source: Tutorials/CFsucrose/Charge Flipping - sucrose.htm @ 1717

Last change on this file since 1717 was 1717, checked in by vondreele, 8 years ago

update the sucrose images
  • Property svn:mime-type set to text/html
File size: 151.9 KB
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412  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
413  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
414  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
415  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
416  <w:LsdException Locked="false" Priority="34" QFormat="true"
417   Name="List Paragraph"/>
418  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
419  <w:LsdException Locked="false" Priority="30" QFormat="true"
420   Name="Intense Quote"/>
421  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
422  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
423  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
424  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
425  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
426  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
427  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
428  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
429  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
430  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
431  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
432  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
433  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
434  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
435  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
436  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
437  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
438  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
439  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
440  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
441  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
442  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
443  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
444  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
445  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
446  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
447  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
448  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
449  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
450  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
451  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
452  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
453  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
454  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
455  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
456  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
457  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
458  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
459  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
460  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
461  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
462  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
463  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
464  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
465  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
466  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
467  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
468  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
469  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
470  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
471  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
472  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
473  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
474  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
475  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
476  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
477  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
478  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
479  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
480  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
481  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
482  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
483  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
484  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
485  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
486  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
487  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
488  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
489  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
490  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
491  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
492  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
493  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
494  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
495  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
496  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
497  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
498  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
499  <w:LsdException Locked="false" Priority="19" QFormat="true"
500   Name="Subtle Emphasis"/>
501  <w:LsdException Locked="false" Priority="21" QFormat="true"
502   Name="Intense Emphasis"/>
503  <w:LsdException Locked="false" Priority="31" QFormat="true"
504   Name="Subtle Reference"/>
505  <w:LsdException Locked="false" Priority="32" QFormat="true"
506   Name="Intense Reference"/>
507  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
508  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
509   UnhideWhenUsed="true" Name="Bibliography"/>
510  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
511   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
512  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
513  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
514  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
515  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
516  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
517  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
518  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
519  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
520  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
521  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
522  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
523  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
524  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
525  <w:LsdException Locked="false" Priority="46"
526   Name="Grid Table 1 Light Accent 1"/>
527  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
528  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
529  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
530  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
531  <w:LsdException Locked="false" Priority="51"
532   Name="Grid Table 6 Colorful Accent 1"/>
533  <w:LsdException Locked="false" Priority="52"
534   Name="Grid Table 7 Colorful Accent 1"/>
535  <w:LsdException Locked="false" Priority="46"
536   Name="Grid Table 1 Light Accent 2"/>
537  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
538  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
539  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
540  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
541  <w:LsdException Locked="false" Priority="51"
542   Name="Grid Table 6 Colorful Accent 2"/>
543  <w:LsdException Locked="false" Priority="52"
544   Name="Grid Table 7 Colorful Accent 2"/>
545  <w:LsdException Locked="false" Priority="46"
546   Name="Grid Table 1 Light Accent 3"/>
547  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
548  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
549  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
550  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
551  <w:LsdException Locked="false" Priority="51"
552   Name="Grid Table 6 Colorful Accent 3"/>
553  <w:LsdException Locked="false" Priority="52"
554   Name="Grid Table 7 Colorful Accent 3"/>
555  <w:LsdException Locked="false" Priority="46"
556   Name="Grid Table 1 Light Accent 4"/>
557  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
558  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
559  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
560  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
561  <w:LsdException Locked="false" Priority="51"
562   Name="Grid Table 6 Colorful Accent 4"/>
563  <w:LsdException Locked="false" Priority="52"
564   Name="Grid Table 7 Colorful Accent 4"/>
565  <w:LsdException Locked="false" Priority="46"
566   Name="Grid Table 1 Light Accent 5"/>
567  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
568  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
569  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
570  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
571  <w:LsdException Locked="false" Priority="51"
572   Name="Grid Table 6 Colorful Accent 5"/>
573  <w:LsdException Locked="false" Priority="52"
574   Name="Grid Table 7 Colorful Accent 5"/>
575  <w:LsdException Locked="false" Priority="46"
576   Name="Grid Table 1 Light Accent 6"/>
577  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
578  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
579  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
580  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
581  <w:LsdException Locked="false" Priority="51"
582   Name="Grid Table 6 Colorful Accent 6"/>
583  <w:LsdException Locked="false" Priority="52"
584   Name="Grid Table 7 Colorful Accent 6"/>
585  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
586  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
587  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
588  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
589  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
590  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
591  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
592  <w:LsdException Locked="false" Priority="46"
593   Name="List Table 1 Light Accent 1"/>
594  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
595  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
596  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
597  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
598  <w:LsdException Locked="false" Priority="51"
599   Name="List Table 6 Colorful Accent 1"/>
600  <w:LsdException Locked="false" Priority="52"
601   Name="List Table 7 Colorful Accent 1"/>
602  <w:LsdException Locked="false" Priority="46"
603   Name="List Table 1 Light Accent 2"/>
604  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
605  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
606  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
607  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
608  <w:LsdException Locked="false" Priority="51"
609   Name="List Table 6 Colorful Accent 2"/>
