source: Tutorials/CFsucrose/Charge Flipping - sucrose.htm @ 1941

Last change on this file since 1941 was 1941, checked in by vondreele, 6 years ago
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414  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
415  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
416  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
417  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
418  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
419  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
420  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
421  <w:LsdException Locked="false" Priority="34" QFormat="true"
422   Name="List Paragraph"/>
423  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
424  <w:LsdException Locked="false" Priority="30" QFormat="true"
425   Name="Intense Quote"/>
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427  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
428  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
429  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
430  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
431  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
432  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
433  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
434  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
435  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
436  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
437  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
438  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
439  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
440  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
441  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
442  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
443  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
444  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
445  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
446  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
447  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
448  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
449  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
450  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
451  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
452  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
453  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
454  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
455  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
456  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
457  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
458  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
459  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
460  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
461  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
462  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
463  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
464  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
465  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
466  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
467  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
468  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
469  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
470  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
471  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
472  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
473  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
474  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
475  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
476  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
477  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
478  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
479  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
480  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
481  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
482  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
483  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
484  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
485  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
486  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
487  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
488  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
489  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
490  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
491  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
492  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
493  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
494  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
495  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
496  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
497  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
498  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
499  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
500  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
501  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
502  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
503  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
504  <w:LsdException Locked="false" Priority="19" QFormat="true"
505   Name="Subtle Emphasis"/>
506  <w:LsdException Locked="false" Priority="21" QFormat="true"
507   Name="Intense Emphasis"/>
508  <w:LsdException Locked="false" Priority="31" QFormat="true"
509   Name="Subtle Reference"/>
510  <w:LsdException Locked="false" Priority="32" QFormat="true"
511   Name="Intense Reference"/>
512  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
513  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
514   UnhideWhenUsed="true" Name="Bibliography"/>
515  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
516   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
517  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
518  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
519  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
520  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
521  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
522  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
523  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
524  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
525  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
526  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
527  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
528  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
529  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
530  <w:LsdException Locked="false" Priority="46"
531   Name="Grid Table 1 Light Accent 1"/>
532  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
533  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
534  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
535  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
536  <w:LsdException Locked="false" Priority="51"
537   Name="Grid Table 6 Colorful Accent 1"/>
538  <w:LsdException Locked="false" Priority="52"
539   Name="Grid Table 7 Colorful Accent 1"/>
540  <w:LsdException Locked="false" Priority="46"
541   Name="Grid Table 1 Light Accent 2"/>
542  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
543  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
544  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
545  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
546  <w:LsdException Locked="false" Priority="51"
547   Name="Grid Table 6 Colorful Accent 2"/>
548  <w:LsdException Locked="false" Priority="52"
549   Name="Grid Table 7 Colorful Accent 2"/>
550  <w:LsdException Locked="false" Priority="46"
551   Name="Grid Table 1 Light Accent 3"/>
552  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
553  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
554  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
555  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
556  <w:LsdException Locked="false" Priority="51"
557   Name="Grid Table 6 Colorful Accent 3"/>
558  <w:LsdException Locked="false" Priority="52"
559   Name="Grid Table 7 Colorful Accent 3"/>
560  <w:LsdException Locked="false" Priority="46"
561   Name="Grid Table 1 Light Accent 4"/>
562  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
563  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
564  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
565  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
566  <w:LsdException Locked="false" Priority="51"
567   Name="Grid Table 6 Colorful Accent 4"/>
568  <w:LsdException Locked="false" Priority="52"
569   Name="Grid Table 7 Colorful Accent 4"/>
570  <w:LsdException Locked="false" Priority="46"
571   Name="Grid Table 1 Light Accent 5"/>
572  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
573  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
574  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
575  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
576  <w:LsdException Locked="false" Priority="51"
577   Name="Grid Table 6 Colorful Accent 5"/>
578  <w:LsdException Locked="false" Priority="52"
579   Name="Grid Table 7 Colorful Accent 5"/>
580  <w:LsdException Locked="false" Priority="46"
581   Name="Grid Table 1 Light Accent 6"/>
582  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
583  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
584  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
585  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
586  <w:LsdException Locked="false" Priority="51"
587   Name="Grid Table 6 Colorful Accent 6"/>
588  <w:LsdException Locked="false" Priority="52"
589   Name="Grid Table 7 Colorful Accent 6"/>
590  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
591  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
592  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
593  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
594  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
595  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
596  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
597  <w:LsdException Locked="false" Priority="46"
598   Name="List Table 1 Light Accent 1"/>
599  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
600  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
601  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
602  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
603  <w:LsdException Locked="false" Priority="51"
604   Name="List Table 6 Colorful Accent 1"/>
605  <w:LsdException Locked="false" Priority="52"
606   Name="List Table 7 Colorful Accent 1"/>
607  <w:LsdException Locked="false" Priority="46"
608   Name="List Table 1 Light Accent 2"/>
609  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
610  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
611  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
612  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
613  <w:LsdException Locked="false" Priority="51"
614   Name="List Table 6 Colorful Accent 2"/>
