source: Tutorials/CFsucrose/Charge Flipping - sucrose.htm @ 4367

Last change on this file since 4367 was 2991, checked in by vondreele, 8 years ago

update to 2-frame version
  • Property svn:mime-type set to text/html
File size: 144.7 KB
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414  <w:LsdException Locked="false" Priority="72" Name="Colorful List"/>
415  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/>
416  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
417  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
418  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
419  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
420  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
421  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
422  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
423  <w:LsdException Locked="false" Priority="34" QFormat="true"
424   Name="List Paragraph"/>
425  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
426  <w:LsdException Locked="false" Priority="30" QFormat="true"
427   Name="Intense Quote"/>
428  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
429  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
430  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
431  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
432  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
433  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
434  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
435  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
436  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
437  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
438  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
439  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
440  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
441  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
442  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
443  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
444  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
445  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
446  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
447  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
448  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
449  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
450  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
451  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
452  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
453  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
454  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
455  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
456  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
457  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
458  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
459  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
460  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
461  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
462  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
463  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
464  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
465  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
466  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
467  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
468  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
469  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
470  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
471  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
472  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
473  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
474  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
475  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
476  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
477  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
478  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
479  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
480  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
481  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
482  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
483  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
484  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
485  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
486  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
487  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
488  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
489  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
490  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
491  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
492  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
493  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
494  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
495  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
496  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
497  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
498  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
499  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
500  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
501  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
502  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
503  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
504  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
505  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
506  <w:LsdException Locked="false" Priority="19" QFormat="true"
507   Name="Subtle Emphasis"/>
508  <w:LsdException Locked="false" Priority="21" QFormat="true"
509   Name="Intense Emphasis"/>
510  <w:LsdException Locked="false" Priority="31" QFormat="true"
511   Name="Subtle Reference"/>
512  <w:LsdException Locked="false" Priority="32" QFormat="true"
513   Name="Intense Reference"/>
514  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
515  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
516   UnhideWhenUsed="true" Name="Bibliography"/>
517  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
518   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
519  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
520  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
521  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
522  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
523  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
524  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
525  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
526  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
527  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
528  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
529  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
530  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
531  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
532  <w:LsdException Locked="false" Priority="46"
533   Name="Grid Table 1 Light Accent 1"/>
534  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
535  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
536  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
537  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
538  <w:LsdException Locked="false" Priority="51"
539   Name="Grid Table 6 Colorful Accent 1"/>
540  <w:LsdException Locked="false" Priority="52"
541   Name="Grid Table 7 Colorful Accent 1"/>
542  <w:LsdException Locked="false" Priority="46"
543   Name="Grid Table 1 Light Accent 2"/>
544  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
545  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
546  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
547  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
548  <w:LsdException Locked="false" Priority="51"
549   Name="Grid Table 6 Colorful Accent 2"/>
550  <w:LsdException Locked="false" Priority="52"
551   Name="Grid Table 7 Colorful Accent 2"/>
552  <w:LsdException Locked="false" Priority="46"
553   Name="Grid Table 1 Light Accent 3"/>
554  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
555  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
556  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
557  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
558  <w:LsdException Locked="false" Priority="51"
559   Name="Grid Table 6 Colorful Accent 3"/>
560  <w:LsdException Locked="false" Priority="52"