610  <w:LsdException Locked="false" Priority="52"
611   Name="List Table 7 Colorful Accent 2"/>
612  <w:LsdException Locked="false" Priority="46"
613   Name="List Table 1 Light Accent 3"/>
614  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
615  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
616  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
617  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
618  <w:LsdException Locked="false" Priority="51"
619   Name="List Table 6 Colorful Accent 3"/>
620  <w:LsdException Locked="false" Priority="52"
621   Name="List Table 7 Colorful Accent 3"/>
622  <w:LsdException Locked="false" Priority="46"
623   Name="List Table 1 Light Accent 4"/>
624  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
625  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
626  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
627  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
628  <w:LsdException Locked="false" Priority="51"
629   Name="List Table 6 Colorful Accent 4"/>
630  <w:LsdException Locked="false" Priority="52"
631   Name="List Table 7 Colorful Accent 4"/>
632  <w:LsdException Locked="false" Priority="46"
633   Name="List Table 1 Light Accent 5"/>
634  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
635  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
636  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
637  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
638  <w:LsdException Locked="false" Priority="51"
639   Name="List Table 6 Colorful Accent 5"/>
640  <w:LsdException Locked="false" Priority="52"
641   Name="List Table 7 Colorful Accent 5"/>
642  <w:LsdException Locked="false" Priority="46"
643   Name="List Table 1 Light Accent 6"/>
644  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
645  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
646  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
647  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
648  <w:LsdException Locked="false" Priority="51"
649   Name="List Table 6 Colorful Accent 6"/>
650  <w:LsdException Locked="false" Priority="52"
651   Name="List Table 7 Colorful Accent 6"/>
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782        mso-ansi-font-size:18.0pt;
783        mso-bidi-font-size:18.0pt;
784        font-family:"Times New Roman",serif;
785        mso-ascii-font-family:"Times New Roman";
786        mso-fareast-font-family:"Times New Roman";
787        mso-fareast-theme-font:minor-fareast;
788        mso-hansi-font-family:"Times New Roman";
789        mso-bidi-font-family:"Times New Roman";
790        font-weight:bold;}
791span.BalloonTextChar
792        {mso-style-name:"Balloon Text Char";
793        mso-style-noshow:yes;
794        mso-style-priority:99;
795        mso-style-unhide:no;
796        mso-style-locked:yes;
797        mso-style-link:"Balloon Text";
798        mso-ansi-font-size:8.0pt;
799        mso-bidi-font-size:8.0pt;
800        font-family:"Tahoma",sans-serif;
801        mso-ascii-font-family:Tahoma;
802        mso-fareast-font-family:"Times New Roman";
803        mso-fareast-theme-font:minor-fareast;
804        mso-hansi-font-family:Tahoma;
805        mso-bidi-font-family:Tahoma;}
806.MsoChpDefault
807        {mso-style-type:export-only;
808        mso-default-props:yes;
809        font-size:12.0pt;
810        mso-ansi-font-size:12.0pt;
811        mso-bidi-font-size:12.0pt;
812        mso-fareast-font-family:Calibri;
813        mso-fareast-theme-font:minor-latin;
814        mso-bidi-font-family:"Times New Roman";
815        mso-bidi-theme-font:minor-bidi;}
816@page WordSection1
817        {size:8.5in 11.0in;
818        margin:1.0in 1.0in 1.0in 1.0in;
819        mso-header-margin:.5in;
820        mso-footer-margin:.5in;
821        mso-paper-source:0;}
822div.WordSection1
823        {page:WordSection1;}
824 /* List Definitions */
825 @list l0
826        {mso-list-id:15232614;
827        mso-list-type:hybrid;
828        mso-list-template-ids:1768441438 -647724540 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
829@list l0:level1
830        {mso-level-tab-stop:none;
831        mso-level-number-position:left;
832        margin-left:.75in;
833        text-indent:-.25in;}
834@list l0:level2
835        {mso-level-number-format:alpha-lower;
836        mso-level-tab-stop:none;
837        mso-level-number-position:left;
838        margin-left:1.25in;
839        text-indent:-.25in;}
840@list l0:level3
841        {mso-level-number-format:roman-lower;
842        mso-level-tab-stop:none;
843        mso-level-number-position:right;
844        margin-left:1.75in;
845        text-indent:-9.0pt;}
846@list l0:level4
847        {mso-level-tab-stop:none;
848        mso-level-number-position:left;
849        margin-left:2.25in;
850        text-indent:-.25in;}
851@list l0:level5
852        {mso-level-number-format:alpha-lower;
853        mso-level-tab-stop:none;
854        mso-level-number-position:left;
855        margin-left:2.75in;
856        text-indent:-.25in;}
857@list l0:level6
858        {mso-level-number-format:roman-lower;
859        mso-level-tab-stop:none;
860        mso-level-number-position:right;
861        margin-left:3.25in;
862        text-indent:-9.0pt;}
863@list l0:level7
864        {mso-level-tab-stop:none;
865        mso-level-number-position:left;
866        margin-left:3.75in;
867        text-indent:-.25in;}
868@list l0:level8
869        {mso-level-number-format:alpha-lower;
870        mso-level-tab-stop:none;
871        mso-level-number-position:left;
872        margin-left:4.25in;
873        text-indent:-.25in;}
874@list l0:level9
875        {mso-level-number-format:roman-lower;
876        mso-level-tab-stop:none;
877        mso-level-number-position:right;
878        margin-left:4.75in;
879        text-indent:-9.0pt;}
880@list l1
881        {mso-list-id:82917343;
882        mso-list-type:hybrid;
883        mso-list-template-ids:-1527319822 -2100533712 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
884@list l1:level1
885        {mso-level-tab-stop:none;
886        mso-level-number-position:left;
887        margin-left:.75in;
888        text-indent:-.25in;}
889@list l1:level2
890        {mso-level-number-format:alpha-lower;
891        mso-level-tab-stop:none;
892        mso-level-number-position:left;
893        margin-left:1.25in;
894        text-indent:-.25in;}
895@list l1:level3
896        {mso-level-number-format:roman-lower;
897        mso-level-tab-stop:none;
898        mso-level-number-position:right;
899        margin-left:1.75in;
900        text-indent:-9.0pt;}
901@list l1:level4
902        {mso-level-tab-stop:none;
903        mso-level-number-position:left;
904        margin-left:2.25in;
905        text-indent:-.25in;}
906@list l1:level5
907        {mso-level-number-format:alpha-lower;
908        mso-level-tab-stop:none;
909        mso-level-number-position:left;
910        margin-left:2.75in;
911        text-indent:-.25in;}
912@list l1:level6
913        {mso-level-number-format:roman-lower;
914        mso-level-tab-stop:none;
915        mso-level-number-position:right;
916        margin-left:3.25in;
917        text-indent:-9.0pt;}
918@list l1:level7
919        {mso-level-tab-stop:none;
920        mso-level-number-position:left;
921        margin-left:3.75in;
922        text-indent:-.25in;}
923@list l1:level8
924        {mso-level-number-format:alpha-lower;
925        mso-level-tab-stop:none;
926        mso-level-number-position:left;
927        margin-left:4.25in;
928        text-indent:-.25in;}
929@list l1:level9
930        {mso-level-number-format:roman-lower;
931        mso-level-tab-stop:none;
932        mso-level-number-position:right;
933        margin-left:4.75in;
934        text-indent:-9.0pt;}
935@list l2
936        {mso-list-id:236667377;
937        mso-list-type:hybrid;
938        mso-list-template-ids:-513138304 1385070818 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
939@list l2:level1
940        {mso-level-tab-stop:none;
941        mso-level-number-position:left;
942        margin-left:.75in;
943        text-indent:-.25in;}
944@list l2:level2
945        {mso-level-number-format:alpha-lower;
946        mso-level-tab-stop:none;
947        mso-level-number-position:left;
948        margin-left:1.25in;
949        text-indent:-.25in;}
950@list l2:level3
951        {mso-level-number-format:roman-lower;
952        mso-level-tab-stop:none;
953        mso-level-number-position:right;
954        margin-left:1.75in;
955        text-indent:-9.0pt;}
956@list l2:level4
957        {mso-level-tab-stop:none;
958        mso-level-number-position:left;
959        margin-left:2.25in;
960        text-indent:-.25in;}
961@list l2:level5
962        {mso-level-number-format:alpha-lower;
963        mso-level-tab-stop:none;
964        mso-level-number-position:left;
965        margin-left:2.75in;
966        text-indent:-.25in;}
967@list l2:level6
968        {mso-level-number-format:roman-lower;
969        mso-level-tab-stop:none;
970        mso-level-number-position:right;
971        margin-left:3.25in;
972        text-indent:-9.0pt;}
973@list l2:level7
974        {mso-level-tab-stop:none;
975        mso-level-number-position:left;
976        margin-left:3.75in;
977        text-indent:-.25in;}
978@list l2:level8
979        {mso-level-number-format:alpha-lower;
980        mso-level-tab-stop:none;
981        mso-level-number-position:left;
982        margin-left:4.25in;
983        text-indent:-.25in;}
984@list l2:level9
985        {mso-level-number-format:roman-lower;
986        mso-level-tab-stop:none;
987        mso-level-number-position:right;
988        margin-left:4.75in;
989        text-indent:-9.0pt;}
990@list l3
991        {mso-list-id:533275380;
992        mso-list-type:hybrid;
993        mso-list-template-ids:-1319630076 -1606007952 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
994@list l3:level1
995        {mso-level-tab-stop:none;
996        mso-level-number-position:left;
997        margin-left:.75in;
998        text-indent:-.25in;}
999@list l3:level2
1000        {mso-level-number-format:alpha-lower;
1001        mso-level-tab-stop:none;
1002        mso-level-number-position:left;
1003        margin-left:1.25in;
1004        text-indent:-.25in;}
1005@list l3:level3
1006        {mso-level-number-format:roman-lower;
1007        mso-level-tab-stop:none;
1008        mso-level-number-position:right;
1009        margin-left:1.75in;
1010        text-indent:-9.0pt;}
1011@list l3:level4
1012        {mso-level-tab-stop:none;
1013        mso-level-number-position:left;
1014        margin-left:2.25in;
1015        text-indent:-.25in;}
1016@list l3:level5
1017        {mso-level-number-format:alpha-lower;
1018        mso-level-tab-stop:none;
1019        mso-level-number-position:left;
1020        margin-left:2.75in;
1021        text-indent:-.25in;}
1022@list l3:level6
1023        {mso-level-number-format:roman-lower;
1024        mso-level-tab-stop:none;
1025        mso-level-number-position:right;
1026        margin-left:3.25in;
1027        text-indent:-9.0pt;}
1028@list l3:level7
1029        {mso-level-tab-stop:none;
1030        mso-level-number-position:left;
1031        margin-left:3.75in;
1032        text-indent:-.25in;}