615  <w:LsdException Locked="false" Priority="52"
616   Name="List Table 7 Colorful Accent 2"/>
617  <w:LsdException Locked="false" Priority="46"
618   Name="List Table 1 Light Accent 3"/>
619  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
620  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
621  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
622  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
623  <w:LsdException Locked="false" Priority="51"
624   Name="List Table 6 Colorful Accent 3"/>
625  <w:LsdException Locked="false" Priority="52"
626   Name="List Table 7 Colorful Accent 3"/>
627  <w:LsdException Locked="false" Priority="46"
628   Name="List Table 1 Light Accent 4"/>
629  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
630  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
631  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
632  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
633  <w:LsdException Locked="false" Priority="51"
634   Name="List Table 6 Colorful Accent 4"/>
635  <w:LsdException Locked="false" Priority="52"
636   Name="List Table 7 Colorful Accent 4"/>
637  <w:LsdException Locked="false" Priority="46"
638   Name="List Table 1 Light Accent 5"/>
639  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
640  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
641  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
642  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
643  <w:LsdException Locked="false" Priority="51"
644   Name="List Table 6 Colorful Accent 5"/>
645  <w:LsdException Locked="false" Priority="52"
646   Name="List Table 7 Colorful Accent 5"/>
647  <w:LsdException Locked="false" Priority="46"
648   Name="List Table 1 Light Accent 6"/>
649  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
650  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
651  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
652  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
653  <w:LsdException Locked="false" Priority="51"
654   Name="List Table 6 Colorful Accent 6"/>
655  <w:LsdException Locked="false" Priority="52"
656   Name="List Table 7 Colorful Accent 6"/>
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783        mso-style-priority:9;
784        mso-style-unhide:no;
785        mso-style-locked:yes;
786        mso-style-link:"Heading 2";
787        mso-ansi-font-size:18.0pt;
788        mso-bidi-font-size:18.0pt;
789        font-family:"Times New Roman",serif;
790        mso-ascii-font-family:"Times New Roman";
791        mso-fareast-font-family:"Times New Roman";
792        mso-fareast-theme-font:minor-fareast;
793        mso-hansi-font-family:"Times New Roman";
794        mso-bidi-font-family:"Times New Roman";
795        font-weight:bold;}
796span.BalloonTextChar
797        {mso-style-name:"Balloon Text Char";
798        mso-style-noshow:yes;
799        mso-style-priority:99;
800        mso-style-unhide:no;
801        mso-style-locked:yes;
802        mso-style-link:"Balloon Text";
803        mso-ansi-font-size:8.0pt;
804        mso-bidi-font-size:8.0pt;
805        font-family:"Tahoma",sans-serif;
806        mso-ascii-font-family:Tahoma;
807        mso-fareast-font-family:"Times New Roman";
808        mso-fareast-theme-font:minor-fareast;
809        mso-hansi-font-family:Tahoma;
810        mso-bidi-font-family:Tahoma;}
811span.SpellE
812        {mso-style-name:"";
813        mso-spl-e:yes;}
814span.GramE
815        {mso-style-name:"";
816        mso-gram-e:yes;}
817.MsoChpDefault
818        {mso-style-type:export-only;
819        mso-default-props:yes;
820        font-size:12.0pt;
821        mso-ansi-font-size:12.0pt;
822        mso-bidi-font-size:12.0pt;
823        mso-fareast-font-family:Calibri;
824        mso-fareast-theme-font:minor-latin;
825        mso-bidi-font-family:"Times New Roman";
826        mso-bidi-theme-font:minor-bidi;}
827@page WordSection1
828        {size:8.5in 11.0in;
829        margin:1.0in 1.0in 1.0in 1.0in;
830        mso-header-margin:.5in;
831        mso-footer-margin:.5in;
832        mso-paper-source:0;}
833div.WordSection1
834        {page:WordSection1;}
835 /* List Definitions */
836 @list l0
837        {mso-list-id:82917343;
838        mso-list-type:hybrid;
839        mso-list-template-ids:-1527319822 -2100533712 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
840@list l0:level1
841        {mso-level-tab-stop:none;
842        mso-level-number-position:left;
843        margin-left:.75in;
844        text-indent:-.25in;}
845@list l0:level2
846        {mso-level-number-format:alpha-lower;
847        mso-level-tab-stop:none;
848        mso-level-number-position:left;
849        margin-left:1.25in;
850        text-indent:-.25in;}
851@list l0:level3
852        {mso-level-number-format:roman-lower;
853        mso-level-tab-stop:none;
854        mso-level-number-position:right;
855        margin-left:1.75in;
856        text-indent:-9.0pt;}
857@list l0:level4
858        {mso-level-tab-stop:none;
859        mso-level-number-position:left;
860        margin-left:2.25in;
861        text-indent:-.25in;}
862@list l0:level5
863        {mso-level-number-format:alpha-lower;
864        mso-level-tab-stop:none;
865        mso-level-number-position:left;
866        margin-left:2.75in;
867        text-indent:-.25in;}
868@list l0:level6
869        {mso-level-number-format:roman-lower;
870        mso-level-tab-stop:none;
871        mso-level-number-position:right;
872        margin-left:3.25in;
873        text-indent:-9.0pt;}
874@list l0:level7
875        {mso-level-tab-stop:none;
876        mso-level-number-position:left;
877        margin-left:3.75in;
878        text-indent:-.25in;}
879@list l0:level8
880        {mso-level-number-format:alpha-lower;
881        mso-level-tab-stop:none;
882        mso-level-number-position:left;
883        margin-left:4.25in;
884        text-indent:-.25in;}
885@list l0:level9
886        {mso-level-number-format:roman-lower;
887        mso-level-tab-stop:none;
888        mso-level-number-position:right;
889        margin-left:4.75in;
890        text-indent:-9.0pt;}
891@list l1
892        {mso-list-id:236667377;
893        mso-list-type:hybrid;
894        mso-list-template-ids:-513138304 1385070818 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
895@list l1:level1
896        {mso-level-tab-stop:none;
897        mso-level-number-position:left;
898        margin-left:.75in;
899        text-indent:-.25in;}
900@list l1:level2
901        {mso-level-number-format:alpha-lower;
902        mso-level-tab-stop:none;
903        mso-level-number-position:left;
904        margin-left:1.25in;
905        text-indent:-.25in;}
906@list l1:level3
907        {mso-level-number-format:roman-lower;
908        mso-level-tab-stop:none;
909        mso-level-number-position:right;
910        margin-left:1.75in;
911        text-indent:-9.0pt;}
912@list l1:level4
913        {mso-level-tab-stop:none;
914        mso-level-number-position:left;
915        margin-left:2.25in;
916        text-indent:-.25in;}
917@list l1:level5
918        {mso-level-number-format:alpha-lower;
919        mso-level-tab-stop:none;
920        mso-level-number-position:left;
921        margin-left:2.75in;
922        text-indent:-.25in;}
923@list l1:level6
924        {mso-level-number-format:roman-lower;
925        mso-level-tab-stop:none;
926        mso-level-number-position:right;
927        margin-left:3.25in;
928        text-indent:-9.0pt;}
929@list l1:level7
930        {mso-level-tab-stop:none;
931        mso-level-number-position:left;
932        margin-left:3.75in;
933        text-indent:-.25in;}
934@list l1:level8
935        {mso-level-number-format:alpha-lower;
936        mso-level-tab-stop:none;
937        mso-level-number-position:left;
938        margin-left:4.25in;
939        text-indent:-.25in;}
940@list l1:level9
941        {mso-level-number-format:roman-lower;
942        mso-level-tab-stop:none;
943        mso-level-number-position:right;
944        margin-left:4.75in;
945        text-indent:-9.0pt;}
946@list l2
947        {mso-list-id:533275380;
948        mso-list-type:hybrid;
949        mso-list-template-ids:-1319630076 -1606007952 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
950@list l2:level1
951        {mso-level-tab-stop:none;
952        mso-level-number-position:left;
953        margin-left:.75in;
954        text-indent:-.25in;}
955@list l2:level2
956        {mso-level-number-format:alpha-lower;
957        mso-level-tab-stop:none;
958        mso-level-number-position:left;
959        margin-left:1.25in;
960        text-indent:-.25in;}
961@list l2:level3
962        {mso-level-number-format:roman-lower;
963        mso-level-tab-stop:none;
964        mso-level-number-position:right;
965        margin-left:1.75in;
966        text-indent:-9.0pt;}
967@list l2:level4
968        {mso-level-tab-stop:none;
969        mso-level-number-position:left;
970        margin-left:2.25in;
971        text-indent:-.25in;}
972@list l2:level5
973        {mso-level-number-format:alpha-lower;
974        mso-level-tab-stop:none;
975        mso-level-number-position:left;
976        margin-left:2.75in;
977        text-indent:-.25in;}
978@list l2:level6
979        {mso-level-number-format:roman-lower;
980        mso-level-tab-stop:none;
981        mso-level-number-position:right;
982        margin-left:3.25in;
983        text-indent:-9.0pt;}
984@list l2:level7
985        {mso-level-tab-stop:none;
986        mso-level-number-position:left;
987        margin-left:3.75in;
988        text-indent:-.25in;}
989@list l2:level8
990        {mso-level-number-format:alpha-lower;
991        mso-level-tab-stop:none;
992        mso-level-number-position:left;
993        margin-left:4.25in;
994        text-indent:-.25in;}
995@list l2:level9
996        {mso-level-number-format:roman-lower;
997        mso-level-tab-stop:none;
998        mso-level-number-position:right;
999        margin-left:4.75in;
1000        text-indent:-9.0pt;}
1001@list l3
1002        {mso-list-id:588542776;
1003        mso-list-type:hybrid;
1004        mso-list-template-ids:477805396 -2056748102 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1005@list l3:level1
1006        {mso-level-tab-stop:none;
1007        mso-level-number-position:left;
1008        margin-left:.75in;
1009        text-indent:-.25in;}
1010@list l3:level2
1011        {mso-level-number-format:alpha-lower;
1012        mso-level-tab-stop:none;
1013        mso-level-number-position:left;
1014        margin-left:1.25in;
1015        text-indent:-.25in;}
1016@list l3:level3
1017        {mso-level-number-format:roman-lower;
1018        mso-level-tab-stop:none;
1019        mso-level-number-position:right;
1020        margin-left:1.75in;
1021        text-indent:-9.0pt;}
1022@list l3:level4
1023        {mso-level-tab-stop:none;
1024        mso-level-number-position:left;
1025        margin-left:2.25in;
1026        text-indent:-.25in;}
1027@list l3:level5
1028        {mso-level-number-format:alpha-lower;
1029        mso-level-tab-stop:none;
1030        mso-level-number-position:left;
1031        margin-left:2.75in;
1032        text-indent:-.25in;}
1033@list l3:level6
1034        {mso-level-number-format:roman-lower;
1035        mso-level-tab-stop:none;
1036        mso-level-number-position:right;
1037        margin-left:3.25in;
1038        text-indent:-9.0pt;}