561   Name="Grid Table 7 Colorful Accent 3"/>
562  <w:LsdException Locked="false" Priority="46"
563   Name="Grid Table 1 Light Accent 4"/>
564  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
565  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
566  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
567  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
568  <w:LsdException Locked="false" Priority="51"
569   Name="Grid Table 6 Colorful Accent 4"/>
570  <w:LsdException Locked="false" Priority="52"
571   Name="Grid Table 7 Colorful Accent 4"/>
572  <w:LsdException Locked="false" Priority="46"
573   Name="Grid Table 1 Light Accent 5"/>
574  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
575  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
576  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
577  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
578  <w:LsdException Locked="false" Priority="51"
579   Name="Grid Table 6 Colorful Accent 5"/>
580  <w:LsdException Locked="false" Priority="52"
581   Name="Grid Table 7 Colorful Accent 5"/>
582  <w:LsdException Locked="false" Priority="46"
583   Name="Grid Table 1 Light Accent 6"/>
584  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
585  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
586  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
587  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
588  <w:LsdException Locked="false" Priority="51"
589   Name="Grid Table 6 Colorful Accent 6"/>
590  <w:LsdException Locked="false" Priority="52"
591   Name="Grid Table 7 Colorful Accent 6"/>
592  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
593  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
594  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
595  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
596  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
597  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
598  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
599  <w:LsdException Locked="false" Priority="46"
600   Name="List Table 1 Light Accent 1"/>
601  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
602  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
603  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
604  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
605  <w:LsdException Locked="false" Priority="51"
606   Name="List Table 6 Colorful Accent 1"/>
607  <w:LsdException Locked="false" Priority="52"
608   Name="List Table 7 Colorful Accent 1"/>
609  <w:LsdException Locked="false" Priority="46"
610   Name="List Table 1 Light Accent 2"/>
611  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
612  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
613  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
614  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
615  <w:LsdException Locked="false" Priority="51"
616   Name="List Table 6 Colorful Accent 2"/>
617  <w:LsdException Locked="false" Priority="52"
618   Name="List Table 7 Colorful Accent 2"/>
619  <w:LsdException Locked="false" Priority="46"
620   Name="List Table 1 Light Accent 3"/>
621  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
622  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
623  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
624  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
625  <w:LsdException Locked="false" Priority="51"
626   Name="List Table 6 Colorful Accent 3"/>
627  <w:LsdException Locked="false" Priority="52"
628   Name="List Table 7 Colorful Accent 3"/>
629  <w:LsdException Locked="false" Priority="46"
630   Name="List Table 1 Light Accent 4"/>
631  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
632  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
633  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
634  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
635  <w:LsdException Locked="false" Priority="51"
636   Name="List Table 6 Colorful Accent 4"/>
637  <w:LsdException Locked="false" Priority="52"
638   Name="List Table 7 Colorful Accent 4"/>
639  <w:LsdException Locked="false" Priority="46"
640   Name="List Table 1 Light Accent 5"/>
641  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
642  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
643  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
644  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
645  <w:LsdException Locked="false" Priority="51"
646   Name="List Table 6 Colorful Accent 5"/>
647  <w:LsdException Locked="false" Priority="52"
648   Name="List Table 7 Colorful Accent 5"/>
649  <w:LsdException Locked="false" Priority="46"
650   Name="List Table 1 Light Accent 6"/>
651  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
652  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
653  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
654  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
655  <w:LsdException Locked="false" Priority="51"
656   Name="List Table 6 Colorful Accent 6"/>
657  <w:LsdException Locked="false" Priority="52"
658   Name="List Table 7 Colorful Accent 6"/>
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782        {mso-style-name:"Heading 2 Char";
783        mso-style-noshow:yes;
784        mso-style-priority:9;
785        mso-style-unhide:no;
786        mso-style-locked:yes;
787        mso-style-link:"Heading 2";
788        mso-ansi-font-size:18.0pt;
789        mso-bidi-font-size:18.0pt;
790        font-family:"Times New Roman",serif;
791        mso-ascii-font-family:"Times New Roman";
792        mso-fareast-font-family:"Times New Roman";
793        mso-fareast-theme-font:minor-fareast;
794        mso-hansi-font-family:"Times New Roman";
795        mso-bidi-font-family:"Times New Roman";
796        font-weight:bold;}
797p.msonormal0, li.msonormal0, div.msonormal0
798        {mso-style-name:msonormal;
799        mso-style-unhide:no;
800        mso-margin-top-alt:auto;
801        margin-right:0in;
802        mso-margin-bottom-alt:auto;
803        margin-left:0in;
804        mso-pagination:widow-orphan;
805        font-size:12.0pt;
806        font-family:"Times New Roman",serif;
807        mso-fareast-font-family:"Times New Roman";
808        mso-fareast-theme-font:minor-fareast;}
809span.BalloonTextChar
810        {mso-style-name:"Balloon Text Char";
811        mso-style-noshow:yes;
812        mso-style-priority:99;
813        mso-style-unhide:no;
814        mso-style-locked:yes;
815        mso-style-link:"Balloon Text";
816        mso-ansi-font-size:8.0pt;
817        mso-bidi-font-size:8.0pt;
818        font-family:"Tahoma",sans-serif;
819        mso-ascii-font-family:Tahoma;
820        mso-fareast-font-family:"Times New Roman";
821        mso-fareast-theme-font:minor-fareast;
822        mso-hansi-font-family:Tahoma;
823        mso-bidi-font-family:Tahoma;}
824span.SpellE
825        {mso-style-name:"";
826        mso-spl-e:yes;}
827span.GramE
828        {mso-style-name:"";
829        mso-gram-e:yes;}
830.MsoChpDefault
831        {mso-style-type:export-only;
832        mso-default-props:yes;
833        font-size:12.0pt;
834        mso-ansi-font-size:12.0pt;
835        mso-bidi-font-size:12.0pt;
836        mso-fareast-font-family:Calibri;
837        mso-fareast-theme-font:minor-latin;
838        mso-bidi-font-family:"Times New Roman";
839        mso-bidi-theme-font:minor-bidi;}
840@page WordSection1
841        {size:8.5in 11.0in;
842        margin:1.0in 1.0in 1.0in 1.0in;
843        mso-header-margin:.5in;
844        mso-footer-margin:.5in;
845        mso-paper-source:0;}
846div.WordSection1
847        {page:WordSection1;}
848 /* List Definitions */
849 @list l0
850        {mso-list-id:82917343;
851        mso-list-type:hybrid;
852        mso-list-template-ids:-1527319822 -2100533712 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
853@list l0:level1
854        {mso-level-tab-stop:none;
855        mso-level-number-position:left;
856        margin-left:.75in;
857        text-indent:-.25in;}
858@list l0:level2
859        {mso-level-number-format:alpha-lower;
860        mso-level-tab-stop:none;
861        mso-level-number-position:left;
862        margin-left:1.25in;
863        text-indent:-.25in;}
864@list l0:level3
865        {mso-level-number-format:roman-lower;
866        mso-level-tab-stop:none;
867        mso-level-number-position:right;
868        margin-left:1.75in;
869        text-indent:-9.0pt;}
870@list l0:level4
871        {mso-level-tab-stop:none;
872        mso-level-number-position:left;
873        margin-left:2.25in;
874        text-indent:-.25in;}