1033@list l3:level8
1034        {mso-level-number-format:alpha-lower;
1035        mso-level-tab-stop:none;
1036        mso-level-number-position:left;
1037        margin-left:4.25in;
1038        text-indent:-.25in;}
1039@list l3:level9
1040        {mso-level-number-format:roman-lower;
1041        mso-level-tab-stop:none;
1042        mso-level-number-position:right;
1043        margin-left:4.75in;
1044        text-indent:-9.0pt;}
1045@list l4
1046        {mso-list-id:588542776;
1047        mso-list-type:hybrid;
1048        mso-list-template-ids:477805396 -2056748102 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1049@list l4:level1
1050        {mso-level-tab-stop:none;
1051        mso-level-number-position:left;
1052        margin-left:.75in;
1053        text-indent:-.25in;}
1054@list l4:level2
1055        {mso-level-number-format:alpha-lower;
1056        mso-level-tab-stop:none;
1057        mso-level-number-position:left;
1058        margin-left:1.25in;
1059        text-indent:-.25in;}
1060@list l4:level3
1061        {mso-level-number-format:roman-lower;
1062        mso-level-tab-stop:none;
1063        mso-level-number-position:right;
1064        margin-left:1.75in;
1065        text-indent:-9.0pt;}
1066@list l4:level4
1067        {mso-level-tab-stop:none;
1068        mso-level-number-position:left;
1069        margin-left:2.25in;
1070        text-indent:-.25in;}
1071@list l4:level5
1072        {mso-level-number-format:alpha-lower;
1073        mso-level-tab-stop:none;
1074        mso-level-number-position:left;
1075        margin-left:2.75in;
1076        text-indent:-.25in;}
1077@list l4:level6
1078        {mso-level-number-format:roman-lower;
1079        mso-level-tab-stop:none;
1080        mso-level-number-position:right;
1081        margin-left:3.25in;
1082        text-indent:-9.0pt;}
1083@list l4:level7
1084        {mso-level-tab-stop:none;
1085        mso-level-number-position:left;
1086        margin-left:3.75in;
1087        text-indent:-.25in;}
1088@list l4:level8
1089        {mso-level-number-format:alpha-lower;
1090        mso-level-tab-stop:none;
1091        mso-level-number-position:left;
1092        margin-left:4.25in;
1093        text-indent:-.25in;}
1094@list l4:level9
1095        {mso-level-number-format:roman-lower;
1096        mso-level-tab-stop:none;
1097        mso-level-number-position:right;
1098        margin-left:4.75in;
1099        text-indent:-9.0pt;}
1100@list l5
1101        {mso-list-id:854225785;
1102        mso-list-type:hybrid;
1103        mso-list-template-ids:-2071413312 1417604178 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1104@list l5:level1
1105        {mso-level-tab-stop:none;
1106        mso-level-number-position:left;
1107        margin-left:.75in;
1108        text-indent:-.25in;}
1109@list l5:level2
1110        {mso-level-number-format:alpha-lower;
1111        mso-level-tab-stop:none;
1112        mso-level-number-position:left;
1113        margin-left:1.25in;
1114        text-indent:-.25in;}
1115@list l5:level3
1116        {mso-level-number-format:roman-lower;
1117        mso-level-tab-stop:none;
1118        mso-level-number-position:right;
1119        margin-left:1.75in;
1120        text-indent:-9.0pt;}
1121@list l5:level4
1122        {mso-level-tab-stop:none;
1123        mso-level-number-position:left;
1124        margin-left:2.25in;
1125        text-indent:-.25in;}
1126@list l5:level5
1127        {mso-level-number-format:alpha-lower;
1128        mso-level-tab-stop:none;
1129        mso-level-number-position:left;
1130        margin-left:2.75in;
1131        text-indent:-.25in;}
1132@list l5:level6
1133        {mso-level-number-format:roman-lower;
1134        mso-level-tab-stop:none;
1135        mso-level-number-position:right;
1136        margin-left:3.25in;
1137        text-indent:-9.0pt;}
1138@list l5:level7
1139        {mso-level-tab-stop:none;
1140        mso-level-number-position:left;
1141        margin-left:3.75in;
1142        text-indent:-.25in;}
1143@list l5:level8
1144        {mso-level-number-format:alpha-lower;
1145        mso-level-tab-stop:none;
1146        mso-level-number-position:left;
1147        margin-left:4.25in;
1148        text-indent:-.25in;}
1149@list l5:level9
1150        {mso-level-number-format:roman-lower;
1151        mso-level-tab-stop:none;
1152        mso-level-number-position:right;
1153        margin-left:4.75in;
1154        text-indent:-9.0pt;}
1155@list l6
1156        {mso-list-id:1022125565;
1157        mso-list-type:hybrid;
1158        mso-list-template-ids:-482838388 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1159@list l6:level1
1160        {mso-level-tab-stop:none;
1161        mso-level-number-position:left;
1162        margin-left:1.0in;
1163        text-indent:-.25in;}
1164@list l6:level2
1165        {mso-level-number-format:alpha-lower;
1166        mso-level-tab-stop:none;
1167        mso-level-number-position:left;
1168        margin-left:1.5in;
1169        text-indent:-.25in;}
1170@list l6:level3
1171        {mso-level-number-format:roman-lower;
1172        mso-level-tab-stop:none;
1173        mso-level-number-position:right;
1174        margin-left:2.0in;
1175        text-indent:-9.0pt;}
1176@list l6:level4
1177        {mso-level-tab-stop:none;
1178        mso-level-number-position:left;
1179        margin-left:2.5in;
1180        text-indent:-.25in;}
1181@list l6:level5
1182        {mso-level-number-format:alpha-lower;
1183        mso-level-tab-stop:none;
1184        mso-level-number-position:left;
1185        margin-left:3.0in;
1186        text-indent:-.25in;}
1187@list l6:level6
1188        {mso-level-number-format:roman-lower;
1189        mso-level-tab-stop:none;
1190        mso-level-number-position:right;
1191        margin-left:3.5in;
1192        text-indent:-9.0pt;}
1193@list l6:level7
1194        {mso-level-tab-stop:none;
1195        mso-level-number-position:left;
1196        margin-left:4.0in;
1197        text-indent:-.25in;}
1198@list l6:level8
1199        {mso-level-number-format:alpha-lower;
1200        mso-level-tab-stop:none;
1201        mso-level-number-position:left;
1202        margin-left:4.5in;
1203        text-indent:-.25in;}
1204@list l6:level9
1205        {mso-level-number-format:roman-lower;
1206        mso-level-tab-stop:none;
1207        mso-level-number-position:right;
1208        margin-left:5.0in;
1209        text-indent:-9.0pt;}
1210ol
1211        {margin-bottom:0in;}
1212ul
1213        {margin-bottom:0in;}
1214-->
1215</style>
1216<!--[if gte mso 10]>
1217<style>
1218 /* Style Definitions */
1219 table.MsoNormalTable
1220        {mso-style-name:"Table Normal";
1221        mso-tstyle-rowband-size:0;
1222        mso-tstyle-colband-size:0;
1223        mso-style-noshow:yes;
1224        mso-style-priority:99;
1225        mso-style-parent:"";
1226        mso-padding-alt:0in 5.4pt 0in 5.4pt;
1227        mso-para-margin:0in;
1228        mso-para-margin-bottom:.0001pt;
1229        mso-pagination:widow-orphan;
1230        font-size:12.0pt;
1231        font-family:"Times New Roman",serif;
1232        mso-bidi-font-family:"Times New Roman";
1233        mso-bidi-theme-font:minor-bidi;}
1234</style>
1235<![endif]--><!--[if gte mso 9]><xml>
1236 <o:shapedefaults v:ext="edit" spidmax="1029"/>
1237</xml><![endif]--><!--[if gte mso 9]><xml>
1238 <o:shapelayout v:ext="edit">
1239  <o:idmap v:ext="edit" data="1"/>
1240 </o:shapelayout></xml><![endif]-->
1241</head>
1242
1243<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1244
1245<div class=WordSection1>
1246
1247<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in
1248GSAS-II - sucrose<o:p></o:p></span></h1>
1249
1250<h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1>
1251
1252<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1253of sucrose from powder diffraction data via charge flipping. This structure was
1254originally solved from single crystal data in the space group P2<sub>1</sub>.
1255It is a difficult exercise to complete as the charge flipping does not always
1256yield a solution and to even have a chance the Pawley refinement must be done
1257with particular care. We have given a route that sometimes works.</p>
1258
1259<p class=MsoNormal>If you have not done so already, <a
1260href="../../../GSASII/help/Starting%20GSAS.htm">start GSAS-II</a> and open the
1261GSAS-II project file (I called it <b style='mso-bidi-font-weight:normal'><span
1262style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1263mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b>) you saved from the
1264third part of the <a
1265href="../../../GSASII/help/Fit%20Peaks.htm#sucrose_peak_fit">peak
1266fitting-indexing exercise</a>. If you didn’t do that exercise, do it now.</p>
1267
1268<h2>Step 1: Setup for Pawley refinement</h2>
1269
1270<p class=MsoNormal>There are a number of steps that must be done in preparation
1271for a Pawley refinement after having completed the unit cell indexing and new
1272phase creation. These cover two things: one is to prepare the powder pattern
1273(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1274
1275<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1276style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1277style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1278<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1279mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
1280in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1281region near d=1.0Å is readily seen. This is ~24deg 2<span style='font-family:
1282Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1283mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1284symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
1285relatively clear of peaks that makes a good place to end the calculations with
1286a reflection set of d<sub>min</sub> ~1Å resolution needed for charge flipping.
1287Enter <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1288mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>23.55</span></b>
1289for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1290mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b>
1291as the upper limit and make a note of the exact d-spacing (1.0125Å) using the
1292mouse cursor on the plot.</p>
1293
1294<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1295style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1296style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1297<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1298mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1299Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1300style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1301mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1302style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1303mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1304profile</span></b> to recover the default values. The peak fitting done earlier
1305is over a much more limited range of 2<span style='font-family:Symbol;
1306mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1307mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1308symbol;mso-symbol-font-family:Symbol'>Q</span></span> giving values that might
1309not extrapolate well over the wider range to be used in the Pawley refinement.