1039@list l3:level7
1040        {mso-level-tab-stop:none;
1041        mso-level-number-position:left;
1042        margin-left:3.75in;
1043        text-indent:-.25in;}
1044@list l3:level8
1045        {mso-level-number-format:alpha-lower;
1046        mso-level-tab-stop:none;
1047        mso-level-number-position:left;
1048        margin-left:4.25in;
1049        text-indent:-.25in;}
1050@list l3:level9
1051        {mso-level-number-format:roman-lower;
1052        mso-level-tab-stop:none;
1053        mso-level-number-position:right;
1054        margin-left:4.75in;
1055        text-indent:-9.0pt;}
1056@list l4
1057        {mso-list-id:854225785;
1058        mso-list-type:hybrid;
1059        mso-list-template-ids:-2071413312 1417604178 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1060@list l4:level1
1061        {mso-level-tab-stop:none;
1062        mso-level-number-position:left;
1063        margin-left:.75in;
1064        text-indent:-.25in;}
1065@list l4:level2
1066        {mso-level-number-format:alpha-lower;
1067        mso-level-tab-stop:none;
1068        mso-level-number-position:left;
1069        margin-left:1.25in;
1070        text-indent:-.25in;}
1071@list l4:level3
1072        {mso-level-number-format:roman-lower;
1073        mso-level-tab-stop:none;
1074        mso-level-number-position:right;
1075        margin-left:1.75in;
1076        text-indent:-9.0pt;}
1077@list l4:level4
1078        {mso-level-tab-stop:none;
1079        mso-level-number-position:left;
1080        margin-left:2.25in;
1081        text-indent:-.25in;}
1082@list l4:level5
1083        {mso-level-number-format:alpha-lower;
1084        mso-level-tab-stop:none;
1085        mso-level-number-position:left;
1086        margin-left:2.75in;
1087        text-indent:-.25in;}
1088@list l4:level6
1089        {mso-level-number-format:roman-lower;
1090        mso-level-tab-stop:none;
1091        mso-level-number-position:right;
1092        margin-left:3.25in;
1093        text-indent:-9.0pt;}
1094@list l4:level7
1095        {mso-level-tab-stop:none;
1096        mso-level-number-position:left;
1097        margin-left:3.75in;
1098        text-indent:-.25in;}
1099@list l4:level8
1100        {mso-level-number-format:alpha-lower;
1101        mso-level-tab-stop:none;
1102        mso-level-number-position:left;
1103        margin-left:4.25in;
1104        text-indent:-.25in;}
1105@list l4:level9
1106        {mso-level-number-format:roman-lower;
1107        mso-level-tab-stop:none;
1108        mso-level-number-position:right;
1109        margin-left:4.75in;
1110        text-indent:-9.0pt;}
1111@list l5
1112        {mso-list-id:1022125565;
1113        mso-list-type:hybrid;
1114        mso-list-template-ids:-482838388 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1115@list l5:level1
1116        {mso-level-tab-stop:none;
1117        mso-level-number-position:left;
1118        margin-left:1.0in;
1119        text-indent:-.25in;}
1120@list l5:level2
1121        {mso-level-number-format:alpha-lower;
1122        mso-level-tab-stop:none;
1123        mso-level-number-position:left;
1124        margin-left:1.5in;
1125        text-indent:-.25in;}
1126@list l5:level3
1127        {mso-level-number-format:roman-lower;
1128        mso-level-tab-stop:none;
1129        mso-level-number-position:right;
1130        margin-left:2.0in;
1131        text-indent:-9.0pt;}
1132@list l5:level4
1133        {mso-level-tab-stop:none;
1134        mso-level-number-position:left;
1135        margin-left:2.5in;
1136        text-indent:-.25in;}
1137@list l5:level5
1138        {mso-level-number-format:alpha-lower;
1139        mso-level-tab-stop:none;
1140        mso-level-number-position:left;
1141        margin-left:3.0in;
1142        text-indent:-.25in;}
1143@list l5:level6
1144        {mso-level-number-format:roman-lower;
1145        mso-level-tab-stop:none;
1146        mso-level-number-position:right;
1147        margin-left:3.5in;
1148        text-indent:-9.0pt;}
1149@list l5:level7
1150        {mso-level-tab-stop:none;
1151        mso-level-number-position:left;
1152        margin-left:4.0in;
1153        text-indent:-.25in;}
1154@list l5:level8
1155        {mso-level-number-format:alpha-lower;
1156        mso-level-tab-stop:none;
1157        mso-level-number-position:left;
1158        margin-left:4.5in;
1159        text-indent:-.25in;}
1160@list l5:level9
1161        {mso-level-number-format:roman-lower;
1162        mso-level-tab-stop:none;
1163        mso-level-number-position:right;
1164        margin-left:5.0in;
1165        text-indent:-9.0pt;}
1166@list l6
1167        {mso-list-id:2020618629;
1168        mso-list-type:hybrid;
1169        mso-list-template-ids:-199700640 470186964 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1170@list l6:level1
1171        {mso-level-tab-stop:none;
1172        mso-level-number-position:left;
1173        margin-left:.75in;
1174        text-indent:-.25in;}
1175@list l6:level2
1176        {mso-level-number-format:alpha-lower;
1177        mso-level-tab-stop:none;
1178        mso-level-number-position:left;
1179        margin-left:1.25in;
1180        text-indent:-.25in;}
1181@list l6:level3
1182        {mso-level-number-format:roman-lower;
1183        mso-level-tab-stop:none;
1184        mso-level-number-position:right;
1185        margin-left:1.75in;
1186        text-indent:-9.0pt;}
1187@list l6:level4
1188        {mso-level-tab-stop:none;
1189        mso-level-number-position:left;
1190        margin-left:2.25in;
1191        text-indent:-.25in;}
1192@list l6:level5
1193        {mso-level-number-format:alpha-lower;
1194        mso-level-tab-stop:none;
1195        mso-level-number-position:left;
1196        margin-left:2.75in;
1197        text-indent:-.25in;}
1198@list l6:level6
1199        {mso-level-number-format:roman-lower;
1200        mso-level-tab-stop:none;
1201        mso-level-number-position:right;
1202        margin-left:3.25in;
1203        text-indent:-9.0pt;}
1204@list l6:level7
1205        {mso-level-tab-stop:none;
1206        mso-level-number-position:left;
1207        margin-left:3.75in;
1208        text-indent:-.25in;}
1209@list l6:level8
1210        {mso-level-number-format:alpha-lower;
1211        mso-level-tab-stop:none;
1212        mso-level-number-position:left;
1213        margin-left:4.25in;
1214        text-indent:-.25in;}
1215@list l6:level9
1216        {mso-level-number-format:roman-lower;
1217        mso-level-tab-stop:none;
1218        mso-level-number-position:right;
1219        margin-left:4.75in;
1220        text-indent:-9.0pt;}
1221ol
1222        {margin-bottom:0in;}
1223ul
1224        {margin-bottom:0in;}
1225-->
1226</style>
1227<!--[if gte mso 10]>
1228<style>
1229 /* Style Definitions */
1230 table.MsoNormalTable
1231        {mso-style-name:"Table Normal";
1232        mso-tstyle-rowband-size:0;
1233        mso-tstyle-colband-size:0;
1234        mso-style-noshow:yes;
1235        mso-style-priority:99;
1236        mso-style-parent:"";
1237        mso-padding-alt:0in 5.4pt 0in 5.4pt;
1238        mso-para-margin:0in;
1239        mso-para-margin-bottom:.0001pt;
1240        mso-pagination:widow-orphan;
1241        font-size:12.0pt;
1242        font-family:"Times New Roman",serif;
1243        mso-bidi-font-family:"Times New Roman";
1244        mso-bidi-theme-font:minor-bidi;}
1245</style>
1246<![endif]--><!--[if gte mso 9]><xml>
1247 <o:shapedefaults v:ext="edit" spidmax="1029"/>
1248</xml><![endif]--><!--[if gte mso 9]><xml>
1249 <o:shapelayout v:ext="edit">
1250  <o:idmap v:ext="edit" data="1"/>
1251 </o:shapelayout></xml><![endif]-->
1252</head>
1253
1254<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1255
1256<div class=WordSection1>
1257
1258<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in
1259GSAS-II - sucrose<o:p></o:p></span></h1>
1260
1261<h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1>
1262
1263<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1264of sucrose from powder diffraction data via charge flipping. This structure was
1265originally solved from single crystal data in the space group P2<sub>1</sub>.
1266It is a difficult exercise to complete as the charge flipping does not always
1267yield a solution and to even have a chance the Pawley refinement must be done
1268with particular care. We have given a route that sometimes works.</p>
1269
1270<p class=MsoNormal>If you have not done so already, start GSAS-II and open the
1271GSAS-II project file (I called it <span class=SpellE><b style='mso-bidi-font-weight:
1272normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1273minor-latin;mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b></span>)
1274you saved from the third part of the peak fitting-indexing exercise. If you
1275didn’t do that exercise, do it now.</p>
1276
1277<h2>Step 1: Setup for Pawley refinement</h2>
1278
1279<p class=MsoNormal>There are a number of steps that must be done in preparation
1280for a Pawley refinement after having completed the unit cell indexing and new
1281phase creation. These cover two things: one is to prepare the powder pattern
1282(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1283
1284<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1285style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1286style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1287<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'>Limits</span></b>
1289in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1290region near d=1.0Å is readily seen. This is ~24deg 2<span style='font-family:
1291Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1292mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1293symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
1294relatively clear of peaks that makes a good place to end the calculations with
1295a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution
1296needed for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span
1297style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1298mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span class=SpellE><b
1299style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1300mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b></span>
1301as the upper limit and make a note of the exact d-spacing (1.0125Å) using the
1302mouse cursor on the plot.</p>
1303
1304<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1305style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1306style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1307<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1308mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1309Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1310style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1311mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1312style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1313mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1314profile</span></b> to recover the default values. The peak fitting done earlier
1315is over a much more limited range of 2<span style='font-family:Symbol;
1316mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1317mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1318symbol;mso-symbol-font-family:Symbol'>Q</span></span> giving values that might
1319not extrapolate well over the wider range to be used in the Pawley refinement.