875@list l0:level5
876        {mso-level-number-format:alpha-lower;
877        mso-level-tab-stop:none;
878        mso-level-number-position:left;
879        margin-left:2.75in;
880        text-indent:-.25in;}
881@list l0:level6
882        {mso-level-number-format:roman-lower;
883        mso-level-tab-stop:none;
884        mso-level-number-position:right;
885        margin-left:3.25in;
886        text-indent:-9.0pt;}
887@list l0:level7
888        {mso-level-tab-stop:none;
889        mso-level-number-position:left;
890        margin-left:3.75in;
891        text-indent:-.25in;}
892@list l0:level8
893        {mso-level-number-format:alpha-lower;
894        mso-level-tab-stop:none;
895        mso-level-number-position:left;
896        margin-left:4.25in;
897        text-indent:-.25in;}
898@list l0:level9
899        {mso-level-number-format:roman-lower;
900        mso-level-tab-stop:none;
901        mso-level-number-position:right;
902        margin-left:4.75in;
903        text-indent:-9.0pt;}
904@list l1
905        {mso-list-id:236667377;
906        mso-list-type:hybrid;
907        mso-list-template-ids:-513138304 1385070818 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
908@list l1:level1
909        {mso-level-tab-stop:none;
910        mso-level-number-position:left;
911        margin-left:.75in;
912        text-indent:-.25in;}
913@list l1:level2
914        {mso-level-number-format:alpha-lower;
915        mso-level-tab-stop:none;
916        mso-level-number-position:left;
917        margin-left:1.25in;
918        text-indent:-.25in;}
919@list l1:level3
920        {mso-level-number-format:roman-lower;
921        mso-level-tab-stop:none;
922        mso-level-number-position:right;
923        margin-left:1.75in;
924        text-indent:-9.0pt;}
925@list l1:level4
926        {mso-level-tab-stop:none;
927        mso-level-number-position:left;
928        margin-left:2.25in;
929        text-indent:-.25in;}
930@list l1:level5
931        {mso-level-number-format:alpha-lower;
932        mso-level-tab-stop:none;
933        mso-level-number-position:left;
934        margin-left:2.75in;
935        text-indent:-.25in;}
936@list l1:level6
937        {mso-level-number-format:roman-lower;
938        mso-level-tab-stop:none;
939        mso-level-number-position:right;
940        margin-left:3.25in;
941        text-indent:-9.0pt;}
942@list l1:level7
943        {mso-level-tab-stop:none;
944        mso-level-number-position:left;
945        margin-left:3.75in;
946        text-indent:-.25in;}
947@list l1:level8
948        {mso-level-number-format:alpha-lower;
949        mso-level-tab-stop:none;
950        mso-level-number-position:left;
951        margin-left:4.25in;
952        text-indent:-.25in;}
953@list l1:level9
954        {mso-level-number-format:roman-lower;
955        mso-level-tab-stop:none;
956        mso-level-number-position:right;
957        margin-left:4.75in;
958        text-indent:-9.0pt;}
959@list l2
960        {mso-list-id:533275380;
961        mso-list-type:hybrid;
962        mso-list-template-ids:-1319630076 -1606007952 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
963@list l2:level1
964        {mso-level-tab-stop:none;
965        mso-level-number-position:left;
966        margin-left:.75in;
967        text-indent:-.25in;}
968@list l2:level2
969        {mso-level-number-format:alpha-lower;
970        mso-level-tab-stop:none;
971        mso-level-number-position:left;
972        margin-left:1.25in;
973        text-indent:-.25in;}
974@list l2:level3
975        {mso-level-number-format:roman-lower;
976        mso-level-tab-stop:none;
977        mso-level-number-position:right;
978        margin-left:1.75in;
979        text-indent:-9.0pt;}
980@list l2:level4
981        {mso-level-tab-stop:none;
982        mso-level-number-position:left;
983        margin-left:2.25in;
984        text-indent:-.25in;}
985@list l2:level5
986        {mso-level-number-format:alpha-lower;
987        mso-level-tab-stop:none;
988        mso-level-number-position:left;
989        margin-left:2.75in;
990        text-indent:-.25in;}
991@list l2:level6
992        {mso-level-number-format:roman-lower;
993        mso-level-tab-stop:none;
994        mso-level-number-position:right;
995        margin-left:3.25in;
996        text-indent:-9.0pt;}
997@list l2:level7
998        {mso-level-tab-stop:none;
999        mso-level-number-position:left;
1000        margin-left:3.75in;
1001        text-indent:-.25in;}
1002@list l2:level8
1003        {mso-level-number-format:alpha-lower;
1004        mso-level-tab-stop:none;
1005        mso-level-number-position:left;
1006        margin-left:4.25in;
1007        text-indent:-.25in;}
1008@list l2:level9
1009        {mso-level-number-format:roman-lower;
1010        mso-level-tab-stop:none;
1011        mso-level-number-position:right;
1012        margin-left:4.75in;
1013        text-indent:-9.0pt;}
1014@list l3
1015        {mso-list-id:588542776;
1016        mso-list-type:hybrid;
1017        mso-list-template-ids:477805396 -2056748102 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1018@list l3:level1
1019        {mso-level-tab-stop:none;
1020        mso-level-number-position:left;
1021        margin-left:.75in;
1022        text-indent:-.25in;}
1023@list l3:level2
1024        {mso-level-number-format:alpha-lower;
1025        mso-level-tab-stop:none;
1026        mso-level-number-position:left;
1027        margin-left:1.25in;
1028        text-indent:-.25in;}
1029@list l3:level3
1030        {mso-level-number-format:roman-lower;
1031        mso-level-tab-stop:none;
1032        mso-level-number-position:right;
1033        margin-left:1.75in;
1034        text-indent:-9.0pt;}
1035@list l3:level4
1036        {mso-level-tab-stop:none;
1037        mso-level-number-position:left;
1038        margin-left:2.25in;
1039        text-indent:-.25in;}
1040@list l3:level5
1041        {mso-level-number-format:alpha-lower;
1042        mso-level-tab-stop:none;
1043        mso-level-number-position:left;
1044        margin-left:2.75in;
1045        text-indent:-.25in;}
1046@list l3:level6
1047        {mso-level-number-format:roman-lower;
1048        mso-level-tab-stop:none;
1049        mso-level-number-position:right;
1050        margin-left:3.25in;
1051        text-indent:-9.0pt;}
1052@list l3:level7
1053        {mso-level-tab-stop:none;
1054        mso-level-number-position:left;
1055        margin-left:3.75in;
1056        text-indent:-.25in;}
1057@list l3:level8
1058        {mso-level-number-format:alpha-lower;
1059        mso-level-tab-stop:none;
1060        mso-level-number-position:left;
1061        margin-left:4.25in;
1062        text-indent:-.25in;}
1063@list l3:level9
1064        {mso-level-number-format:roman-lower;
1065        mso-level-tab-stop:none;
1066        mso-level-number-position:right;
1067        margin-left:4.75in;
1068        text-indent:-9.0pt;}
1069@list l4
1070        {mso-list-id:854225785;
1071        mso-list-type:hybrid;
1072        mso-list-template-ids:-2071413312 1417604178 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1073@list l4:level1
1074        {mso-level-tab-stop:none;
1075        mso-level-number-position:left;
1076        margin-left:.75in;
1077        text-indent:-.25in;}
1078@list l4:level2
1079        {mso-level-number-format:alpha-lower;
1080        mso-level-tab-stop:none;
1081        mso-level-number-position:left;
1082        margin-left:1.25in;
1083        text-indent:-.25in;}
1084@list l4:level3
1085        {mso-level-number-format:roman-lower;
1086        mso-level-tab-stop:none;
1087        mso-level-number-position:right;
1088        margin-left:1.75in;
1089        text-indent:-9.0pt;}
1090@list l4:level4
1091        {mso-level-tab-stop:none;
1092        mso-level-number-position:left;
1093        margin-left:2.25in;
1094        text-indent:-.25in;}
1095@list l4:level5
1096        {mso-level-number-format:alpha-lower;
1097        mso-level-tab-stop:none;
1098        mso-level-number-position:left;
1099        margin-left:2.75in;
1100        text-indent:-.25in;}
1101@list l4:level6
1102        {mso-level-number-format:roman-lower;
1103        mso-level-tab-stop:none;
1104        mso-level-number-position:right;
1105        margin-left:3.25in;
1106        text-indent:-9.0pt;}
1107@list l4:level7
1108        {mso-level-tab-stop:none;
1109        mso-level-number-position:left;
1110        margin-left:3.75in;
1111        text-indent:-.25in;}
1112@list l4:level8
1113        {mso-level-number-format:alpha-lower;
1114        mso-level-tab-stop:none;
1115        mso-level-number-position:left;
1116        margin-left:4.25in;
