b style='mso-bidi-font-weight:normal'><span
1867style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1868mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The
1869latter is most important; if you forget you will just get another Pawley
1870refinement!</p>
1871
1872<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1873style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1874mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
1875GSAS-II data tree menu; all that was refined is scale and background. I got <span
1876class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear
1877intensity differences; the atom positions obviously need refinement.</p>
1878
1879<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1880 id="Picture_x0020_21" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:502.5pt;
1881 height:430.5pt;visibility:visible;mso-wrap-style:square'>
1882 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/>
1883</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=574
1884src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
1885
1886<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
1887obvious.</p>
1888
1889<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
1890style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1891mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and select the <b
1892style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1893mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1894tab. Note the warning at the bottom of the window; the origin in space group P
18952<sub>1</sub> has an arbitrary location along the y-axis. Then double click the
1896<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1897mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1898column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight:
1899normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1900minor-latin;mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and
1901press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1902mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1903The atoms table will show the refinement controls</p>
1904
1905<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1906 id="Picture_x0020_22" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
1907 height:225pt;visibility:visible;mso-wrap-style:square'>
1908 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/>
1909</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
1910src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
1911
1912<p class=MsoNormal>To deal with the warning we need to set a “Hold” on one atom
1913y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span
1914style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1915mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II
1916data tree.</p>
1917
1918<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1919 id="Picture_x0020_23" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:225pt;
1920 height:187.5pt;visibility:visible;mso-wrap-style:square'>
1921 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image030.png" o:title=""/>
1922</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
1923src="Charge%20Flipping%20-%20sucrose_files/image030.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
1924
1925<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
1926style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1927mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
1928style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1929mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
1930class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will
1931fix the shift along y for the <span class=GramE>O(</span>1) atom.</p>
1932
1933<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1934 id="Picture_x0020_53" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:259.5pt;
1935 height:271.5pt;visibility:visible;mso-wrap-style:square'>
1936 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/>
1937</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=362
1938src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
1939
1940<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
1941style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1942mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will
1943show the hold</p>
1944
1945<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1946 id="Picture_x0020_54" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:225pt;
1947 height:187.5pt;visibility:visible;mso-wrap-style:square'>
1948 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image032.png" o:title=""/>
1949</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
1950src="Charge%20Flipping%20-%20sucrose_files/image032.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
1951
1952<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
1953style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1954mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
1955class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice
1956parameters (in the <b style='mso-bidi-font-weight:normal'><span
1957style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1958mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
1959style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1960mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>),
1961the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1962mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1963parameters</span></b> <b style='mso-bidi-font-weight:normal'><span
1964style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1965mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
1966normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1967minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b
1968style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1969mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
1970<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1971mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
1972&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1973mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
1974and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1975mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1976class=SpellE>displ</span></span></b>. You can also include refinement of atom
1977thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
1978refinement improved slightly to Rwp~10.0%. Let’s see if a difference Fourier
1979map will show anything.<br>
1980Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1981mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose
1982General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
1983style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1984mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway
1985down the window.</p>
1986
1987<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1988mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
1989"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1990</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
1991normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1992minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
1993style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1994mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
1995for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1996mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
1997
1998<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1999mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2000"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2001</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
2002style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2003mso-hansi-theme-font:minor-latin'>PWDR 11bmb_8716.fxye Bank 1</span></b> for
2004the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2005mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