1320We will refine them again later.</p>
1321
1322<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1323style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1324style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1325<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1326mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1327Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1328normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1329minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.
1330While you are here set <b style='mso-bidi-font-weight:normal'><span
1331style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1332mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> to <b
1333style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1334mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>.</p>
1335
1336<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1337style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1338style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1339to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1340mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1341to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1342"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1343minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1344normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1345minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
1346box and enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
1347style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1348mso-hansi-theme-font:minor-latin'>1.0125</span></b>) into the <b
1349style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1350mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1351class=SpellE>dmin</span></span></b> box.</p>
1352
1353<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1354style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1355mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1356
1357<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1358 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1359 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1360 <v:stroke joinstyle="miter"/>
1361 <v:formulas>
1362  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1363  <v:f eqn="sum @0 1 0"/>
1364  <v:f eqn="sum 0 0 @1"/>
1365  <v:f eqn="prod @2 1 2"/>
1366  <v:f eqn="prod @3 21600 pixelWidth"/>
1367  <v:f eqn="prod @3 21600 pixelHeight"/>
1368  <v:f eqn="sum @0 0 1"/>
1369  <v:f eqn="prod @6 1 2"/>
1370  <v:f eqn="prod @7 21600 pixelWidth"/>
1371  <v:f eqn="sum @8 21600 0"/>
1372  <v:f eqn="prod @7 21600 pixelHeight"/>
1373  <v:f eqn="sum @10 21600 0"/>
1374 </v:formulas>
1375 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1376 <o:lock v:ext="edit" aspectratio="t"/>
1377</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1062" type="#_x0000_t75"
1378 style='width:542.25pt;height:375pt;visibility:visible;mso-wrap-style:square'>
1379 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image001.png" o:title=""/>
1380</v:shape><![endif]--><![if !vml]><img width=723 height=500
1381src="Charge%20Flipping%20-%20sucrose_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
1382
1383<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1384style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1385mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1386for some text. Do <b style='mso-bidi-font-weight:normal'><span
1387style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1388mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
1389dialog box will appear</p>
1390
1391<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1392 id="Picture_x0020_2" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:240pt;
1393 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1394 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image002.png" o:title=""/>
1395</v:shape><![endif]--><![if !vml]><img width=320 height=310
1396src="Charge%20Flipping%20-%20sucrose_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1397
1398<p class=MsoNormal>Select the only choice and press <b style='mso-bidi-font-weight:
1399normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1400minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>; the desired data
1401set will be added to this phase for analysis. The data tab now shows the new
1402data set.</p>
1403
1404<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1405 id="Picture_x0020_3" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:359.25pt;
1406 height:375pt;visibility:visible;mso-wrap-style:square'>
1407 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image003.png" o:title=""/>
1408</v:shape><![endif]--><![if !vml]><img width=479 height=500
1409src="Charge%20Flipping%20-%20sucrose_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
1410
1411<p class=MsoNormal>I’ve stretched the window slightly to see the entire
1412contents. This is the location for all the phase dependent parameters for this
1413histogram. Notice that it includes phase fraction, size &amp; <span
1414class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1415and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1416intended for protein work where a significant region of the structure is disordered
1417solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1418surfaces as well as preferred orientation correction curves.</p>
1419
1420<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1421style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1422mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1423empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
1424style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1425mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
1426makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
1427normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1428minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>.
1429The table should list reflections 0~780. Select and check the refine column
1430using the same technique you used for the peak list. </p>
1431
1432<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1433 id="Picture_x0020_4" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:375pt;
1434 height:225pt;visibility:visible;mso-wrap-style:square'>
1435 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image004.png" o:title=""/>
1436</v:shape><![endif]--><![if !vml]><img width=500 height=300
1437src="Charge%20Flipping%20-%20sucrose_files/image004.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
1438
1439<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1440you didn’t skip a step as it might not work correctly if you did.</p>
1441
1442<h2>Step 2: Pawley refinement</h2>
1443
1444<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1445normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1446minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1447the main GSAS-II data tree window. Before it begins a backup of the project
1448file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
1449style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1450mso-hansi-theme-font:minor-latin'>sucrose.bck0.gpx</span></b>. It can be used
1451to recover from a bad refinement. A progress dialog box will appear showing the
1452residual as the refinement proceeds. Notice that there was a singular matrix
1453warning on the console window and perhaps the last reflection (781) was removed
1454from the refinement because it was off the end of the used part of the pattern.
1455This is the GSAS-II singular matrix recovery mechanism; you can go to the <b
1456style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1457mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1458reflections</span></b> tab and uncheck the last reflection. Then repeat <b
1459style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1460mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1461to make sure it has essentially minimized. My refinement completed with <span
1462class=SpellE>Rwp</span> ~25% (NB: here and after succeeding refinements your <span
1463class=SpellE>Rwp</span> values may be slightly different from what I show here);
1464a dialog box appears asking if you wish to load the result. Press <b
1465style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1466mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1467To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
1468the width and height).</p>
1469
1470<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1471 id="Picture_x0020_5" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:525pt;
1472 height:450pt;visibility:visible;mso-wrap-style:square'>
1473 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image005.png" o:title=""/>
1474</v:shape><![endif]--><![if !vml]><img width=700 height=600
1475src="Charge%20Flipping%20-%20sucrose_files/image005.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
1476
1477<p class=MsoNormal>It is evident from examining the plot that some improvement
1478can be had by refining the lattice and profile parameters and perhaps the
1479sample X position. Go to <b style='mso-bidi-font-weight:normal'><span
1480style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1481mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> in the GSAS-II data
1482tree and check the <b style='mso-bidi-font-weight:normal'><span
1483style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1484mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> box. Now select <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'>Instrument
1487parameters</span></b> for the PWDR data set in the GSAS-II data tree and check <b
1488style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1489mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>,
1490<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1491mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>,
1492<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1493mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,<b
1494style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1495mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
1496class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
1497style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1498mso-hansi-theme-font:minor-latin'> Y</span></b>. The go to <b style='mso-bidi-font-weight:
1499normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1500minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and
1501check <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1502mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1503class=SpellE>displ</span></span></b>.; make the <b style='mso-bidi-font-weight:
1504normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1505minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> <b
1506style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1507mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1508if you didn’t do this earlier. Repeat <b style='mso-bidi-font-weight:normal'><span
1509style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1510mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged; I
1511obtained an improved residual of ~7.3% with a much better fit at the high angle
1512part of the pattern but still not fit well for the lower part.</p>
1513
1514<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1515 id="Picture_x0020_6" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:504.75pt;
1516 height:432.75pt;visibility:visible;mso-wrap-style:square'>
1517 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image006.png" o:title=""/>
1518</v:shape><![endif]--><![if !vml]><img width=673 height=577
1519src="Charge%20Flipping%20-%20sucrose_files/image006.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
1520
1521<p class=MsoNormal>What you see is that the background has a substantial
1522diffuse scattering feature at ~5deg and there are some peak shape issues (which
1523may be a consequence of the poor background fit). We’d like the fit to be
1524better before trying charge flipping. First select <b style='mso-bidi-font-weight:
1525normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1526minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>, set <b
1527style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1528mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peaks in
1529background: No. peaks</span></b> to <b style='mso-bidi-font-weight:normal'><span
1530style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1531mso-hansi-theme-font:minor-latin'>1</span></b> from the pull down box; the
1532window changes to </p>
1533
1534<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1535 id="Picture_x0020_7" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:366.75pt;
1536 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1537 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image007.png" o:title=""/>
1538</v:shape><![endif]--><![if !vml]><img width=489 height=263
1539src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_7"><![endif]></span><span
1540style='mso-spacerun:yes'> </span></p>
1541
1542<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
1543style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1544mso-hansi-theme-font:minor-latin'>5.0</span></b> for <span class=SpellE><b
1545style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1546mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span>,
1547<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1548mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
1549for <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1550style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1551mso-hansi-theme-font:minor-latin'>int</span></b></span> and <b
1552style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1553mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1554for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1555mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
1556(as appropriate for broad diffuse peaks) and then check all three refine boxes.