1310We will refine them again later.</p>
1311
1312<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1313style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1314style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1315<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1316mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1317Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1318normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1319minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.
1320While you are here set <b style='mso-bidi-font-weight:normal'><span
1321style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1322mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> to <b
1323style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1324mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>.</p>
1325
1326<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1327style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1328style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1329to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1330mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1331to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1332"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1333minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1334normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1335minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
1336box and enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
1337style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1338mso-hansi-theme-font:minor-latin'>1.0125</span></b>) into the <b
1339style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1340mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>
1341box.</p>
1342
1343<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1344style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1345mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1346
1347<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1348 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1349 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1350 <v:stroke joinstyle="miter"/>
1351 <v:formulas>
1352  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1353  <v:f eqn="sum @0 1 0"/>
1354  <v:f eqn="sum 0 0 @1"/>
1355  <v:f eqn="prod @2 1 2"/>
1356  <v:f eqn="prod @3 21600 pixelWidth"/>
1357  <v:f eqn="prod @3 21600 pixelHeight"/>
1358  <v:f eqn="sum @0 0 1"/>
1359  <v:f eqn="prod @6 1 2"/>
1360  <v:f eqn="prod @7 21600 pixelWidth"/>
1361  <v:f eqn="sum @8 21600 0"/>
1362  <v:f eqn="prod @7 21600 pixelHeight"/>
1363  <v:f eqn="sum @10 21600 0"/>
1364 </v:formulas>
1365 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1366 <o:lock v:ext="edit" aspectratio="t"/>
1367</v:shapetype><v:shape id="Picture_x0020_25" o:spid="_x0000_i1064" type="#_x0000_t75"
1368 style='width:545.25pt;height:303.75pt;visibility:visible;mso-wrap-style:square'>
1369 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image001.png" o:title=""/>
1370</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
1371src="Charge%20Flipping%20-%20sucrose_files/image001.png" v:shapes="Picture_x0020_25"><![endif]></span></p>
1372
1373<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1374style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1375mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1376for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
1377style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1378mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
1379dialog box will appear</p>
1380
1381<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1382 id="Picture_x0020_2" o:spid="_x0000_i1063" type="#_x0000_t75" style='width:259.5pt;
1383 height:252pt;visibility:visible;mso-wrap-style:square'>
1384 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image002.png" o:title=""/>
1385</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1386src="Charge%20Flipping%20-%20sucrose_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1387
1388<p class=MsoNormal>Select either choice; the desired data set will be added to
1389this phase for analysis. The data tab now shows the new data set; check the <b
1390style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1391mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
1392button to see the full information</p>
1393
1394<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1395 id="Picture_x0020_3" o:spid="_x0000_i1062" type="#_x0000_t75" style='width:480pt;
1396 height:393pt;visibility:visible;mso-wrap-style:square'>
1397 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image003.png" o:title=""/>
1398</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=524
1399src="Charge%20Flipping%20-%20sucrose_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
1400
1401<p class=MsoNormal>I’ve stretched the window slightly to see the entire
1402contents. This is the location for all the phase dependent parameters for this
1403histogram. Notice that it includes phase fraction, size &amp; mustrain as well
1404as preferred orientation, elastic strain and extinction corrections. The
1405Babinet correction is intended for protein work where a significant region of
1406the structure is disordered solvent. There are buttons for plotting size and
1407mustrain surfaces</p>
1408
1409<p class=MsoNormal>as well as preferred orientation correction curves.</p>
1410
1411<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1412style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1413mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1414empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
1415style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1416mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
1417makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
1418normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1419minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>. The table
1420should list reflections 0-781. Select and check the refine column using the
1421same technique you used for the peak list. </p>
1422
1423<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1424 id="Picture_x0020_4" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:375pt;
1425 height:225pt;visibility:visible;mso-wrap-style:square'>
1426 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image004.png" o:title=""/>
1427</v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300
1428src="Charge%20Flipping%20-%20sucrose_files/image004.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
1429
1430<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1431you didn’t skip a step as it might not work correctly if you did.</p>
1432
1433<h2>Step 2: Pawley refinement</h2>
1434
1435<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1436normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1437minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1438the main GSAS-II data tree window. Before it begins a backup of the project
1439file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
1440style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1441mso-hansi-theme-font:minor-latin'>sucrose.bck0.gpx</span></b>. It can be used
1442to recover from a bad refinement. A progress dialog box will appear showing the
1443residual as the refinement proceeds. Notice that there was a singular matrix
1444warning on the console window and the last reflection (781) was removed from
1445the refinement because it was off the end of the used part of the pattern. This
1446is the GSAS-II singular matrix recovery mechanism; you can go to the <b
1447style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1448mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1449reflections</span></b> tab and uncheck the last reflection. Then repeat <b
1450style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1451mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1452to make sure it has essentially minimized. My refinement completed with Rwp
1453~26.3%; a dialog box appears asking if you wish to load the result. Press <b
1454style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1455mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1456To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
1457the width and height).</p>
1458
1459<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1460 id="Picture_x0020_5" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:503.25pt;
1461 height:431.25pt;visibility:visible;mso-wrap-style:square'>
1462 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image005.png" o:title=""/>
1463</v:shape><![endif]--><![if !vml]><img border=0 width=671 height=575
1464src="Charge%20Flipping%20-%20sucrose_files/image005.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
1465
1466<p class=MsoNormal>It is evident from examining the plot that some improvement
1467can be had by refining the lattice and profile parameters and perhaps the
1468sample X position. Go to <b style='mso-bidi-font-weight:normal'><span
1469style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1470mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> in the GSAS-II data
1471tree and check the <b style='mso-bidi-font-weight:normal'><span
1472style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1473mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> box. Now select <b
1474style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1475mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1476parameters</span></b> for the PWDR data set in the GSAS-II data tree and check <b
1477style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1478mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>,
1479<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1480mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>,
1481<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1482mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,<b
1483style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1484mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> X </span></b>&amp;<b
1485style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1486mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Y</span></b>.
1487The go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1488mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1489Parameters</span></b> and check <b style='mso-bidi-font-weight:normal'><span
1490style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1491mso-hansi-theme-font:minor-latin'>Sample X displ</span></b>.; make the <b
1492style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1493mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer
1494radius</span></b> <b style='mso-bidi-font-weight:normal'><span
1495style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1496mso-hansi-theme-font:minor-latin'>1000</span></b> if you didn’t do this earlier.
1497Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1498mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine
1499</span></b>until converged; I obtained an improved residual of ~9.05% with a
1500much better fit at the high angle part of the pattern but still not fit well
1501for the lower part.</p>
1502
1503<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1504 id="Picture_x0020_26" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:504.75pt;
1505 height:432.75pt;visibility:visible;mso-wrap-style:square'>
1506 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image006.png" o:title=""/>
1507</v:shape><![endif]--><![if !vml]><img border=0 width=673 height=577
1508src="Charge%20Flipping%20-%20sucrose_files/image006.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
1509
1510<p class=MsoNormal>What you see is that the background has a substantial
1511diffuse scattering feature at ~5deg and there are some peak shape issues (which
1512may be a consequence of the poor background fit). We’d like the fit to be
1513better before trying charge flipping. First select <b style='mso-bidi-font-weight:
1514normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1515minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>, set <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'>Peaks in
1518background: No. peaks</span></b> to <b style='mso-bidi-font-weight:normal'><span
1519style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1520mso-hansi-theme-font:minor-latin'>1</span></b> from the pull down box; the
1521window changes to </p>
1522
1523<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1524 id="Picture_x0020_27" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:366.75pt;
1525 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1526 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image007.png" o:title=""/>
1527</v:shape><![endif]--><![if !vml]><img border=0 width=489 height=263
1528src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span><span
1529style='mso-spacerun:yes'> </span></p>
1530
1531<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
1532style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1533mso-hansi-theme-font:minor-latin'>5.0</span></b> for <b style='mso-bidi-font-weight:
1534normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1535minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b>, <b
1536style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1537mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
1538for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1539mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b>
1540and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1541mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1542for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1543mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
1544(as appropriate for broad diffuse peaks) and then check all three refine boxes.