2006set from</span></b> item (the only choice). The Fourier calculation will use the
2007structure factors shown in the <b style='mso-bidi-font-weight:normal'><span
2008style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2009mso-hansi-theme-font:minor-latin'>Reflection list</span></b> item for this PWDR
2010data set.</p>
2011
2012<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2013mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2014"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2015</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2016style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2017mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b
2018style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2019mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2020tab window. The map will be computed via fast Fourier techniques and is very
2021fast. A few lines summarizing the map is printed on the console, the structure
2022plot may show a single green dot somewhere (it could be hidden beneath an
2023atom!), this is the highest point in the map.</p>
2024
2025<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2026mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2027"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2028</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2029style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2030mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b
2031style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2032mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
2033level</span></b> slider until something appears on the map. You can also reduce
2034the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2035mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
2036to help clarify the view.</p>
2037
2038<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2039 id="Picture_x0020_35" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:502.5pt;
2040 height:435.75pt;visibility:visible;mso-wrap-style:square'>
2041 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title=""
2042  croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/>
2043</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=581
2044src="Charge%20Flipping%20-%20sucrose_files/image034.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
2045
2046<p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots
2047whose size are proportional to the electron density. There are peaks that might
2048be H-atom positions as well as features that suggest C &amp; O-atoms out of
2049position. Recall that the refinement was just done without any H-atoms; it will
2050make the best fit compensating for the missing H-atoms by displacing the C
2051&amp;O atoms in the direction of the missing H-atoms. </p>
2052
2053<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2054mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2055"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2056</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2057style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2058mso-hansi-theme-font:minor-latin'>Phases/<span class=GramE>sucrose<span
2059style='mso-spacerun:yes'>  </span>Draw</span> Atoms</span></b> tab.</p>
2060
2061<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2062mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2063"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2064</span></span></span><![endif]>Select a C or O atoms with possible H-atom
2065density nearby. It will appear green. Do <b style='mso-bidi-font-weight:normal'><span
2066style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2067mso-hansi-theme-font:minor-latin'>Edit/View point</span></b>; this will
2068position the cross on the selected atom.</p>
2069
2070<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2071mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2072"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2073</span></span></span><![endif]>Using the mouse, position the multicolored cross
2074directly in the center of the nearby H atom peak. Rotate the drawing around
2075with the left mouse button and shift the cross with the right mouse button. You
2076can zoom in using the roll wheel on the mouse (or else use the <b
2077style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2078mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Camera
2079distance</span></b> slider in the <b style='mso-bidi-font-weight:normal'><span
2080style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2081mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab if your mouse
2082lacks a wheel).</p>
2083
2084<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2085 id="Picture_x0020_36" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:7in;
2086 height:435.75pt;visibility:visible;mso-wrap-style:square'>
2087 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""
2088  croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/>
2089</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=581
2090src="Charge%20Flipping%20-%20sucrose_files/image036.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
2091
2092<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2093mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2094"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2095</span></span></span><![endif]>Go to the Atoms tab and do <b style='mso-bidi-font-weight:
2096normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2097minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>,
2098a white ball will appear at the selected position and an H-atom (name = <b
2099style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2100mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>)
2101will be appended to the end of the atom list. Repeat steps 1-4 for as many
2102recognizable H-atom positions you can find; the goal is to find all 22 of them
2103(you probably will find less than that, but you could guess many of the rest).
2104I found all but 5 of them.</p>
2105
2106<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2107 id="Picture_x0020_38" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:7in;
2108 height:427.5pt;visibility:visible;mso-wrap-style:square'>
2109 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image037.png" o:title=""
2110  croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/>
2111</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=570
2112src="Charge%20Flipping%20-%20sucrose_files/image038.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
2113
2114<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2115mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2116"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2117</span></span></span><![endif]>Change their <b style='mso-bidi-font-weight:
2118normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2119minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> to <b
2120style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2121mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>,
2122they will be renamed and make then all ball &amp; stick. Do a <b
2123style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2124mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
2125there should be a drop in <span class=SpellE>Rwp</span>. Then repeat the <b
2126style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2127mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier
2128map</span></b> in the <b style='mso-bidi-font-weight:normal'><span
2129style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2130mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust the <b
2131style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2132mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour level</span></b>
2133and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2134mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
2135as desired. Look for the remaining H-atoms; you may have to guess positions for