1117        text-indent:-.25in;}
1118@list l4:level9
1119        {mso-level-number-format:roman-lower;
1120        mso-level-tab-stop:none;
1121        mso-level-number-position:right;
1122        margin-left:4.75in;
1123        text-indent:-9.0pt;}
1124@list l5
1125        {mso-list-id:1022125565;
1126        mso-list-type:hybrid;
1127        mso-list-template-ids:-482838388 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1128@list l5:level1
1129        {mso-level-tab-stop:none;
1130        mso-level-number-position:left;
1131        margin-left:1.0in;
1132        text-indent:-.25in;}
1133@list l5:level2
1134        {mso-level-number-format:alpha-lower;
1135        mso-level-tab-stop:none;
1136        mso-level-number-position:left;
1137        margin-left:1.5in;
1138        text-indent:-.25in;}
1139@list l5:level3
1140        {mso-level-number-format:roman-lower;
1141        mso-level-tab-stop:none;
1142        mso-level-number-position:right;
1143        margin-left:2.0in;
1144        text-indent:-9.0pt;}
1145@list l5:level4
1146        {mso-level-tab-stop:none;
1147        mso-level-number-position:left;
1148        margin-left:2.5in;
1149        text-indent:-.25in;}
1150@list l5:level5
1151        {mso-level-number-format:alpha-lower;
1152        mso-level-tab-stop:none;
1153        mso-level-number-position:left;
1154        margin-left:3.0in;
1155        text-indent:-.25in;}
1156@list l5:level6
1157        {mso-level-number-format:roman-lower;
1158        mso-level-tab-stop:none;
1159        mso-level-number-position:right;
1160        margin-left:3.5in;
1161        text-indent:-9.0pt;}
1162@list l5:level7
1163        {mso-level-tab-stop:none;
1164        mso-level-number-position:left;
1165        margin-left:4.0in;
1166        text-indent:-.25in;}
1167@list l5:level8
1168        {mso-level-number-format:alpha-lower;
1169        mso-level-tab-stop:none;
1170        mso-level-number-position:left;
1171        margin-left:4.5in;
1172        text-indent:-.25in;}
1173@list l5:level9
1174        {mso-level-number-format:roman-lower;
1175        mso-level-tab-stop:none;
1176        mso-level-number-position:right;
1177        margin-left:5.0in;
1178        text-indent:-9.0pt;}
1179@list l6
1180        {mso-list-id:2020618629;
1181        mso-list-type:hybrid;
1182        mso-list-template-ids:-199700640 470186964 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1183@list l6:level1
1184        {mso-level-tab-stop:none;
1185        mso-level-number-position:left;
1186        margin-left:.75in;
1187        text-indent:-.25in;}
1188@list l6:level2
1189        {mso-level-number-format:alpha-lower;
1190        mso-level-tab-stop:none;
1191        mso-level-number-position:left;
1192        margin-left:1.25in;
1193        text-indent:-.25in;}
1194@list l6:level3
1195        {mso-level-number-format:roman-lower;
1196        mso-level-tab-stop:none;
1197        mso-level-number-position:right;
1198        margin-left:1.75in;
1199        text-indent:-9.0pt;}
1200@list l6:level4
1201        {mso-level-tab-stop:none;
1202        mso-level-number-position:left;
1203        margin-left:2.25in;
1204        text-indent:-.25in;}
1205@list l6:level5
1206        {mso-level-number-format:alpha-lower;
1207        mso-level-tab-stop:none;
1208        mso-level-number-position:left;
1209        margin-left:2.75in;
1210        text-indent:-.25in;}
1211@list l6:level6
1212        {mso-level-number-format:roman-lower;
1213        mso-level-tab-stop:none;
1214        mso-level-number-position:right;
1215        margin-left:3.25in;
1216        text-indent:-9.0pt;}
1217@list l6:level7
1218        {mso-level-tab-stop:none;
1219        mso-level-number-position:left;
1220        margin-left:3.75in;
1221        text-indent:-.25in;}
1222@list l6:level8
1223        {mso-level-number-format:alpha-lower;
1224        mso-level-tab-stop:none;
1225        mso-level-number-position:left;
1226        margin-left:4.25in;
1227        text-indent:-.25in;}
1228@list l6:level9
1229        {mso-level-number-format:roman-lower;
1230        mso-level-tab-stop:none;
1231        mso-level-number-position:right;
1232        margin-left:4.75in;
1233        text-indent:-9.0pt;}
1234ol
1235        {margin-bottom:0in;}
1236ul
1237        {margin-bottom:0in;}
1238-->
1239</style>
1240<!--[if gte mso 10]>
1241<style>
1242 /* Style Definitions */
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1265</head>
1266
1267<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1268
1269<div class=WordSection1>
1270
1271<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in
1272GSAS-II - sucrose<o:p></o:p></span></h1>
1273
1274<h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1>
1275
1276<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1277of sucrose from powder diffraction data via charge flipping. This structure was
1278originally solved from single crystal data in the space group P2<sub>1</sub>.
1279It is a difficult exercise to complete as the charge flipping does not always
1280yield a solution and to even have a chance the Pawley refinement must be done
1281with particular care. We have given a route that sometimes works.</p>
1282
1283<p class=MsoNormal>If you have not done so already, start GSAS-II and open the
1284GSAS-II project file (I called it <span class=SpellE><b style='mso-bidi-font-weight:
1285normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1286minor-latin;mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b></span>)
1287you saved from the third part of the peak fitting-indexing exercise. If you
1288didn’t do that exercise, do it now.</p>
1289
1290<h2>Step 1: Setup for Pawley refinement</h2>
1291
1292<p class=MsoNormal>There are a number of steps that must be done in preparation
1293for a Pawley refinement after having completed the unit cell indexing and new
1294phase creation. These cover two things: one is to prepare the powder pattern
1295(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1296
1297<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1298style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1299style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1300<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1301mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
1302in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1303region near d=1.0Å is readily seen. This is ~24deg 2<span style='font-family:
1304Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1305mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1306symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
1307relatively clear of peaks that makes a good place to end the calculations with
1308a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution
1309needed for charge flipping. Enter <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'>23.55</span></b> for <span class=SpellE><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'>Tmax</span></b></span>
1314as the upper limit and make a note of the exact d-spacing (1.0125Å) using the
1315mouse cursor on the plot.</p>
1316
1317<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1318style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1319style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1320<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1321mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1322Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1323style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1324mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1325style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1326mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1327profile</span></b> to recover the default values. The peak fitting done earlier
1328is over a much more limited range of 2<span style='font-family:Symbol;
1329mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1330mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1331symbol;mso-symbol-font-family:Symbol'>Q</span></span> giving values that might
1332not extrapolate well over the wider range to be used in the Pawley refinement.
1333We will refine them again later.</p>
1334
1335<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1336style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1337style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1338<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1339mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1340Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1341normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1342minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.