1557Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1558mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
1559class=SpellE>coeff</span>.</span></b> <span class=GramE>pulldown</span> to <b
1560style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1561mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>
1562for the <span class=SpellE>Chebyschev</span> part of the background. The window
1563should look like</p>
1564
1565<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1566 id="Picture_x0020_8" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:439.5pt;
1567 height:199.5pt;visibility:visible;mso-wrap-style:square'>
1568 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image008.png" o:title=""/>
1569</v:shape><![endif]--><![if !vml]><img width=586 height=266
1570src="Charge%20Flipping%20-%20sucrose_files/image008.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1571
1572<p class=MsoNormal>Go to the <b style='mso-bidi-font-weight:normal'><span
1573style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1574mso-hansi-theme-font:minor-latin'>Controls</span></b> item in the GSAS-II data
1575tree and set the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1576"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1577minor-latin'>Max cycles</span></b> to <b style='mso-bidi-font-weight:normal'><span
1578style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1579mso-hansi-theme-font:minor-latin'>5</span></b>. Now do <b style='mso-bidi-font-weight:
1580normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1581minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until
1582the refinement converges. After a set of refinement cycles go to the <b
1583style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1584mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1585reflections</span></b> tab and check the intensities. If there are many
1586negatives amongst the highest angle reflections do <b style='mso-bidi-font-weight:
1587normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1588minor-latin;mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this
1589replaces all the values with those in the extracted from the profile as listed
1590in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1591mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1592list</span></b> for the PWDR data set each multiplied by 0.5. Additionally
1593their refinement flags are turned off. Do <b style='mso-bidi-font-weight:normal'><span
1594style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1595mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b><span
1596style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1597mso-hansi-theme-font:minor-latin'>; this will adjust all the reflections in the
1598vicinity of the reset ones</span>. You may repeat this process to suppress any
1599new negatives that may appear. Then set all the Pawley refinement flags back on
1600(excluding any that lead to a singular matrix) and repeat the refinement. After
1601refinement, mine converged to ~5.3% with very few negatives and the plot looked
1602like</p>
1603
1604<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1605 id="Picture_x0020_9" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:525pt;
1606 height:450pt;visibility:visible;mso-wrap-style:square'>
1607 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image009.png" o:title=""/>
1608</v:shape><![endif]--><![if !vml]><img width=700 height=600
1609src="Charge%20Flipping%20-%20sucrose_files/image009.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
1610
1611<p class=MsoNormal>Let’s see if this is good enough for charge flipping.</p>
1612
1613<h2>Step 3: Charge flipping</h2>
1614
1615<p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
1616Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1617mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1618and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1619"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1620minor-latin'>Charge flip controls</span></b> in the middle of the <b
1621style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1622mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1623tab.</p>
1624
1625<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1626mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1627"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1628</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
1629style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1630mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b
1631style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1632mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
163311bmb_8716.fxye Bank 1</span></b> (the only choice!). This makes the reflection
1634set to be used those in <b style='mso-bidi-font-weight:normal'><span
1635style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1636mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
1637data set; these should match the <b style='mso-bidi-font-weight:normal'><span
1638style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1639mso-hansi-theme-font:minor-latin'>Pawley reflection</span></b> set.</p>
1640
1641<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1642mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1643"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1644</span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span
1645style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1646mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b
1647style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1648mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map
1649controls</span></b>) to <b style='mso-bidi-font-weight:normal'><span
1650style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1651mso-hansi-theme-font:minor-latin'>20%</span></b>. This controls the map search
1652routine.</p>
1653
1654<p class=MsoNormal>For powder data it is not usually advisable to select a <b
1655style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1656mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing
1657element</span></b>; if selected a periodic table appears – select an element or
1658‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1659mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None’</span></b>.
1660The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1661mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1662defines the map spacing and thus the extent of the reflection set; the observed
1663reflection set is zero filled to this limit for charge flipping. The <b
1664style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1665mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b>
1666and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1667mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b>
1668determine the lower threshold and upper limit for charge flipping,
1669respectively. The latter is used to avoid “Uranium solutions” in the result.
1670Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1671"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1672minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
1673ones. For sucrose set it to <b style='mso-bidi-font-weight:normal'><span
1674style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1675mso-hansi-theme-font:minor-latin'>12.</span></b> When ready select <b
1676style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1677mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1678flipping</span></b>; a progress bar dialog will appear that tracks the residual
1679found in each charge flipping cycle. It will quickly drop to some level
1680(42-44%) and then for a successful charge flipping run perhaps drop again into
1681the 20-25% range after a considerable length of time. You should save the
1682project if you get an apparently good solution. Many times it will not drop
1683below ~40%; just try <b style='mso-bidi-font-weight:normal'><span
1684style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1685mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b> again. If
1686several tries fail to yield a solution, go back to the last step of the Pawley
1687refinement and just repeat it (that is do <b style='mso-bidi-font-weight:normal'><span
1688style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1689mso-hansi-theme-font:minor-latin'>Pawley update</span></b> and <b
1690style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1691mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>).
1692This will generate a different set of intensities for the highly overlapped
1693part of the powder pattern; perhaps they will give a successful charge flip
1694solution. Unless otherwise interrupted, GSAS-II will try 10000 times for a
1695charge flip solution (for sucrose this takes 5-10min on my laptop). Press <b
1696style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1697mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b>
1698to stop the charge flipping; a peak list and a drawing of the solution will
1699appear. One of my runs gave</p>
1700
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1707
1708<p class=MsoNormal><o:p>&nbsp;</o:p></p>
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1808 </v:shape></v:group><![endif]--><![if !vml]><span style='mso-ignore:vglayout;
1809position:absolute;z-index:251662336;margin-left:315px;margin-top:308px;
1810width:16px;height:35px'><img width=16 height=35
1811src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
1812style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_11"
1813 o:spid="_x0000_i1052" type="#_x0000_t75" style='width:502.5pt;height:431.25pt;
1814 visibility:visible;mso-wrap-style:square'>
1815 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image012.png" o:title=""
1816  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
1817</v:shape><![endif]--><![if !vml]><img width=670 height=575
1818src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_11"><![endif]></span></p>
1819
1820<p class=MsoNormal>The result looks very promising! Charge flipping operates
1821without regard to symmetry and GSAS-II attempts to locate the map with respect
1822to the symmetry elements from the computed reflection phases. (NB: charge
1823flipping also will give a solution without regard to handedness; this solution
1824may be either the correct one for sucrose or its inverse.) Errors in these
1825phases can disrupt this process so that the map and peak positions are offset
1826from their true positions. To discover this and fix it, rotate the drawing
1827around to check that atom positions are related via the 2<sub>1</sub> screw
1828axis (through the multicolored cross in the center of the cell and parallel to
1829the y-axis – the green cell edge). Avoid motions with the right mouse button
1830pressed, this moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:
1831normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1832minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the
1833cross to the cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my
1834drawing above to show where I think it should be. If you find an offset to the
1835map, orient it so the offset is horizontal or vertical and then press the <b
1836style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1837mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>,
1838<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1839mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>,
1840<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1841mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
1842or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1843mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
1844keys to shift the map and peaks as needed. The shift is in resolution units
1845(0.5Å) so the fix can only be approximate. Repeat as needed. Notice that the
1846peak positions in the table are updated as the offset is changed. In this case,
1847I needed just a few steps to correct the map offset. NB: you can use these keys
1848to move the result anywhere you wish, e.g. to select a different origin for the
1849structure but pay attention to the location of symmetry elements. After
1850adjustment, my solution looked like</p>
1851
1852<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1853 id="Picture_x0020_12" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:500.25pt;
1854 height:424.5pt;visibility:visible;mso-wrap-style:square'>
1855 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image014.png" o:title=""
1856  croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/>
1857</v:shape><![endif]--><![if !vml]><img width=667 height=566
1858src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
1859
1860<h2>Step 4: Obtain solution from charge flip result</h2>
1861
1862<p class=MsoNormal>The next step is to extract the unique peak positions from
1863the map and make atoms out of them. The map peak list is initially sorted by
1864peak magnitude; you can change the sorting to be along any of the column
1865headings in the table by a single click on the desired heading. The <span
1866class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1867"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1868minor-latin'>dzero</span></b></span> column gives the distance of each peak
1869from the origin. The menu items under Map peaks give you several tools to aid
1870in the peak selection process; we will just use a couple in this example. I have
1871chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:normal'><span
1872style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1873mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and then finding
1874the unique ones. </p>
1875
1876<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1877mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1878"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1879</span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight:
1880normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1881minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> column heading. This
1882will sort the peaks in increasing z-axis coordinate.</p>
1883
1884<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1885mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1886"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1887</span></span></span><![endif]>Do a single click on the upper left (empty) box
1888of the table. All entries will be colored grey indicating their selection.</p>
1889
1890<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1891mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1892"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1893</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1894style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1895mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That
1896should select (grey) 23 out of 46 peak positions in the table and all should be
1897near the top of the list. The console displays this as both the number of unique
1898peaks and the fraction found (the ideal value<span class=GramE>,0.5</span>, for
1899the latter is easily inferred from the space group). Given the formula for
1900sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub> that would be all the C
1901&amp; O atoms! They will be colored green in the plot. If more are selected
1902then check the map offset – it may need a slight correction.</p>
1903
1904<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1905 id="Picture_x0020_13" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:337.5pt;
1906 height:411.75pt;visibility:visible;mso-wrap-style:square'>
1907 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image016.png" o:title=""/>
1908</v:shape><![endif]--><![if !vml]><img width=450 height=549
1909src="Charge%20Flipping%20-%20sucrose_files/image016.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1910
1911<p class=MsoNormal>The drawing shows the selected atoms in green.</p>
1912
1913<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1914 id="Picture_x0020_14" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:7in;
1915 height:429pt;visibility:visible;mso-wrap-style:square'>
1916 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image017.png" o:title=""
1917  croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/>
1918</v:shape><![endif]--><![if !vml]><img width=672 height=572
1919src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
1920
1921<p class=MsoNormal>Notice that in my case one atom is in a neighboring
1922molecule, one can deselect it and then pick the desired equivalent. Hold the <b
1923style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1924mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1925key down and use the right mouse button to pick/unpick atoms in the drawing.