2136some of them using known stereochemistry rules. My model looked like</p>
2137
2138<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2139 id="Picture_x0020_39" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:502.5pt;
2140 height:421.5pt;visibility:visible;mso-wrap-style:square'>
2141 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image039.png" o:title=""
2142  croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/>
2143</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=562
2144src="Charge%20Flipping%20-%20sucrose_files/image040.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
2145
2146<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2147style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2148mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> to finish this
2149stage in the structure analysis. My <span class=SpellE>Rwp</span> was ~8.02%
2150with all the H-atoms included (but not refined). The fit looks pretty good</p>
2151
2152<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2153 id="Picture_x0020_40" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
2154 height:450pt;visibility:visible;mso-wrap-style:square'>
2155 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image041.png" o:title=""/>
2156</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2157src="Charge%20Flipping%20-%20sucrose_files/image041.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
2158
2159<h2>Step 6: Final refinement</h2>
2160
2161<p class=MsoNormal>Looking at the fit, there may be room for improvement and
2162we’d like to refine the H-atom positions. First we need to change the profile
2163model to include crystallite size and <span class=SpellE>mustrain</span>
2164broadening. Go to <b style='mso-bidi-font-weight:normal'><span
2165style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2166mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>, set <b
2167style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2168mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2169and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2170mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2171to <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'>zero</span></b>
2173and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2174"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2175minor-latin'>Refine</span></b> flags for them.</p>
2176
2177<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
2178style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2179mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and look at the <b
2180style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2181mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
2182tab; make sure the <b style='mso-bidi-font-weight:normal'><span
2183style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2184mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the
2185boxes for both <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2186style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2187mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b style='mso-bidi-font-weight:
2188normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2189minor-latin;mso-hansi-theme-font:minor-latin'>. <span class=GramE>size</span></span></b>
2190and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2191style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2192mso-hansi-theme-font:minor-latin'>microstrain</span></b></span>.</p>
2193
2194<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2195 id="Picture_x0020_41" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:480pt;
2196 height:339pt;visibility:visible;mso-wrap-style:square'>
2197 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/>
2198</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=452
2199src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
2200
2201<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2202style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2203mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2204class=SpellE>Rwp</span> will start out high but should converge to where it was
2205before this change. I got 8.08% and the Data tab looked like</p>
2206
2207<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2208 id="Picture_x0020_42" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:480pt;
2209 height:334.5pt;visibility:visible;mso-wrap-style:square'>
2210 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image043.png" o:title=""/>
2211</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=446
2212src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
2213
2214<p class=MsoNormal>This no change in model yet but next select <b
2215style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2216mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Generalized</span></b>
2217for the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2218style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2219mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span><b
2220style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2221mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> model</span></b>;
2222this is the Stephens phenomenological model for <span class=SpellE>microstrain</span>
2223which has 9 terms for monoclinic structures. Check all the boxes for it.</p>
2224
2225<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2226 id="Picture_x0020_43" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:480pt;
2227 height:303.75pt;visibility:visible;mso-wrap-style:square'>
2228 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image044.png" o:title=""/>
2229</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=405
2230src="Charge%20Flipping%20-%20sucrose_files/image044.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
2231
2232<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2233style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2234mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2235class=SpellE>Rwp</span> will start out high but should converge lower than
2236where it was before this change. I got 7.65% and the Data tab looked like. If
2237you check the <span class=SpellE>Mustrain</span> button in the Select plot type
2238box, you will see the interesting <span class=SpellE>mustrain</span> surface
2239plot for ground sucrose.</p>
2240
2241<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2242 id="Picture_x0020_45" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:480pt;
2243 height:305.25pt;visibility:visible;mso-wrap-style:square'>
2244 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image045.png" o:title=""/>
2245</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=407
2246src="Charge%20Flipping%20-%20sucrose_files/image045.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
2247
2248<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2249style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2250mso-hansi-theme-font:minor-latin;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2251 id="Picture_x0020_47" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
2252 height:450pt;visibility:visible;mso-wrap-style:square'>
2253 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image046.png" o:title=""/>
2254</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2255src="Charge%20Flipping%20-%20sucrose_files/image046.png" v:shapes="Picture_x0020_47"><![endif]></span></b></p>
2256
2257<p class=MsoNormal>Before refining H-atom positions it would be wise to create
2258restraints on their bond distances and angles. Locate <b style='mso-bidi-font-weight:
2259normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2260minor-latin;mso-hansi-theme-font:minor-latin'>Restraints</span></b> in the main
2261GSAS-II data tree; there will be an almost blank window telling you there are
2262no bond restraints for sucrose. Do <b style='mso-bidi-font-weight:normal'><span