1343While you are here set <b style='mso-bidi-font-weight:normal'><span
1344style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1345mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> to <b
1346style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1347mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>.</p>
1348
1349<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1350style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1351style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1352to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1353mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1354to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1355"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1356minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1357normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1358minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
1359box and enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
1360style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1361mso-hansi-theme-font:minor-latin'>1.0125</span></b>) into the <b
1362style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1363mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1364class=SpellE>dmin</span></span></b> box. Set the <b style='mso-bidi-font-weight:
1365normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1366minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Pawley
1367neg. wt.</span></b> to <b style='mso-bidi-font-weight:normal'><span
1368style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1369mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.001</span></b></p>
1370
1371<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1372style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1373mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1374
1375<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1376 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1377 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1378 <v:stroke joinstyle="miter"/>
1379 <v:formulas>
1380  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1381  <v:f eqn="sum @0 1 0"/>
1382  <v:f eqn="sum 0 0 @1"/>
1383  <v:f eqn="prod @2 1 2"/>
1384  <v:f eqn="prod @3 21600 pixelWidth"/>
1385  <v:f eqn="prod @3 21600 pixelHeight"/>
1386  <v:f eqn="sum @0 0 1"/>
1387  <v:f eqn="prod @6 1 2"/>
1388  <v:f eqn="prod @7 21600 pixelWidth"/>
1389  <v:f eqn="sum @8 21600 0"/>
1390  <v:f eqn="prod @7 21600 pixelHeight"/>
1391  <v:f eqn="sum @10 21600 0"/>
1392 </v:formulas>
1393 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1394 <o:lock v:ext="edit" aspectratio="t"/>
1395</v:shapetype><v:shape id="Picture_x0020_42" o:spid="_x0000_i1062" type="#_x0000_t75"
1396 style='width:451.5pt;height:180.75pt;visibility:visible;mso-wrap-style:square'>
1397 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image049.png" o:title=""/>
1398</v:shape><![endif]--><![if !vml]><img width=602 height=241
1399src="Charge%20Flipping%20-%20sucrose_files/image050.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
1400
1401<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1402style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1403mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1404for some text. Do <b style='mso-bidi-font-weight:normal'><span
1405style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1406mso-hansi-theme-font:minor-latin'>Edit Phase/Add powder histograms</span></b>;
1407a dialog box will appear</p>
1408
1409<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1410 id="Picture_x0020_43" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:241.5pt;
1411 height:228.75pt;visibility:visible;mso-wrap-style:square'>
1412 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image051.png" o:title=""/>
1413</v:shape><![endif]--><![if !vml]><img width=322 height=305
1414src="Charge%20Flipping%20-%20sucrose_files/image051.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
1415
1416<p class=MsoNormal>Select the only choice and press <b style='mso-bidi-font-weight:
1417normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1418minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>; the desired data
1419set will be added to this phase for analysis. The data tab now shows the new
1420data set.</p>
1421
1422<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1423 id="Picture_x0020_44" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:6in;
1424 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1425 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image052.png" o:title=""/>
1426</v:shape><![endif]--><![if !vml]><img width=576 height=502
1427src="Charge%20Flipping%20-%20sucrose_files/image053.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
1428
1429<p class=MsoNormal>I’ve stretched the window slightly to see the entire
1430contents. This is the location for all the phase dependent parameters for this
1431histogram. Notice that it includes phase fraction, size &amp; <span
1432class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1433and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1434intended for protein work where a significant region of the structure is disordered
1435solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1436surfaces as well as preferred orientation correction curves.</p>
1437
1438<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1439style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1440mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1441empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
1442style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1443mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
1444makes the reflection set over the range covered by setting <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'>Pawley <span class=SpellE>dmin</span></span></b>.
1447The table should list reflections 0~780. Select and check the refine column
1448using the same technique you used for the peak list. </p>
1449
1450<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1451 id="Picture_x0020_45" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:468pt;
1452 height:238.5pt;visibility:visible;mso-wrap-style:square'>
1453 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image054.png" o:title=""/>
1454</v:shape><![endif]--><![if !vml]><img width=624 height=318
1455src="Charge%20Flipping%20-%20sucrose_files/image054.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
1456
1457<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1458you didn’t skip a step as it might not work correctly if you did.</p>
1459
1460<h2>Step 2: Pawley refinement</h2>
1461
1462<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1463normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1464minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1465the main GSAS-II data tree window. Before it begins a backup of the project
1466file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
1467style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1468mso-hansi-theme-font:minor-latin'>sucrose.bck0.gpx</span></b>. It can be used
1469to recover from a bad refinement. A progress dialog box will appear showing the
1470residual as the refinement proceeds. Notice that there was a singular matrix
1471warning on the console window and perhaps the last reflection (781) was removed
1472from the refinement because it was off the end of the used part of the pattern.
1473This is the GSAS-II singular matrix recovery mechanism; you can go to the <b
1474style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1475mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1476reflections</span></b> tab and uncheck the last reflection. Then repeat <b
1477style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1478mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1479to make sure it has essentially minimized. My refinement completed with <span
1480class=SpellE>Rwp</span> ~25% (NB: here and after succeeding refinements your <span
1481class=SpellE>Rwp</span> values may be slightly different from what I show
1482here); a dialog box appears asking if you wish to load the result. Press <b
1483style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1484mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1485To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
1486the width and height).</p>
1487
1488<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1489 id="Picture_x0020_46" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:420.75pt;
1490 height:360.75pt;visibility:visible;mso-wrap-style:square'>
1491 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image055.png" o:title=""/>
1492</v:shape><![endif]--><![if !vml]><img width=561 height=481
1493src="Charge%20Flipping%20-%20sucrose_files/image056.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
1494
1495<p class=MsoNormal>It is evident from examining the plot that some improvement
1496can be had by refining the lattice and profile parameters and perhaps the
1497sample X position. Go to <b style='mso-bidi-font-weight:normal'><span
1498style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1499mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> in the GSAS-II data
1500tree and check the <b style='mso-bidi-font-weight:normal'><span
1501style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1502mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> box. Now select <b
1503style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1504mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1505parameters</span></b> for the PWDR data set in the GSAS-II data tree and check <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'>U</span></b>,
1508<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1509mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>,
1510<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1511mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,<b
1512style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1513mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
1514class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
1515style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1516mso-hansi-theme-font:minor-latin'> Y</span></b>. The go to <b style='mso-bidi-font-weight:
1517normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1518minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and
1519check <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1520mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1521class=SpellE>displ</span></span></b>.; make the <b style='mso-bidi-font-weight:
1522normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1523minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> <b
1524style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1525mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1526if you didn’t do this earlier. Repeat <b style='mso-bidi-font-weight:normal'><span
1527style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1528mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged;
1529I obtained an improved residual of ~7.3% with a much better fit at the high
1530angle part of the pattern but still not fit well for the lower part.</p>
1531
1532<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1533 id="Picture_x0020_47" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:417.75pt;
1534 height:358.5pt;visibility:visible;mso-wrap-style:square'>
1535 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image057.png" o:title=""/>
1536</v:shape><![endif]--><![if !vml]><img width=557 height=478
1537src="Charge%20Flipping%20-%20sucrose_files/image058.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
1538
1539<p class=MsoNormal>What you see is that the background has a substantial
1540diffuse scattering feature at ~5deg and there are some peak shape issues (which
1541may be a consequence of the poor background fit). We’d like the fit to be
1542better before trying charge flipping. First select <b style='mso-bidi-font-weight:
1543normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1544minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>, set <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'>Peaks in background:
1547No. peaks</span></b> to <b style='mso-bidi-font-weight:normal'><span
1548style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1549mso-hansi-theme-font:minor-latin'>1</span></b> from the pull down box; the
1550window changes to </p>
1551
1552<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1553 id="Picture_x0020_48" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:325.5pt;
1554 height:165pt;visibility:visible;mso-wrap-style:square'>
1555 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image059.png" o:title=""/>
1556</v:shape><![endif]--><![if !vml]><img width=434 height=220
1557src="Charge%20Flipping%20-%20sucrose_files/image060.png" v:shapes="Picture_x0020_48"><![endif]></span><span
1558style='mso-spacerun:yes'> </span></p>
1559
1560<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
1561style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1562mso-hansi-theme-font:minor-latin'>5.0</span></b> for <span class=SpellE><b
1563style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1564mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span>,
1565<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1566mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
1567for <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1568style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1569mso-hansi-theme-font:minor-latin'>int</span></b></span> and <b
1570style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1571mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1572for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1573mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
1574(as appropriate for broad diffuse peaks) and then check all three refine boxes.