1545Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1546mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. coeff.</span></b>
1547pulldown to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1548"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1549minor-latin'>5</span></b> for the chebyschev part of the background. The window
1550should look like</p>
1551
1552<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1553 id="Picture_x0020_28" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:402pt;
1554 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1555 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image008.png" o:title=""/>
1556</v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
1557src="Charge%20Flipping%20-%20sucrose_files/image008.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1558
1559<p class=MsoNormal>Go to the <b style='mso-bidi-font-weight:normal'><span
1560style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1561mso-hansi-theme-font:minor-latin'>Controls</span></b> item in the GSAS-II data
1562tree and set the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1563"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1564minor-latin'>Max cycles</span></b> to <b style='mso-bidi-font-weight:normal'><span
1565style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1566mso-hansi-theme-font:minor-latin'>5</span></b>. Now do <b style='mso-bidi-font-weight:
1567normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1568minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until
1569the refinement converges. After a set of refinement cycles go to the <b
1570style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1571mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1572reflections</span></b> tab and check the intensities. If there are many
1573negatives amongst the highest angle reflections do <b style='mso-bidi-font-weight:
1574normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1575minor-latin;mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this
1576replaces all the values with those in the extracted from the profile as listed
1577in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1578mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1579list</span></b> for the PWDR data set each multiplied by 0.5. Additionally
1580their refinement flags are turned off. Do <b style='mso-bidi-font-weight:normal'><span
1581style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1582mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b><span
1583style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1584mso-hansi-theme-font:minor-latin'>; this will adjust all the reflections in the
1585vicinity of the reset ones</span>. You may repeat this process to suppress any
1586new negatives that may appear. Then set all the Pawley refinement flags back on
1587(excluding any that lead to a singular matrix) and repeat the refinement. After
1588refinement, mine converged to ~5.7% with very few negatives and and the plot
1589looked like</p>
1590
1591<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1592 id="Picture_x0020_29" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:507pt;
1593 height:434.25pt;visibility:visible;mso-wrap-style:square'>
1594 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image009.png" o:title=""/>
1595</v:shape><![endif]--><![if !vml]><img border=0 width=676 height=579
1596src="Charge%20Flipping%20-%20sucrose_files/image009.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
1597
1598<p class=MsoNormal>Let’s see if this is good enough for charge flipping.</p>
1599
1600<h2>Step 3: Charge flipping</h2>
1601
1602<p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
1603Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1604mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1605and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1606"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1607minor-latin'>Charge flip controls</span></b> in the middle of the <b
1608style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1609mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1610tab.</p>
1611
1612<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1613mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1614"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1615</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
1616style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1617mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b
1618style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1619mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
162011bmb_8716.fxye Bank 1</span></b> (the only choice!). This makes the reflection
1621set to be used those in <b style='mso-bidi-font-weight:normal'><span
1622style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1623mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
1624data set; these should match the <b style='mso-bidi-font-weight:normal'><span
1625style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1626mso-hansi-theme-font:minor-latin'>Pawley reflection</span></b> set.</p>
1627
1628<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1629mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1630"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1631</span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span
1632style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1633mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b
1634style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1635mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map
1636controls</span></b>) to <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'>20%</span></b>. This controls the map search
1639routine.</p>
1640
1641<p class=MsoNormal>For powder data it is not usually advisable to select a <b
1642style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1643mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing
1644element</span></b>; if selected a periodic table appears – select an element or
1645‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1646mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None’</span></b>.
1647The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1648mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1649defines the map spacing and thus the extent of the reflection set; the observed
1650reflection set is zero filled to this limit for charge flipping. The <b
1651style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1652mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b>
1653and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1654mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b>
1655determine the lower threshold and upper limit for charge flipping, respectively.
1656The latter is used to avoid “Uranium solutions” in the result. Set this to <b
1657style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1658mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>10-12</span></b>
1659for equal atom problems and larger for heavy atom ones. For sucrose set it to <b
1660style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1661mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>12.</span></b>
1662When ready select <b style='mso-bidi-font-weight:normal'><span
1663style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1664mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b>; a
1665progress bar dialog will appear that tracks the residual found in each charge
1666flipping cycle. It will quickly drop to some level (42-44%) and then for a
1667successful charge flipping run perhaps drop again into the 20-25% range after a
1668considerable length of time. You should save the project if you get an
1669apparently good solution. Many times it will not drop below ~40%; just try <b
1670style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1671mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1672flipping</span></b> again. If several tries fail to yield a solution, go back
1673to the last step of the Pawley refinement and just repeat it (that is do <b
1674style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1675mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1676update</span></b> and <b style='mso-bidi-font-weight:normal'><span
1677style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1678mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>). This will
1679generate a different set of intensities for the highly overlapped part of the
1680powder pattern; perhaps they will give a successful charge flip solution.
1681Unless otherwise interrupted, GSAS-II will try 10000 times for a charge flip solution
1682(for sucrose this takes 5-10min on my laptop). Press <b style='mso-bidi-font-weight:
1683normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1684minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
1685charge flipping; a peak list and a drawing of the solution will appear. One of
1686my runs gave</p>
1687
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1693src="Charge%20Flipping%20-%20sucrose_files/image010.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1694
1695<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1696
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1795 </v:shape></v:group><![endif]--><![if !vml]><span style='mso-ignore:vglayout;
1796position:absolute;z-index:251662336;margin-left:315px;margin-top:308px;
1797width:16px;height:35px'><img width=16 height=35
1798src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
1799style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
1800 o:spid="_x0000_i1054" type="#_x0000_t75" style='width:502.5pt;height:431.25pt;
1801 visibility:visible;mso-wrap-style:square'>
1802 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image012.png" o:title=""
1803  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
1804</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=575
1805src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
1806
1807<p class=MsoNormal>The result looks very promising! Charge flipping operates
1808without regard to symmetry and GSAS-II attempts to locate the map with respect
1809to the symmetry elements from the computed reflection phases. (NB: charge
1810flipping also will give a solution without regard to handedness; this solution
1811may be either the correct one for sucrose or its inverse.) Errors in these
1812phases can disrupt this process so that the map and peak positions are offset from
1813their true positions. To discover this and fix it, rotate the drawing around to
1814check that atom positions are related via the 2<sub>1</sub> screw axis (through
1815the multicolored cross in the center of the cell and parallel to the y-axis –
1816the green cell edge). Avoid motions with the right mouse button pressed, this
1817moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:normal'><span
1818style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1819mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the cross to the
1820cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my drawing
1821above to show where I think it should be. If you find an offset to the map,
1822orient it so the offset is horizontal or vertical and then press the <b
1823style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1824mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>,
1825<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1826mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>,
1827<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1828mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
1829or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1830mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
1831keys to shift the map and peaks as needed. The shift is in resolution units
1832(0.5Å) so the fix can only be approximate. Repeat as needed. Notice that the
1833peak positions in the table are updated as the offset is changed. In this case,
1834I needed just a few steps to correct the map offset. NB: you can use these keys
1835to move the result anywhere you wish, e.g. to select a different origin for the
1836structure but pay attention to the location of symmetry elements. After
1837adjustment, my solution looked like</p>
1838
1839<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1840 id="Picture_x0020_12" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:500.25pt;
1841 height:424.5pt;visibility:visible;mso-wrap-style:square'>
1842 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image014.png" o:title=""
1843  croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/>
1844</v:shape><![endif]--><![if !vml]><img border=0 width=667 height=566
1845src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
1846
1847<h2>Step 4: Obtain solution from charge flip result</h2>
1848
1849<p class=MsoNormal>The next step is to extract the unique peak positions from
1850the map and make atoms out of them. The map peak list is initially sorted by
1851peak magnitude; you can change the sorting to be along any of the column
1852headings in the table by a single click on the desired heading. The <b
1853style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1854mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b>
1855column gives the distance of each peak from the origin. The menu items under
1856Map peaks give you several tools to aid in the peak selection process; we will
1857just use a couple in this example. I have chosen to proceed by sorting the
1858atoms by <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1859mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>,
1860selecting all and then finding the unique ones. </p>
1861
1862<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1863mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1864"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1865</span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight:
1866normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1867minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> column heading. This
1868will sort the peaks in increasing z-axis coordinate.</p>
1869
1870<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1871mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1872"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1873</span></span></span><![endif]>Do a single click on the upper left (empty) box
1874of the table. All entries will be colored grey indicating their selection.</p>
1875
1876<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1877mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1878"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1879</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1880style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1881mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That
1882should select (grey) 23 out of 46 peak positions in the table and all should be
1883near the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
1884that would be all the C &amp; O atoms! They will be colored green in the plot. If
1885more are selected then check the map offset – it may need a slight correction.</p>
1886
1887<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1888 id="Picture_x0020_13" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:337.5pt;
1889 height:411.75pt;visibility:visible;mso-wrap-style:square'>
1890 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image016.png" o:title=""/>
1891</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=549
1892src="Charge%20Flipping%20-%20sucrose_files/image016.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1893
1894<p class=MsoNormal>The drawing shows the selected atoms in green.</p>
1895
1896<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1897 id="Picture_x0020_14" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:7in;
1898 height:429pt;visibility:visible;mso-wrap-style:square'>
1899 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image017.png" o:title=""
1900  croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/>
1901</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=572
1902src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
1903
1904<p class=MsoNormal>Notice that in my case one atom is in a neighboring
1905molecule, one can deselect it and then pick the desired equivalent. Hold the <b
1906style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1907mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1908key down and use the right mouse button to pick/unpick atoms in the drawing.