2263style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2264mso-hansi-theme-font:minor-latin'>Edit/Add <span class=GramE>restraints<span
2265style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
2266a dialog box will appear asking for the origin atom for the bond. </p>
2267
2268<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2269 id="Picture_x0020_48" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:259.5pt;
2270 height:252pt;visibility:visible;mso-wrap-style:square'>
2271 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image047.png" o:title=""/>
2272</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
2273src="Charge%20Flipping%20-%20sucrose_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
2274
2275<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2276style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2277mso-hansi-theme-font:minor-latin'>all H</span></b> and press <b
2278style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2279mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2280A new dialog box will appear asking for the target atoms for the bonds.</p>
2281
2282<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2283 id="Picture_x0020_49" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:259.5pt;
2284 height:252pt;visibility:visible;mso-wrap-style:square'>
2285 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image048.png" o:title=""/>
2286</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
2287src="Charge%20Flipping%20-%20sucrose_files/image048.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
2288
2289<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2290style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2291mso-hansi-theme-font:minor-latin'>all C</span></b> and <b style='mso-bidi-font-weight:
2292normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2293minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b> and a third
2294dialog box appears asking for the bond length</p>
2295
2296<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2297 id="Picture_x0020_50" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:147pt;
2298 height:78.75pt;visibility:visible;mso-wrap-style:square'>
2299 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image049.png" o:title=""/>
2300</v:shape><![endif]--><![if !vml]><img border=0 width=196 height=105
2301src="Charge%20Flipping%20-%20sucrose_files/image049.png" v:shapes="Picture_x0020_50"><![endif]></span><span
2302style='mso-spacerun:yes'> </span></p>
2303
2304<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
2305style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2306mso-hansi-theme-font:minor-latin'>1.09</span></b> and press <b
2307style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2308mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2309I got a short list of 8 H-C and H-O restraints, but I expect 22 of them. Change
2310the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2311mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Search range</span></b>
2312to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2313mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.5</span></b>
2314and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
2315"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2316minor-latin'>Edit/Add restraints</span></b>. There are now 22 restraints on H-C
2317and H-O bond lengths.</p>
2318
2319<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2320 id="Picture_x0020_51" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:450pt;
2321 height:423pt;visibility:visible;mso-wrap-style:square'>
2322 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image050.png" o:title=""/>
2323</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=564
2324src="Charge%20Flipping%20-%20sucrose_files/image050.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
2325
2326<p class=MsoNormal>Next select the <b style='mso-bidi-font-weight:normal'><span
2327style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2328mso-hansi-theme-font:minor-latin'>Angle restraints</span></b> tab and again
2329there aren’t any. Do <b style='mso-bidi-font-weight:normal'><span
2330style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2331mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
2332will appear asking for the A atom in the angle A-B-C. Select <b
2333style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2334mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all H</span></b>.
2335The next dialog asks for the B atom in the A-B-C angle, select <b
2336style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2337mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all C</span></b>
2338and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2339mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b>.
2340The third dialog asks for the angle and has a default of <b style='mso-bidi-font-weight:
2341normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2342minor-latin;mso-hansi-theme-font:minor-latin'>109.54</span></b>. This is the
2343tetrahedral angle so just press OK. 36 restraints will be listed; they are
2344listed in order of the B atom. O-atoms should have one angle apiece; C-atoms
2345will have more. </p>
2346
2347<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2348 id="Picture_x0020_52" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:450pt;
2349 height:365.25pt;visibility:visible;mso-wrap-style:square'>
2350 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image051.png" o:title=""/>
2351</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=487
2352src="Charge%20Flipping%20-%20sucrose_files/image051.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
2353
2354<p class=MsoNormal>Now go back the <b style='mso-bidi-font-weight:normal'><span
2355style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2356mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab in <b style='mso-bidi-font-weight:
2357normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2358minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>, select
2359<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2360mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>
2361from the dialog box by double clicking on the <b style='mso-bidi-font-weight:
2362normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2363minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column. Then do <b
2364style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2365mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Set
2366atom refinement flags</span></b>. Select <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'>X-coordinates</span></b>; this will set those
2369for all H-atoms. Now do <span style='font-family:"Calibri","sans-serif";
2370mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span>,
2371the console will list progress on the “Penalty function” (i.e. the restraints)
2372and the <span class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase
2373the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2374mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Restraint
2375weight factors</span></b> to tighten them up at some expense in <span
2376class=SpellE>Rwp</span>. In the end I chose <b style='mso-bidi-font-weight:
2377normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2378minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b> for both <b
2379style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2380mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond</span></b>
2381and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2382mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b>
2383restraints to give a final <span class=SpellE>Rwp</span> ~7.1%.</p>
2384
2385<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2386
2387<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2388
2389</div>
2390
2391</body>
2392
2393</html>
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