1575Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1576mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
1577class=SpellE>coeff</span>.</span></b> <span class=GramE>pulldown</span> to <b
1578style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1579mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>
1580for the <span class=SpellE>Chebyschev</span> part of the background. The window
1581should look like</p>
1582
1583<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1584 id="Picture_x0020_49" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:418.5pt;
1585 height:184.5pt;visibility:visible;mso-wrap-style:square'>
1586 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image061.png" o:title=""/>
1587</v:shape><![endif]--><![if !vml]><img width=558 height=246
1588src="Charge%20Flipping%20-%20sucrose_files/image062.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
1589
1590<p class=MsoNormal>Go to the <b style='mso-bidi-font-weight:normal'><span
1591style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1592mso-hansi-theme-font:minor-latin'>Controls</span></b> item in the GSAS-II data
1593tree and set the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1594"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1595minor-latin'>Max cycles</span></b> to <b style='mso-bidi-font-weight:normal'><span
1596style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1597mso-hansi-theme-font:minor-latin'>5</span></b>. Now do <b style='mso-bidi-font-weight:
1598normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1599minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until
1600the refinement converges. After a set of refinement cycles go to the <b
1601style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1602mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1603reflections</span></b> tab and check the intensities. If there are many
1604negatives amongst the highest angle reflections do <b style='mso-bidi-font-weight:
1605normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1606minor-latin;mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this
1607replaces all the values with those in the extracted from the profile as listed
1608in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1609mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1610list</span></b> for the PWDR data set each multiplied by 0.5. Additionally
1611their refinement flags are turned off. Do <b style='mso-bidi-font-weight:normal'><span
1612style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1613mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b><span
1614style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1615mso-hansi-theme-font:minor-latin'>; this will adjust all the reflections in the
1616vicinity of the reset ones</span>. You may repeat this process to suppress any
1617new negatives that may appear. Then set all the Pawley refinement flags back on
1618(excluding any that lead to a singular matrix) and repeat the refinement. After
1619refinement, mine converged to ~5.3% with very few negatives and the plot looked
1620like</p>
1621
1622<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1623 id="_x0000_i1054" type="#_x0000_t75" style='width:383.25pt;height:328.5pt;
1624 visibility:visible;mso-wrap-style:square'>
1625 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image063.png" o:title=""/>
1626</v:shape><![endif]--><![if !vml]><img width=511 height=438
1627src="Charge%20Flipping%20-%20sucrose_files/image064.png" v:shapes="_x0000_i1054"><![endif]></span></p>
1628
1629<p class=MsoNormal>Let’s see if this is good enough for charge flipping.</p>
1630
1631<h2>Step 3: Charge flipping</h2>
1632
1633<p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
1634Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1635mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1636and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1637"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1638minor-latin'>Charge flip controls</span></b> in the middle of the <b
1639style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1640mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1641tab.</p>
1642
1643<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1644mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1645"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1646</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
1647style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1648mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b
1649style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1650mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
165111bmb_8716.fxye Bank 1</span></b> (the only choice!). This makes the reflection
1652set to be used those in <b style='mso-bidi-font-weight:normal'><span
1653style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1654mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
1655data set; these should match the <b style='mso-bidi-font-weight:normal'><span
1656style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1657mso-hansi-theme-font:minor-latin'>Pawley reflection</span></b> set.</p>
1658
1659<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1660mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1661"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1662</span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span
1663style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1664mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b
1665style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1666mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map
1667controls</span></b>) to <b style='mso-bidi-font-weight:normal'><span
1668style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1669mso-hansi-theme-font:minor-latin'>20%</span></b>. This controls the map search
1670routine.</p>
1671
1672<p class=MsoNormal>For powder data it is not usually advisable to select a <b
1673style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1674mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing
1675element</span></b>; if selected a periodic table appears – select an element or
1676‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1677mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None’</span></b>.
1678The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1679mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1680defines the map spacing and thus the extent of the reflection set; the observed
1681reflection set is zero filled to this limit for charge flipping. The <b
1682style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1683mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b>
1684and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1685mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b>
1686determine the lower threshold and upper limit for charge flipping,
1687respectively. The latter is used to avoid “Uranium solutions” in the result.
1688Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1689"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1690minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
1691ones. For sucrose set it to <b style='mso-bidi-font-weight:normal'><span
1692style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1693mso-hansi-theme-font:minor-latin'>12.</span></b> When ready select <b
1694style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1695mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1696flipping</span></b>; a progress bar dialog will appear that tracks the residual
1697found in each charge flipping cycle. It will quickly drop to some level
1698(42-44%) and then for a successful charge flipping run perhaps drop again into
1699the 20-25% range after a considerable length of time. If it does drop then let
1700it run for a little bit; this “anneals” in the solution and generally gives a
1701better result. You should save the project if you get an apparently good
1702solution. Many times it will not drop below ~40%; just try <b style='mso-bidi-font-weight:
1703normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1704minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b>
1705again. If several tries fail to yield a solution, go back to the last step of
1706the Pawley refinement and just repeat it (that is do <b style='mso-bidi-font-weight:
1707normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1708minor-latin;mso-hansi-theme-font:minor-latin'>Pawley update</span></b> and <b
1709style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1710mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>).