1909NB: the left mouse button will clear all the selections. The other two “lone”
1910atoms belong to molecules in neighboring unit cells; we’ll deal with them
1911later.</p>
1912
1913<p class=MsoNormal>These are now ready to turn into atoms. Do <b
1914style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1915mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1916peaks/Move peaks</span></b>. The drawing will show white balls for each of the
1917selected positions and the <b style='mso-bidi-font-weight:normal'><span
1918style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1919mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 23 new H
1920atoms. </p>
1921
1922<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1923 id="Picture_x0020_15" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:7in;
1924 height:433.5pt;visibility:visible;mso-wrap-style:square'>
1925 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image019.png" o:title=""
1926  croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/>
1927</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=578
1928src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
1929
1930<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1931 id="Picture_x0020_44" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
1932 height:414.75pt;visibility:visible;mso-wrap-style:square'>
1933 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image021.png" o:title=""/>
1934</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=553
1935src="Charge%20Flipping%20-%20sucrose_files/image021.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
1936
1937<p class=MsoNormal>The atom names indicate the peak magnitude to aid
1938identification (M100 for the largest in the <b style='mso-bidi-font-weight:
1939normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1940minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
1941may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
1942style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1943mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
1944them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
1945style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1946mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
1947normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1948minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
1949and then selecting a position in the table with the <b style='mso-bidi-font-weight:
1950normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1951minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
1952Linux machines the <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'>Alt</span></b> key may have been hijacked by
1955the operating system; use <b style='mso-bidi-font-weight:normal'><span
1956style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1957mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms.
1958After sorting by magnitude, my list is now </p>
1959
1960<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1961 id="Picture_x0020_17" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:525pt;
1962 height:417pt;visibility:visible;mso-wrap-style:square'>
1963 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image022.png" o:title=""/>
1964</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=556
1965src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1966
1967<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out
1968into two groups with a clear gap between M79 and M64. The higher ones are
1969likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit
1970of ambiguity in the middle, but just assign the top 11 as O and the rest as C
1971and see what happens. You can do this by selecting a block of atoms, go to <b
1972style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1973mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1974atom parameters</span></b> and select <b style='mso-bidi-font-weight:normal'><span
1975style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1976mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a periodic
1977table will appear. Select the desired element and they will be changed in the
1978list and drawing.</p>
1979
1980<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1981 id="Picture_x0020_18" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:7in;
1982 height:405.75pt;visibility:visible;mso-wrap-style:square'>
1983 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image023.png" o:title=""
1984  croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/>
1985</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=541
1986src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
1987
1988<p class=MsoNormal>The original charge flipping solution is still visible and the
1989atoms are now identified, I’ve changed the drawing to show balls and sticks and
1990labeled the atoms with their names, this is done in the <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'>Draw atoms</span></b> tab. Double
1993click the appropriate column heading and make the selection from the dialog
1994box.<span style='mso-spacerun:yes'>  </span></p>
1995
1996<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1997 id="Picture_x0020_19" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:450pt;
1998 height:415.5pt;visibility:visible;mso-wrap-style:square'>
1999 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image025.png" o:title=""/>
2000</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=554
2001src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
2002
2003<p class=MsoNormal>Now one can safely remove the map peaks (do <b
2004style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2005mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
2006peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span
2007style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2008mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
2009charge flip map (do <b style='mso-bidi-font-weight:normal'><span
2010style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2011mso-hansi-theme-font:minor-latin'>Clear map</span></b> in the <b
2012style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2013mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2014tab). The atom positions I obtained have two atoms (O3 &amp; O4) not connected
2015to the sucrose molecule because they belong to neighboring molecules. We need
2016to discover the equivalent ones that belong to this molecule. Follow the steps:</p>
2017
2018<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2019mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2020"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2021</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2022style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2023mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> tab and select them
2024(hold the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2025mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ctrl</span></b>
2026key down and select the appropriate rows). </p>
2027
2028<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2029mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2030"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2031</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2032style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2033mso-hansi-theme-font:minor-latin'>Edit/Fill unit cell</span></b>; new atoms
2034will appear at end of list and in the drawing. </p>
2035
2036<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2037mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2038"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2039</span></span></span><![endif]>Select all the atoms in the <b style='mso-bidi-font-weight:
2040normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2041minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table by a
2042double click on upper left corner box of the table.</p>
2043
2044<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2045mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2046"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2047</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2048style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2049mso-hansi-theme-font:minor-latin'>Edit/Fill CN-sphere</span></b>; new atoms
2050will appear that are bonded to the molecule.</p>
2051
2052<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2053mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2054"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2055</span></span></span><![endif]>Select these new atoms that are in the molecule;
2056they will probably be outside the unit cell box. Do this on the drawing with <b
2057style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2058mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift left</span></b>
2059for the first one &amp; <b style='mso-bidi-font-weight:normal'><span
2060style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2061mso-hansi-theme-font:minor-latin'>Shift right</span></b> for the rest, they
2062will show in green. </p>
2063
2064<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2065mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2066"Times New Roman"'><span style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2067</span></span></span><![endif]>Look at the <b style='mso-bidi-font-weight:normal'><span
2068style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2069mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the
2070selections and make note of the <b style='mso-bidi-font-weight:normal'><span
2071style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2072mso-hansi-theme-font:minor-latin'>Sym Op</span></b> for each one. In my case
2073they were “<b style='mso-bidi-font-weight:normal'><span style='font-family:
2074"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2075minor-latin'>2+1,0,0</span></b>” for O(4) and “<b style='mso-bidi-font-weight:
2076normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2077minor-latin;mso-hansi-theme-font:minor-latin'>2+2,-1,1</span></b>” for O(3).
2078The first number is the symmetry operator number and the 3 numbers after the ‘<b
2079style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2080mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’
2081are unit cell translations.</p>
2082
2083<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2084mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2085"Times New Roman"'><span style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2086</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2087style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2088mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab.</p>
2089
2090<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2091mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2092"Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2093</span></span></span><![endif]>Select an atom in turn that needs to be moved,
2094e.g. in my case O(3) or O(4). </p>
2095
2096<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2097mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2098"Times New Roman"'><span style='mso-list:Ignore'>9.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2099</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2100style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2101mso-hansi-theme-font:minor-latin'>Edit/Transform atoms</span></b>, select the
2102operator and unit cell translations, then press <b style='mso-bidi-font-weight:
2103normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2104minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom
2105coordinates will be transformed.</p>
2106
2107<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2108mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2109"Times New Roman"'><span style='mso-list:Ignore'>10.<span style='font:7.0pt "Times New Roman"'>&nbsp;
2110</span></span></span><![endif]>Repeat 8 &amp; 9 for any other atoms to be
2111moved.</p>
2112
2113<p class=MsoNormal style='margin-left:.5in'>This will complete the molecule
2114with the extra atoms. Do <b style='mso-bidi-font-weight:normal'><span
2115style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2116mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b> to see the
2117completed molecule. I’ve made it a balls &amp; sticks with names as labels.</p>
2118
2119<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2120 id="Picture_x0020_20" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:7in;
2121 height:6in;visibility:visible;mso-wrap-style:square'>
2122 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image026.png" o:title=""
2123  cropbottom="28348f" cropleft="41090f" cropright="9483f"/>
2124</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=576
2125src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
2126
2127<p class=MsoNormal>Save the project file; the next step is to complete the
2128structure by finding H-atoms and then do the final Rietveld refinements.</p>
2129
2130<h2>Step 5: Complete the structure</h2>
2131
2132<p class=MsoNormal>To complete the structure you will need to perform a
2133preliminary Rietveld refinement. This will make the atom positions more
2134accurate and prepare a set of calculated structure factors needed to generate a
2135difference Fourier map good enough to maybe reveal the H atoms. There are a
2136number of steps needed to set all the controls from the previous Pawley
2137refinement to get a successful start for the Rietveld refinement.</p>
2138
2139<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2140mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2141"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2142</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2143style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2144mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the
2145GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span
2146style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2147mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You don’t want to
2148start with these when the scale factor is unknown.</p>
2149
2150<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2151mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2152"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2153</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
2154style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2155mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b
2156style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2157mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2158scale factor</span></b> box. This is the scale factor for the data set. Uncheck
2159the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2160mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X
2161displ</span></b>.</p>
2162
2163<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2164mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2165"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2166</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
2167style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2168mso-hansi-theme-font:minor-latin'>Phases/sucrose General</span></b> tab and
2169uncheck <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'>Refine unit
2171cell</span></b> and <b style='mso-bidi-font-weight:normal'><span
2172style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2173mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The
2174latter is most important; if you forget you will just get another Pawley
2175refinement!</p>
2176
2177<p class=MsoNormal>Now do <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'>Calculate/Refine</span></b> from the main
2180GSAS-II data tree menu; only scale and background are refined. I got a Rwp
2181~20%. The plot shows clear intensity differences; the atom positions obviously
2182need refinement.</p>
2183
2184<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2185 id="Picture_x0020_21" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:502.5pt;
2186 height:430.5pt;visibility:visible;mso-wrap-style:square'>
2187 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/>
2188</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=574
2189src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
2190
2191<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
2192obvious.</p>
2193
2194<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
2195style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2196mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and select the <b
2197style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2198mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2199tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub>
2200has an arbitrary location along the y-axis. Then double click the <b
2201style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2202mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
2203column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight:
2204normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2205minor-latin;mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and
2206press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2207mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2208The atoms table will show the refinement controls</p>
2209
2210<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2211 id="Picture_x0020_22" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
2212 height:225pt;visibility:visible;mso-wrap-style:square'>
2213 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/>
2214</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
2215src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
2216
2217<p class=MsoNormal>To deal with the warning we need to set a “Hold” on one atom
2218y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span
2219style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2220mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II
2221data tree.</p>
2222
2223<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2224 id="Picture_x0020_23" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:225pt;
2225 height:187.5pt;visibility:visible;mso-wrap-style:square'>