1926NB: the left mouse button will clear all the selections. The other two “lone”
1927atoms belong to molecules in neighboring unit cells; we’ll deal with them
1928later.</p>
1929
1930<p class=MsoNormal>These are now ready to turn into atoms. Do <b
1931style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1932mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1933peaks/Move peaks</span></b>. The drawing will show white balls for each of the
1934selected positions and the <b style='mso-bidi-font-weight:normal'><span
1935style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1936mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 23 new H
1937atoms. </p>
1938
1939<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1940 id="Picture_x0020_15" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:7in;
1941 height:433.5pt;visibility:visible;mso-wrap-style:square'>
1942 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image019.png" o:title=""
1943  croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/>
1944</v:shape><![endif]--><![if !vml]><img width=672 height=578
1945src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
1946
1947<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1948 id="_x0000_i1047" type="#_x0000_t75" style='width:525pt;height:414.75pt;
1949 visibility:visible;mso-wrap-style:square'>
1950 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image021.png" o:title=""/>
1951</v:shape><![endif]--><![if !vml]><img width=700 height=553
1952src="Charge%20Flipping%20-%20sucrose_files/image021.png" v:shapes="_x0000_i1047"><![endif]></span></p>
1953
1954<p class=MsoNormal>The atom names indicate the peak magnitude to aid
1955identification (M100 for the largest in the <b style='mso-bidi-font-weight:
1956normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1957minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
1958may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
1959style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1960mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
1961them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
1962style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1963mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
1964normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1965minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
1966and then selecting a position in the table with the <b style='mso-bidi-font-weight:
1967normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1968minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
1969Linux machines the <b style='mso-bidi-font-weight:normal'><span
1970style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1971mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by
1972the operating system; use <b style='mso-bidi-font-weight:normal'><span
1973style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1974mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms.
1975After sorting by magnitude, my list is now </p>
1976
1977<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1978 id="Picture_x0020_17" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
1979 height:417pt;visibility:visible;mso-wrap-style:square'>
1980 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image022.png" o:title=""/>
1981</v:shape><![endif]--><![if !vml]><img width=700 height=556
1982src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1983
1984<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out into
1985two groups with a clear gap between M79 and M64. The higher ones are likely to
1986be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of
1987ambiguity in the middle, but just assign the top 11 as O and the rest as C and
1988see what happens. You can do this by selecting a block of atoms, go to <b
1989style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1990mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1991atom parameters</span></b> and select <b style='mso-bidi-font-weight:normal'><span
1992style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1993mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a
1994periodic table will appear. Select the desired element and they will be changed
1995in the list and drawing. (NB: I show below the result from a different charge
1996flipping run which had a different origin choice so the sucrose molecule is
1997more fragmented).</p>
1998
1999<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2000 id="Picture_x0020_44" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:363pt;
2001 height:309.75pt;visibility:visible;mso-wrap-style:square'>
2002 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image023.png" o:title=""
2003  croptop="13142f" cropbottom="15218f" cropleft="37794f" cropright="12724f"/>
2004</v:shape><![endif]--><![if !vml]><img width=484 height=413
2005src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_44"><![endif]></span></p>
2006
2007<p class=MsoNormal>The original charge flipping solution is still visible and
2008the atoms are now identified, I’ve changed the drawing to show balls and sticks
2009and labeled the atoms with their names, this is done in the <b
2010style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2011mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b>
2012tab. Double click the appropriate column heading and make the selection from
2013the dialog box.<span style='mso-spacerun:yes'>  </span></p>
2014
2015<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2016 id="Picture_x0020_45" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:525pt;
2017 height:445.5pt;visibility:visible;mso-wrap-style:square'>
2018 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image025.png" o:title=""/>
2019</v:shape><![endif]--><![if !vml]><img width=700 height=594
2020src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
2021
2022<p class=MsoNormal>Now one can safely remove the map peaks (do <b
2023style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2024mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
2025peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span
2026style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2027mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
2028charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
2029style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2030mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
2031normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2032minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
2033style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2034mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2035tab). The atom positions I obtained in this charge flipping run have the
2036sucrose molecule fragmented over several neighboring molecules. We need assemble
2037these into a single molecule. Follow the steps:</p>
2038
2039<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2040mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2041"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2042</span></span></span><![endif]>In the Atoms tab of the Data window do <b
2043style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2044mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload
2045draw <span class=GramE>atoms<span style='font-family:"Times New Roman",serif;
2046font-weight:normal'>.</span></span></span></b> This ensures the drawing is
2047up-to-date with the Atom list.</p>
2048
2049<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2050mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2051"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2052</span></span></span><![endif]>Select one atom in one of the fragments (perhaps
2053<span class=GramE>O(</span>1) in the drawing above as that is likely to be the
2054bridging O-atom between the two rings of sucrose. With the Atoms table showing
2055on the data window, use Shift-Left mouse button on the desired atom; it will
2056turn green indicating selection.</p>
2057
2058<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2059mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2060"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2061</span></span></span><![endif]>Then in the Atoms menu do <b style='mso-bidi-font-weight:
2062normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2063minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b>;
2064a popup dialog offering choices of distances (&amp; angles – not used). Press <b
2065style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2066mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.</p>
2067
2068<p class=MsoNormal style='margin-left:.5in'>The atoms will automatically be
2069reorganized into a single molecule and are ordered in the table according to
2070connectivity.</p>
2071
2072<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2073 id="Picture_x0020_20" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:360.75pt;
2074 height:312pt;visibility:visible;mso-wrap-style:square'>
2075 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image026.png" o:title=""
2076  croptop="14042f" cropbottom="14048f" cropleft="39221f" cropright="11359f"/>
2077</v:shape><![endif]--><![if !vml]><img width=481 height=416
2078src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
2079
2080<p class=MsoNormal>I’ve changed the style to balls &amp; sticks and added the
2081atom names as labels.</p>
2082
2083<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2084 id="Picture_x0020_46" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
2085 height:449.25pt;visibility:visible;mso-wrap-style:square'>
2086 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/>
2087</v:shape><![endif]--><![if !vml]><img width=700 height=599
2088src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
2089
2090<p class=MsoNormal>If it happens that the Assemble molecule routine leaves one
2091or two atoms out, rerun it adjusting the Bond search factor to a slightly
2092larger value (e.g. 0.9 vs 0.85). That should pick up the outliers.</p>
2093
2094<p class=MsoNormal>To rename the atoms, select all the atoms (double click in
2095the empty left upper square of the Atom table; the entries will turn blue or
2096grey. Then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
2097"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2098minor-latin'>Edit/Modify atom parameters</span></b>. Select <b
2099style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2100mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Name</span></b>
2101from the popup window and press <b style='mso-bidi-font-weight:normal'><span
2102style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2103mso-hansi-theme-font:minor-latin'>OK</span></b>; you will be asked to confirm.