1711This will generate a different set of intensities for the highly overlapped
1712part of the powder pattern; perhaps they will give a successful charge flip
1713solution. Unless otherwise interrupted, GSAS-II will try 10000 times for a
1714charge flip solution (for sucrose this takes 5-10min on my laptop). Press <b
1715style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1716mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b>
1717to stop the charge flipping; a peak list and a drawing of the solution will
1718appear. One of my runs gave</p>
1719
1720<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1721 id="Picture_x0020_51" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:468pt;
1722 height:234.75pt;visibility:visible;mso-wrap-style:square'>
1723 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image065.png" o:title=""/>
1724</v:shape><![endif]--><![if !vml]><img width=624 height=313
1725src="Charge%20Flipping%20-%20sucrose_files/image066.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
1726
1727<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1728
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1821</v:group><![endif]--><![if !vml]><span style='mso-ignore:vglayout;position:
1822absolute;z-index:251662336;margin-left:236px;margin-top:204px;width:15px;
1823height:34px'><img width=15 height=34
1824src="Charge%20Flipping%20-%20sucrose_files/image067.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
1825style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_52"
1826 o:spid="_x0000_i1052" type="#_x0000_t75" style='width:366pt;height:315.75pt;
1827 visibility:visible;mso-wrap-style:square'>
1828 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image068.png" o:title=""/>
1829</v:shape><![endif]--><![if !vml]><img width=488 height=421
1830src="Charge%20Flipping%20-%20sucrose_files/image069.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
1831
1832<p class=MsoNormal>The result looks very promising! Charge flipping operates
1833without regard to symmetry and GSAS-II attempts to locate the map with respect
1834to the symmetry elements from the computed reflection phases. (NB: charge flipping
1835also will give a solution without regard to handedness; this solution may be
1836either the correct one for sucrose or its inverse.) Errors in these phases can
1837disrupt this process so that the map and peak positions are offset from their
1838true positions. To discover this and fix it, rotate the drawing around to check
1839that atom positions are related via the 2<sub>1</sub> screw axis (through the
1840multicolored cross in the center of the cell and parallel to the y-axis – the
1841green cell edge). Avoid motions with the right mouse button pressed, this moves
1842the cross. To recover, press the ‘<b style='mso-bidi-font-weight:normal'><span
1843style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1844mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the cross to the
1845cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my drawing
1846above to show where I think it should be. If you find an offset to the map,
1847orient it so the offset is horizontal or vertical and then press the <b
1848style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1849mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>,
1850<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1851mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>,
1852<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1853mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
1854or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1855mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
1856keys to shift the map and peaks as needed. The shift is in resolution units
1857(0.5Å) so the fix can only be approximate. Repeat as needed. Notice that the
1858peak positions in the table are updated as the offset is changed. In this case,
1859I needed just a few steps to correct the map offset. NB: you can use these keys
1860to move the result anywhere you wish, e.g. to select a different origin for the
1861structure but pay attention to the location of symmetry elements. After
1862adjustment, my solution looked like</p>
1863
1864<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1865 id="Picture_x0020_53" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:399pt;
1866 height:345pt;visibility:visible;mso-wrap-style:square'>
1867 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image070.png" o:title=""/>
1868</v:shape><![endif]--><![if !vml]><img width=532 height=460
1869src="Charge%20Flipping%20-%20sucrose_files/image071.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
1870
1871<h2>Step 4: Obtain solution from charge flip result</h2>
1872
1873<p class=MsoNormal>The next step is to extract the unique peak positions from
1874the map and make atoms out of them. The map peak list is initially sorted by
1875peak magnitude; you can change the sorting to be along any of the column
1876headings in the table by a single click on the desired heading. The <span
1877class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1878"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1879minor-latin'>dzero</span></b></span> column gives the distance of each peak
1880from the origin. The menu items under Map peaks give you several tools to aid
1881in the peak selection process; we will just use a couple in this example. I
1882have chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:
1883normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1884minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and
1885then finding the unique ones. </p>
1886
1887<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1888mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1889"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1890</span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight:
1891normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1892minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> column heading. This
1893will sort the peaks in increasing z-axis coordinate.</p>
1894
1895<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1896mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1897"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1898</span></span></span><![endif]>Do a single click on the upper left (empty) box
1899of the table. All entries will be colored grey indicating their selection.</p>
1900
1901<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1902mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1903"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1904</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1905style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1906mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That
1907should select (grey) 23 out of 46 peak positions in the table and all should be
1908near the top of the list. The console displays this as both the number of
1909unique peaks and the fraction found (the ideal value, 0.5, for the latter is
1910easily inferred from the space group). Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
1911that would be all the C &amp; O atoms! They will be colored green in the plot.
1912If more are selected then check the map offset – it may need a slight
1913correction.</p>
1914
1915<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1916 id="Picture_x0020_54" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:382.5pt;
1917 height:309.75pt;visibility:visible;mso-wrap-style:square'>
1918 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image072.png" o:title=""/>
1919</v:shape><![endif]--><![if !vml]><img width=510 height=413
1920src="Charge%20Flipping%20-%20sucrose_files/image073.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
1921
1922<p class=MsoNormal>The drawing shows the selected atoms in green.</p>
1923
1924<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1925 id="Picture_x0020_55" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:394.5pt;
1926 height:342.75pt;visibility:visible;mso-wrap-style:square'>
1927 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image074.png" o:title=""/>
1928</v:shape><![endif]--><![if !vml]><img width=526 height=457
1929src="Charge%20Flipping%20-%20sucrose_files/image075.png" v:shapes="Picture_x0020_55"><![endif]></span></p>
1930
1931<p class=MsoNormal>Notice that in my case one atom is in a neighboring
1932molecule, one can deselect it and then pick the desired equivalent. Hold the <b
1933style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1934mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1935key down and use the right mouse button to pick/unpick atoms in the drawing.