2226 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image030.png" o:title=""/>
2227</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
2228src="Charge%20Flipping%20-%20sucrose_files/image030.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
2229
2230<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
2231style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2232mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
2233style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2234mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0::dAy:0 for
2235O(1)</span></b>’ from the dialog box. This will fix the shift along y for the
2236O(1) atom.</p>
2237
2238<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2239 id="Picture_x0020_53" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:259.5pt;
2240 height:271.5pt;visibility:visible;mso-wrap-style:square'>
2241 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/>
2242</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=362
2243src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
2244
2245<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2246style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2247mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will
2248show the hold</p>
2249
2250<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2251 id="Picture_x0020_54" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:225pt;
2252 height:187.5pt;visibility:visible;mso-wrap-style:square'>
2253 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image032.png" o:title=""/>
2254</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
2255src="Charge%20Flipping%20-%20sucrose_files/image032.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
2256
2257<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
2258style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2259mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my Rwp is
2260now ~10.3%. You can now safely refine lattice parameters (in the <b
2261style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2262mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2263tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2264mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>),
2265the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2266mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
2267parameters</span></b> <b style='mso-bidi-font-weight:normal'><span
2268style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2269mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
2270normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2271minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b
2272style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2273mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
2274<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2275mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2276&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2277mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2278and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2279mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X
2280displ</span></b>. You can also include refinement of atom thermal motion (U<sub>iso</sub>)
2281parameters. My refinement improved slightly to Rwp~10.0%. Let’s see if a
2282difference Fourier map will show anything.<br>
2283Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2284mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose
2285General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
2286style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2287mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway down
2288the window.</p>
2289
2290<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2291mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2292"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2293</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
2294style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2295mso-hansi-theme-font:minor-latin'>delt-F</span></b> for the <b
2296style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2297mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
2298
2299<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2300mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2301"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2302</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
2303style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2304mso-hansi-theme-font:minor-latin'>PWDR 11bmb_8716.fxye Bank 1</span></b> for
2305the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2306mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
2307set from</span></b> item (the only choice). The Fourier calculation will use
2308the structure factors shown in the <b style='mso-bidi-font-weight:normal'><span
2309style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2310mso-hansi-theme-font:minor-latin'>Reflection list</span></b> item for this PWDR
2311data set.</p>
2312
2313<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2314mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2315"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2316</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2317style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2318mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b
2319style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2320mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2321tab window. The map will be computed via fast Fourier techniques and is very
2322fast. A few lines summarizing the map is printed on the console, the structure
2323plot may show a single green dot somewhere (it could be hidden beneath an
2324atom!), this is the highest point in the map.</p>
2325
2326<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2327mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2328"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2329</span></span></span><![endif]>Go to the <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'>Draw Options</span></b> tab and adjust the <b
2332style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2333mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
2334level</span></b> slider until something appears on the map. You can also reduce
2335the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2336mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
2337to help clarify the view.</p>
2338
2339<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2340 id="Picture_x0020_35" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:502.5pt;
2341 height:435.75pt;visibility:visible;mso-wrap-style:square'>
2342 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title=""
2343  croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/>
2344</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=581
2345src="Charge%20Flipping%20-%20sucrose_files/image034.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
2346
2347<p class=MsoNormal>What is drawn here are green dots whose size are
2348proportional to the electron density. There are peaks that might be H-atom
2349positions as well as features that suggest C &amp; O-atoms out of position.
2350Recall that the refinement was just done without any H-atoms; it will make the
2351best fit compensating for the missing H-atoms by displacing the C &amp; O atoms
2352in the direction of the missing H-atoms. </p>
2353
2354<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2355mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2356"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2357</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2358style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2359mso-hansi-theme-font:minor-latin'>Phases/sucrose<span
2360style='mso-spacerun:yes'>  </span>Draw Atoms</span></b> tab.</p>
2361
2362<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2363mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2364"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2365</span></span></span><![endif]>Select a C or O atom with possible H-atom
2366density nearby. It will appear green. Do <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'>Edit/View point</span></b>; this will
2369position the cross on the selected atom.</p>
2370
2371<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2372mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2373"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2374</span></span></span><![endif]>Using the mouse, position the multicolored cross
2375directly in the center of the nearby H atom peak. Rotate the drawing around
2376with the left mouse button and shift the cross with the right mouse button. You
2377can zoom in using the roll wheel on the mouse (or else use the <b
2378style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2379mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Camera
2380distance</span></b> slider in the <b style='mso-bidi-font-weight:normal'><span
2381style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2382mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab if your mouse
2383lacks a wheel).</p>
2384
2385<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2386 id="Picture_x0020_36" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:7in;
2387 height:435.75pt;visibility:visible;mso-wrap-style:square'>
2388 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""
2389  croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/>
2390</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=581
2391src="Charge%20Flipping%20-%20sucrose_files/image036.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
2392
2393<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2394mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2395"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2396</span></span></span><![endif]>Go to the Atoms tab and do <b style='mso-bidi-font-weight:
2397normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2398minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>,
2399a white ball will appear at the selected position and an H-atom (name = <b
2400style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2401mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>)
2402will be appended to the end of the atom list. Repeat steps 1-4 for as many
2403recognizable H-atom positions you can find; the goal is to find all 22 of them
2404(you probably will find less than that, but you could guess many of the rest).
2405I easily found all but 5 of them.</p>
2406
2407<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2408 id="Picture_x0020_38" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:7in;
2409 height:427.5pt;visibility:visible;mso-wrap-style:square'>
2410 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image037.png" o:title=""
2411  croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/>
2412</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=570
2413src="Charge%20Flipping%20-%20sucrose_files/image038.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
2414
2415<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2416mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2417"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2418</span></span></span><![endif]>Change their <b style='mso-bidi-font-weight:
2419normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2420minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> to <b
2421style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2422mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>,
2423they will be renamed and make then all ball &amp; stick. Do a <b
2424style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2425mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
2426there should be a drop in Rwp. Then repeat the <b style='mso-bidi-font-weight:
2427normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2428minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> in
2429the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2430mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2431tab, adjust the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2432"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2433minor-latin'>Contour level</span></b> and <b style='mso-bidi-font-weight:normal'><span
2434style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2435mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for the
2436remaining H-atoms; you may have to guess positions for some of them using known
2437stereochemistry rules. My model looked like</p>
2438
2439<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2440 id="Picture_x0020_39" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:502.5pt;
2441 height:421.5pt;visibility:visible;mso-wrap-style:square'>
2442 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image039.png" o:title=""
2443  croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/>
2444</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=562
2445src="Charge%20Flipping%20-%20sucrose_files/image040.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
2446
2447<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2448style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2449mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> to finish this
2450stage in the structure analysis. My Rwp was ~8.02% with all the H-atoms
2451included (but not refined). The fit looks pretty good</p>
2452
2453<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2454 id="Picture_x0020_40" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
2455 height:450pt;visibility:visible;mso-wrap-style:square'>
2456 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image041.png" o:title=""/>
2457</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2458src="Charge%20Flipping%20-%20sucrose_files/image041.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
2459
2460<h2>Step 6: Final refinement</h2>
2461
2462<p class=MsoNormal>Looking at the fit, there may be room for improvement and
2463we’d like to refine the H-atom positions. First we need to change the profile
2464model to include crystallite size and mustrain broadening. Go to <b
2465style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2466mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
2467Parameters</span></b>, set <b style='mso-bidi-font-weight:normal'><span
2468style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2469mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
2470normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2471minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> to <b
2472style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2473mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>zero</span></b>
2474and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2475"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2476minor-latin'>Refine</span></b> flags for them.</p>
2477
2478<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
2479style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2480mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and look at the <b
2481style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2482mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
2483tab; make sure the <b style='mso-bidi-font-weight:normal'><span
2484style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2485mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the
2486boxes for both <b style='mso-bidi-font-weight:normal'><span style='font-family:
2487"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2488minor-latin'>Cryst. size</span></b> and <b style='mso-bidi-font-weight:normal'><span
2489style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2490mso-hansi-theme-font:minor-latin'>microstrain</span></b>.</p>
2491
2492<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2493 id="Picture_x0020_41" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:480pt;
2494 height:339pt;visibility:visible;mso-wrap-style:square'>
2495 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/>
2496</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=452
2497src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
2498
2499<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2500style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2501mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the Rwp will
2502start out high but should converge to where it was before this change. I got
25038.08% and the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2504"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2505minor-latin'>Data tab</span></b> looked like</p>
2506
2507<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2508 id="Picture_x0020_42" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:480pt;
2509 height:334.5pt;visibility:visible;mso-wrap-style:square'>
2510 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image043.png" o:title=""/>
2511</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=446
2512src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
2513
2514<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
2515style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2516mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <b
2517style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2518mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Mustrain
2519model</span></b>; this is the Stephens phenomenological model for microstrain
2520which has 9 terms for monoclinic structures. Check all the boxes for it.</p>
2521
2522<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2523 id="Picture_x0020_43" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:480pt;
2524 height:303.75pt;visibility:visible;mso-wrap-style:square'>
2525 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image044.png" o:title=""/>
2526</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=405
2527src="Charge%20Flipping%20-%20sucrose_files/image044.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
2528
2529<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2530style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2531mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the Rwp will
2532start out high but should converge lower than where it was before this change.