2104The atoms will be renamed. </p>
2105
2106<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2107 id="Picture_x0020_47" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;
2108 height:450.75pt;visibility:visible;mso-wrap-style:square'>
2109 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/>
2110</v:shape><![endif]--><![if !vml]><img width=700 height=601
2111src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
2112
2113<p class=MsoNormal>You can also reorder the atoms to make the connectivity
2114conform to usual chemical naming rules; use the Alt key to pick &amp; place
2115each atom to be moved just as we did with the Map peak results above.</p>
2116
2117<p class=MsoNormal>Save the project file; the next step is to complete the
2118structure by finding H-atoms and then do the final Rietveld refinements.</p>
2119
2120<h2>Step 5: Complete the structure</h2>
2121
2122<p class=MsoNormal>To complete the structure you will need to perform a
2123preliminary Rietveld refinement. This will make the atom positions more
2124accurate and prepare a set of calculated structure factors needed to generate a
2125difference Fourier map good enough to maybe reveal the H atoms. There are a
2126number of steps needed to set all the controls from the previous Pawley
2127refinement to get a successful start for the Rietveld refinement.</p>
2128
2129<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2130mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2131"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2132</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2133style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2134mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the
2135GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span
2136style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2137mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You don’t want to
2138start with these when the scale factor is unknown.</p>
2139
2140<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2141mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2142"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2143</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
2144style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2145mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b
2146style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2147mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2148scale factor</span></b> box. This is the scale factor for the data set. Uncheck
2149the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2150mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
2151class=SpellE>displ</span></span></b>.</p>
2152
2153<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2154mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2155"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2156</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
2157style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2158mso-hansi-theme-font:minor-latin'>Phases/sucrose General</span></b> tab and
2159uncheck <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'>Refine unit
2161cell</span></b> and <b style='mso-bidi-font-weight:normal'><span
2162style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2163mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The
2164latter is most important; if you forget you will just get another Pawley
2165refinement!</p>
2166
2167<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
2168style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2169mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
2170GSAS-II data tree menu; only scale and background are refined. I got <span
2171class=SpellE>Rwp</span> ~20%. The plot shows clear intensity differences; the
2172atom positions obviously need refinement.</p>
2173
2174<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2175 id="Picture_x0020_21" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
2176 height:450pt;visibility:visible;mso-wrap-style:square'>
2177 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image030.png" o:title=""/>
2178</v:shape><![endif]--><![if !vml]><img width=700 height=600
2179src="Charge%20Flipping%20-%20sucrose_files/image030.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
2180
2181<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
2182obvious.</p>
2183
2184<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
2185style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2186mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and select the <b
2187style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2188mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2189tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub>
2190has an arbitrary location along the y-axis. Then double click the <b
2191style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2192mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
2193column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight:
2194normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2195minor-latin;mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and
2196press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2197mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2198The atoms table will show the refinement controls</p>
2199
2200<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2201 id="Picture_x0020_48" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
2202 height:225pt;visibility:visible;mso-wrap-style:square'>
2203 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/>
2204</v:shape><![endif]--><![if !vml]><img width=700 height=300
2205src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
2206
2207<p class=MsoNormal>To deal with the warning we need to set a “Hold” on one atom
2208y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span
2209style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2210mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II data
2211tree.</p>
2212
2213<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2214 id="Picture_x0020_23" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:225pt;
2215 height:187.5pt;visibility:visible;mso-wrap-style:square'>
2216 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image032.png" o:title=""/>
2217</v:shape><![endif]--><![if !vml]><img width=300 height=250
2218src="Charge%20Flipping%20-%20sucrose_files/image032.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
2219
2220<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
2221style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2222mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
2223style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2224mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
2225class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. Notice the
2226use of a filter to shorten the list. This will fix the shift along y for the <span
2227class=GramE>O(</span>1) atom.</p>
2228
2229<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2230 id="Picture_x0020_49" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468.75pt;
2231 height:300pt;visibility:visible;mso-wrap-style:square'>
2232 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title=""/>
2233</v:shape><![endif]--><![if !vml]><img width=625 height=400
2234src="Charge%20Flipping%20-%20sucrose_files/image033.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
2235
2236<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2237style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2238mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will
2239show the hold</p>
2240
2241<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2242 id="Picture_x0020_27" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:225pt;
2243 height:187.5pt;visibility:visible;mso-wrap-style:square'>
2244 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image034.png" o:title=""/>
2245</v:shape><![endif]--><![if !vml]><img width=300 height=250
2246src="Charge%20Flipping%20-%20sucrose_files/image034.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
2247
2248<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
2249style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2250mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
2251class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice
2252parameters (in the <b style='mso-bidi-font-weight:normal'><span
2253style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2254mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
2255style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2256mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>),
2257the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2258mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
2259parameters</span></b> <b style='mso-bidi-font-weight:normal'><span
2260style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2261mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
2262normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2263minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b
2264style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2265mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
2266<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2267mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2268&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2269mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2270and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2271mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
2272class=SpellE>displ</span></span></b>. You can also include refinement of atom
2273thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
2274refinement improved slightly to Rwp~10.0%. Next we should add the hydrogen
2275atoms that are on carbon as these can be located from the molecular geometry.
2276To do this do the following:</p>
2277
2278<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2279
2280<p class=MsoNormal>Go to the Atoms tab and select the <b style='mso-bidi-font-weight:
2281normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2282minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column; a popup
2283will appear. Select just the <b style='mso-bidi-font-weight:normal'><span
2284style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2285mso-hansi-theme-font:minor-latin'>C</span></b> atoms; these will be highlighted
2286in grey in the Atom table.</p>
2287
2288<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
2289style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2290mso-hansi-theme-font:minor-latin'>Edit/Insert H atoms</span></b> from the Atoms
2291menu; a Distance Angle Controls popup will appear. You can change radii and
2292Bond search factor if needed (rarely). Press <b style='mso-bidi-font-weight:
2293normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2294minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>. A new popup window
2295will appear.<br>
2296<span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_50"
2297 o:spid="_x0000_i1035" type="#_x0000_t75" style='width:300pt;height:363.75pt;
2298 visibility:visible;mso-wrap-style:square'>
2299 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""/>
2300</v:shape><![endif]--><![if !vml]><img width=400 height=485
2301src="Charge%20Flipping%20-%20sucrose_files/image035.png" v:shapes="Picture_x0020_50"><![endif]></span><br>
2302This offers the choice of how many H-atoms to be added for each atom in the
2303table; the maximum is chosen for each atom. If the bonds are sufficiently short
2304this may be fewer reflecting the possibility of sp<sup>2</sup> or <span
2305class=SpellE>sp</span> bonding on the atom. You can override the choices made
2306by default. You also can deselect some of the other attached atoms so they will
2307not be used in the geometry calculations for H-atom placement (e.g. a metal
2308atom in certain organometallics). When you are satisfied with the choices
2309(actually no changes are needed in this case), press <b style='mso-bidi-font-weight:
2310normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2311minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>. The structure will
2312be redrawn with H-atoms shown as van der Waals spheres; they are inserted in
2313the Atom list immediately after the C-atom they are bound to and they are named
2314accordingly. </p>
2315
2316<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2317 id="Picture_x0020_51" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:362.25pt;
2318 height:312pt;visibility:visible;mso-wrap-style:square'>
2319 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image036.png" o:title=""
2320  croptop="15482f" cropbottom="12608f" cropleft="37236f" cropright="13314f"/>
2321</v:shape><![endif]--><![if !vml]><img width=483 height=416
2322src="Charge%20Flipping%20-%20sucrose_files/image037.jpg" v:shapes="Picture_x0020_51"><![endif]></span></p>
2323
2324<p class=MsoNormal>These hydrogen atoms will better describe the scattering
2325density in the vicinity of the carbon atoms; their positions need to be refined
2326to find their better locations. Do <b style='mso-bidi-font-weight:normal'><span
2327style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2328mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (the refinement
2329flags are already set for this – NB: don’t be tempted to refine the H-atom
2330positions as they are likely to move erratically). My result was Rwp~9.2% and
2331the drawing is updated with the new atom positions (as van der Waals spheres).</p>
2332
2333<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2334 id="Picture_x0020_52" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:363pt;
2335 height:311.25pt;visibility:visible;mso-wrap-style:square'>
2336 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image038.png" o:title=""
2337  croptop="15482f" cropbottom="12698f" cropleft="37236f" cropright="13252f"/>
2338</v:shape><![endif]--><![if !vml]><img width=484 height=415
2339src="Charge%20Flipping%20-%20sucrose_files/image039.jpg" v:shapes="Picture_x0020_52"><![endif]></span></p>
2340
2341<p class=MsoNormal>Because the C-atoms have probably moved; the H-atoms (which
2342were fixed) are now no longer in their optimal locations. From the Atom tab
2343menu, do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2344mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/ Update
2345H atoms</span></b>. This will shift their positions slightly. Repeat <b
2346style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2347mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
2348and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2349mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Update
2350H atoms</span></b>; you should see no shift this time. (<span class=SpellE>Rwp</span>
2351may be slightly higher; I got ~9.3%).</p>
2352
2353<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2354
2355<p class=MsoNormal>Now we have to find the hydrogens that are on oxygen; these
2356cannot be geometrically located except that they are somewhere on a circle at
2357the bonding distance from the O-atom. We need a difference Fourier map. Go to
2358the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2359mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose
2360General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
2361style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2362mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway
2363down the window.</p>
2364
2365<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2366mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2367"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2368</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
2369normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2370minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
2371style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2372mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
2373for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2374mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
2375
2376<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2377mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2378"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2379</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
2380style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2381mso-hansi-theme-font:minor-latin'>PWDR 11bmb_8716.fxye Bank 1</span></b> for
2382the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2383mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
2384set from</span></b> item (the only choice). The Fourier calculation will use
2385the structure factors shown in the Reflection list item for this PWDR data set.</p>
2386
2387<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2388mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2389"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2390</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2391style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2392mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b
2393style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2394mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2395tab window. The map will be computed via fast Fourier techniques and is very
2396fast. A few lines summarizing the map is printed on the console, the structure
2397plot may show a single green dot somewhere (it could be hidden beneath an
2398atom!), this is the highest point in the map.</p>
2399
2400<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2401mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2402"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2403</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2404style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2405mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b
2406style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2407mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
2408level</span></b> slider until something appears on the map. You can also reduce
2409the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2410mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
2411and shift the View Point (use right mouse button) to help clarify the view.