2533I got 7.65% and the <b style='mso-bidi-font-weight:normal'><span
2534style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2535mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like. If you check
2536the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2537mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Mustrain</span></b>
2538button in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2539"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2540minor-latin'>Select plot type</span></b> box, you will see the interesting
2541mustrain surface plot for ground sucrose.</p>
2542
2543<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2544 id="Picture_x0020_45" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:480pt;
2545 height:305.25pt;visibility:visible;mso-wrap-style:square'>
2546 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image045.png" o:title=""/>
2547</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=407
2548src="Charge%20Flipping%20-%20sucrose_files/image045.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
2549
2550<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2551style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2552mso-hansi-theme-font:minor-latin;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2553 id="Picture_x0020_47" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
2554 height:450pt;visibility:visible;mso-wrap-style:square'>
2555 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image046.png" o:title=""/>
2556</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2557src="Charge%20Flipping%20-%20sucrose_files/image046.png" v:shapes="Picture_x0020_47"><![endif]></span></b></p>
2558
2559<p class=MsoNormal>Before refining H-atom positions it would be wise to create
2560restraints on their bond distances and angles. Locate <b style='mso-bidi-font-weight:
2561normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2562minor-latin;mso-hansi-theme-font:minor-latin'>Restraints</span></b> in the main
2563GSAS-II data tree; there will be an almost blank window telling you there are
2564no bond restraints for sucrose. Do <b style='mso-bidi-font-weight:normal'><span
2565style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2566mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
2567will appear asking for the origin atom for the bond. </p>
2568
2569<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2570 id="Picture_x0020_48" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:259.5pt;
2571 height:252pt;visibility:visible;mso-wrap-style:square'>
2572 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image047.png" o:title=""/>
2573</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
2574src="Charge%20Flipping%20-%20sucrose_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
2575
2576<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2577style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2578mso-hansi-theme-font:minor-latin'>all H</span></b> and press <b
2579style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2580mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2581A new dialog box will appear asking for the target atoms for the bonds.</p>
2582
2583<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2584 id="Picture_x0020_49" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:259.5pt;
2585 height:252pt;visibility:visible;mso-wrap-style:square'>
2586 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image048.png" o:title=""/>
2587</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
2588src="Charge%20Flipping%20-%20sucrose_files/image048.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
2589
2590<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2591style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2592mso-hansi-theme-font:minor-latin'>all C</span></b> and <b style='mso-bidi-font-weight:
2593normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2594minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b> and a third
2595dialog box appears asking for the bond length</p>
2596
2597<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2598 id="Picture_x0020_50" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:147pt;
2599 height:78.75pt;visibility:visible;mso-wrap-style:square'>
2600 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image049.png" o:title=""/>
2601</v:shape><![endif]--><![if !vml]><img border=0 width=196 height=105
2602src="Charge%20Flipping%20-%20sucrose_files/image049.png" v:shapes="Picture_x0020_50"><![endif]></span><span
2603style='mso-spacerun:yes'> </span></p>
2604
2605<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
2606style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2607mso-hansi-theme-font:minor-latin'>1.09</span></b> and press <b
2608style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2609mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2610I got a short list of 8 H-C and H-O restraints, but I expect 22 of them. Change
2611the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2612mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Search range</span></b>
2613to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2614mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.5</span></b>
2615and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
2616"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2617minor-latin'>Edit/Add restraints</span></b>. There are now 22 restraints on H-C
2618and H-O bond lengths.</p>
2619
2620<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2621 id="Picture_x0020_51" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:450pt;
2622 height:423pt;visibility:visible;mso-wrap-style:square'>
2623 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image050.png" o:title=""/>
2624</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=564
2625src="Charge%20Flipping%20-%20sucrose_files/image050.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
2626
2627<p class=MsoNormal>Next select the <b style='mso-bidi-font-weight:normal'><span
2628style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2629mso-hansi-theme-font:minor-latin'>Angle restraints</span></b> tab and again
2630there aren’t any. Do <b style='mso-bidi-font-weight:normal'><span
2631style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2632mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
2633will appear asking for the A atom in the angle A-B-C. Select <b
2634style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2635mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all H</span></b>.
2636The next dialog asks for the B atom in the A-B-C angle, select <b
2637style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2638mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all C</span></b>
2639and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2640mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b>.
2641The third dialog asks for the angle and has a default of <b style='mso-bidi-font-weight:
2642normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2643minor-latin;mso-hansi-theme-font:minor-latin'>109.54</span></b>. This is the
2644tetrahedral angle so just press <b style='mso-bidi-font-weight:normal'><span
2645style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2646mso-hansi-theme-font:minor-latin'>OK</span></b>. 36 restraints will be listed;
2647they are listed in order of the B atom. O-atoms should have one angle apiece;
2648C-atoms will have more. </p>
2649
2650<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2651 id="Picture_x0020_52" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:450pt;
2652 height:365.25pt;visibility:visible;mso-wrap-style:square'>
2653 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image051.png" o:title=""/>
2654</v:shape><![endif]--><![if !vml]><img border=0 width=600 height=487
2655src="Charge%20Flipping%20-%20sucrose_files/image051.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
2656
2657<p class=MsoNormal>Now go back the <b style='mso-bidi-font-weight:normal'><span
2658style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2659mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab in <b style='mso-bidi-font-weight:
2660normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2661minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>, select
2662<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2663mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>
2664from the dialog box by double clicking on the <b style='mso-bidi-font-weight:
2665normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2666minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column. Then do <b
2667style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2668mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Set
2669atom refinement flags</span></b>. Select <b style='mso-bidi-font-weight:normal'><span
2670style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2671mso-hansi-theme-font:minor-latin'>X-coordinates</span></b>; this will set those
2672for all H-atoms. Now do <b style='mso-bidi-font-weight:normal'><span
2673style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2674mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>, the console will
2675list progress on the “Penalty function” (i.e. the restraints) and the Rwp drops
2676in my case to ~7.05%. One can increase the <b style='mso-bidi-font-weight:normal'><span
2677style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2678mso-hansi-theme-font:minor-latin'>Restraint weight factors</span></b> to
2679tighten them up at some expense in Rwp. In the end I chose <b style='mso-bidi-font-weight:
2680normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2681minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b> for both <b
2682style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2683mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond</span></b>
2684and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2685mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b>
2686restraints to give a final Rwp ~7.1%. NB: the H-atom positions may not be
2687correct even though the refinement apparently succeeded. You should check that
2688the OH ones all give reasonable H-bonds to neighboring O-atoms. As this is
2689powder data such changes will hardly affect the fit but will be more
2690satisfying. At present such checking is outside the scope of GSAS-II.</p>
2691
2692<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2693
2694<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2695
2696</div>
2697
2698</body>
2699
2700</html>
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