2412Note that the map continues to show the density around the View Point even if
2413it is outside the unit cell box.</p>
2414
2415<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2416 id="Picture_x0020_31" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:362.25pt;
2417 height:308.25pt;visibility:visible;mso-wrap-style:square'>
2418 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image040.png" o:title=""
2419  croptop="10982f" cropbottom="17558f" cropleft="37484f" cropright="13065f"/>
2420</v:shape><![endif]--><![if !vml]><img width=483 height=411
2421src="Charge%20Flipping%20-%20sucrose_files/image041.jpg" v:shapes="Picture_x0020_31"><![endif]></span></p>
2422
2423<p class=MsoNormal>What is drawn here are green (&amp; red for negative) dots
2424whose size are proportional to the electron density. There are peaks that might
2425be H-atom positions as well as features that suggest O-atoms out of position.
2426Recall that the refinement was just done without any H-atoms on the oxygen
2427atoms; it will make the best fit compensating for the missing H-atoms by
2428displacing the O atoms in the direction of the missing H-atoms. To add the OH atoms
2429do the following:</p>
2430
2431<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2432mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2433"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2434</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2435style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2436mso-hansi-theme-font:minor-latin'>Phases/sucrose Atoms</span></b> tab.</p>
2437
2438<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2439mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2440"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2441</span></span></span><![endif]>Select all O-atoms in the table (double click
2442the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2443mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b>
2444column heading &amp; select <b style='mso-bidi-font-weight:normal'><span
2445style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2446mso-hansi-theme-font:minor-latin'>O</span></b> atoms from the popup); all will
2447turn grey.</p>
2448
2449<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2450mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2451"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2452</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2453style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2454mso-hansi-theme-font:minor-latin'>Edit/Insert H atoms</span></b> from the menu;
2455a Distance Angle Controls popup will appear. You can change radii and Bond
2456search factor if needed (rarely). Press <b style='mso-bidi-font-weight:normal'><span
2457style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2458mso-hansi-theme-font:minor-latin'>Ok</span></b>. A new popup window will appear</p>
2459
2460<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2461 id="Picture_x0020_32" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:300pt;
2462 height:363.75pt;visibility:visible;mso-wrap-style:square'>
2463 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/>
2464</v:shape><![endif]--><![if !vml]><img width=400 height=485
2465src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
2466
2467<p class=MsoNormal style='margin-left:.5in'>This offers the choice of how many
2468H-atoms to be added for each O-atom in the table; one is chosen in this case
2469for each atom. Press <b style='mso-bidi-font-weight:normal'><span
2470style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2471mso-hansi-theme-font:minor-latin'>Ok</span></b>. The structure will be redrawn
2472showing the added H-atoms.</p>
2473
2474<p class=MsoNormal style='margin-left:.5in'><o:p>&nbsp;</o:p></p>
2475
2476<p class=MsoNormal style='margin-left:.5in'>These OH hydrogens are found by
2477finding the highest point in the delta-F map for all possible orientations of
2478this bond at a fixed angle (109.5°). The new hydrogen atoms are named in sequence
2479and are appended to the end of the Atom list.</p>
2480
2481<p class=MsoNormal style='margin-left:.5in'><o:p>&nbsp;</o:p></p>
2482
2483<p class=MsoNormal>Do the set of <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'>Calculate/Refine, Edit/Update H atoms</span></b>
2486at least twice to finish this stage in the structure analysis; end with a <b
2487style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2488mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>.
2489My <span class=SpellE>Rwp</span> was ~8.14% with all the H-atoms included (but
2490not refined). The fit looks pretty good</p>
2491
2492<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2493 id="Picture_x0020_40" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
2494 height:450pt;visibility:visible;mso-wrap-style:square'>
2495 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image043.png" o:title=""/>
2496</v:shape><![endif]--><![if !vml]><img width=700 height=600
2497src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
2498
2499<h2>Step 6: Final refinement</h2>
2500
2501<p class=MsoNormal>Looking at the fit, there may be room for improvement. First
2502we need to change the profile model to include crystallite size and <span
2503class=SpellE>mustrain</span> broadening. Go to <b style='mso-bidi-font-weight:
2504normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2505minor-latin;mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>,
2506set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2507mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2508and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2509mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2510to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2511mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>zero</span></b>
2512and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2513"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2514minor-latin'>Refine</span></b> flags for them.</p>
2515
2516<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
2517style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2518mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and look at the <b
2519style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2520mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
2521tab; make sure the <b style='mso-bidi-font-weight:normal'><span
2522style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2523mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the
2524boxes for both <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2525style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2526mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b style='mso-bidi-font-weight:
2527normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2528minor-latin;mso-hansi-theme-font:minor-latin'>. <span class=GramE>size</span></span></b>
2529and <span class=SpellE><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'>microstrain</span></b></span>.</p>
2532
2533<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2534 id="Picture_x0020_41" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:480pt;
2535 height:339pt;visibility:visible;mso-wrap-style:square'>
2536 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image044.png" o:title=""/>
2537</v:shape><![endif]--><![if !vml]><img width=640 height=452
2538src="Charge%20Flipping%20-%20sucrose_files/image044.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
2539
2540<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2541style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2542mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2543class=SpellE>Rwp</span> will start out high but should converge to where it was
2544before this change. I got 8.09% and the <b style='mso-bidi-font-weight:normal'><span
2545style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2546mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>
2547
2548<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2549 id="Picture_x0020_42" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:480pt;
2550 height:334.5pt;visibility:visible;mso-wrap-style:square'>
2551 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image045.png" o:title=""/>
2552</v:shape><![endif]--><![if !vml]><img width=640 height=446
2553src="Charge%20Flipping%20-%20sucrose_files/image045.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
2554
2555<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
2556style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2557mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span
2558class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2559"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2560minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span
2561style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2562mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
2563phenomenological model for <span class=SpellE>microstrain</span> which has 9 terms
2564for monoclinic structures. Check all the boxes for it and press <b
2565style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2566mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reset</span></b>.
2567This will convert the isotropic strain value to the equivalent generalized
2568values.</p>
2569
2570<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2571 id="Picture_x0020_55" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:402pt;
2572 height:375pt;visibility:visible;mso-wrap-style:square'>
2573 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image046.png" o:title=""/>
2574</v:shape><![endif]--><![if !vml]><img width=536 height=500
2575src="Charge%20Flipping%20-%20sucrose_files/image046.png" v:shapes="Picture_x0020_55"><![endif]></span></p>
2576
2577<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2578style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2579mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2580class=SpellE>Rwp</span> will start out high but should converge lower than
2581where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight:
2582normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2583minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like.
2584If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2585style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2586mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b
2587style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2588mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot
2589type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span>
2590surface plot for ground sucrose.</p>
2591
2592<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2593 id="Picture_x0020_56" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:402pt;
2594 height:375pt;visibility:visible;mso-wrap-style:square'>
2595 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image047.png" o:title=""/>
2596</v:shape><![endif]--><![if !vml]><img width=536 height=500
2597src="Charge%20Flipping%20-%20sucrose_files/image047.png" v:shapes="Picture_x0020_56"><![endif]></span></p>
2598
2599<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2600 id="Picture_x0020_58" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
2601 height:450pt;visibility:visible;mso-wrap-style:square'>
2602 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image048.png" o:title=""/>
2603</v:shape><![endif]--><![if !vml]><img width=700 height=600
2604src="Charge%20Flipping%20-%20sucrose_files/image048.png" v:shapes="Picture_x0020_58"><![endif]></span></p>
2605
2606<p class=MsoNormal>This completes the exercise.</p>
2607
2608</div>
2609
2610</body>
2611
2612</html>
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