1936NB: the left mouse button will clear all the selections. The other two “lone”
1937atoms belong to molecules in neighboring unit cells; we’ll deal with them
1938later.</p>
1939
1940<p class=MsoNormal>These are now ready to turn into atoms. Do <b
1941style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1942mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1943peaks/Move peaks</span></b>. The drawing will show white balls for each of the
1944selected positions and the <b style='mso-bidi-font-weight:normal'><span
1945style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1946mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 23 new H
1947atoms. </p>
1948
1949<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1950 id="Picture_x0020_56" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:375.75pt;
1951 height:326.25pt;visibility:visible;mso-wrap-style:square'>
1952 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image076.png" o:title=""/>
1953</v:shape><![endif]--><![if !vml]><img width=501 height=435
1954src="Charge%20Flipping%20-%20sucrose_files/image077.png" v:shapes="Picture_x0020_56"><![endif]></span></p>
1955
1956<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1957 id="Picture_x0020_57" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:417.75pt;
1958 height:332.25pt;visibility:visible;mso-wrap-style:square'>
1959 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image078.png" o:title=""/>
1960</v:shape><![endif]--><![if !vml]><img width=557 height=443
1961src="Charge%20Flipping%20-%20sucrose_files/image079.png" v:shapes="Picture_x0020_57"><![endif]></span></p>
1962
1963<p class=MsoNormal>The atom names indicate the peak magnitude to aid
1964identification (M100 for the largest in the <b style='mso-bidi-font-weight:
1965normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1966minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
1967may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
1968style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1969mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
1970them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
1971style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1972mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
1973normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1974minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
1975and then selecting a position in the table with the <b style='mso-bidi-font-weight:
1976normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1977minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
1978Linux machines the <b style='mso-bidi-font-weight:normal'><span
1979style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1980mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by
1981the operating system; use <b style='mso-bidi-font-weight:normal'><span
1982style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1983mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms.
1984After sorting by magnitude, my list is now </p>
1985
1986<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1987 id="Picture_x0020_58" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:468pt;
1988 height:372.75pt;visibility:visible;mso-wrap-style:square'>
1989 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image080.png" o:title=""/>
1990</v:shape><![endif]--><![if !vml]><img width=624 height=497
1991src="Charge%20Flipping%20-%20sucrose_files/image081.png" v:shapes="Picture_x0020_58"><![endif]></span></p>
1992
1993<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out
1994into two groups with a clear gap between M80 and M64. The higher ones are
1995likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit
1996of ambiguity in the middle, but just assign the top 11 as O and the rest as C
1997and see what happens. You can do this by selecting a block of atoms, go to <b
1998style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1999mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit
2000Atoms/On selected atoms…/Modify atom parameters</span></b> and select <b
2001style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2002mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b>
2003from the dialog box; a periodic table will appear. Select the desired element
2004and they will be changed in the list and drawing. <span style='mso-no-proof:
2005yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_59" o:spid="_x0000_i1045"
2006 type="#_x0000_t75" style='width:407.25pt;height:351pt;visibility:visible;
2007 mso-wrap-style:square'>
2008 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image082.png" o:title=""/>
2009</v:shape><![endif]--><![if !vml]><img width=543 height=468
2010src="Charge%20Flipping%20-%20sucrose_files/image083.png" v:shapes="Picture_x0020_59"><![endif]></span></p>
2011
2012<p class=MsoNormal>The original charge flipping solution is still visible and
2013the atoms are now identified, I’ve changed the drawing to show balls and sticks
2014and labeled the atoms with their names, this is done in the <b
2015style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2016mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b>
2017tab. Double click the appropriate column heading and make the selection from
2018the dialog box.<span style='mso-spacerun:yes'>  </span></p>
2019
2020<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2021 id="Picture_x0020_60" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:405pt;
2022 height:323.25pt;visibility:visible;mso-wrap-style:square'>
2023 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image084.png" o:title=""/>
2024</v:shape><![endif]--><![if !vml]><img width=540 height=431
2025src="Charge%20Flipping%20-%20sucrose_files/image085.png" v:shapes="Picture_x0020_60"><![endif]></span></p>
2026
2027<p class=MsoNormal>Now one can safely remove the map peaks (do <b
2028style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2029mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
2030peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span
2031style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2032mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
2033charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
2034style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2035mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
2036normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2037minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
2038style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2039mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2040tab). The atom positions I obtained in this charge flipping run have the sucrose
2041molecule fragmented over several neighboring molecules. We need assemble these
2042into a single molecule. Follow the steps:</p>
2043
2044<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2045mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2046"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2047</span></span></span><![endif]>In the Atoms tab of the Data window do <b
2048style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2049mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Atoms/Reload
2050draw <span class=GramE>atoms<span style='font-family:"Times New Roman",serif;
2051font-weight:normal'>.</span></span></span></b> This ensures the drawing is
2052up-to-date with the Atom list.</p>
2053
2054<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2055mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2056"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2057</span></span></span><![endif]>Select one atom in one of the fragments (perhaps
2058<span class=GramE>O(</span>1) in the drawing above as that is likely to be the
2059bridging O-atom between the two rings of sucrose. With the Atoms table showing
2060on the data window, use Shift-Left mouse button on the desired atom; it will turn
2061green indicating selection.</p>
2062
2063<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2064mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2065"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2066</span></span></span><![endif]>Then in the Atoms menu do <b style='mso-bidi-font-weight:
2067normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2068minor-latin;mso-hansi-theme-font:minor-latin'>Edit Atoms/Assemble molecule</span></b>;
2069a popup dialog offering choices of distances (&amp; angles – not used). Press <b
2070style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2071mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.</p>
2072
2073<p class=MsoNormal style='margin-left:.5in'>The atoms will automatically be
2074reorganized into a single molecule and are ordered in the table according to
2075connectivity.</p>
2076
2077<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2078 id="Picture_x0020_61" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:360.75pt;
2079 height:312.75pt;visibility:visible;mso-wrap-style:square'>
2080 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image086.png" o:title=""/>
2081</v:shape><![endif]--><![if !vml]><img width=481 height=417
2082src="Charge%20Flipping%20-%20sucrose_files/image087.png" v:shapes="Picture_x0020_61"><![endif]></span></p>
2083
2084<p class=MsoNormal>I’ve changed the style to balls &amp; sticks and added the
2085atom names as labels.</p>
2086
2087<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2088 id="Picture_x0020_62" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:430.5pt;
2089 height:342.75pt;visibility:visible;mso-wrap-style:square'>
2090 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image088.png" o:title=""/>
2091</v:shape><![endif]--><![if !vml]><img width=574 height=457
2092src="Charge%20Flipping%20-%20sucrose_files/image089.png" v:shapes="Picture_x0020_62"><![endif]></span></p>
2093
2094<p class=MsoNormal>If it happens that the Assemble molecule routine leaves one
2095or two atoms out, rerun it adjusting <span class=GramE>the</span> Bond search
2096factor to a slightly larger value (e.g. 0.9 vs 0.85). That should pick up the
2097outliers.</p>
2098
2099<p class=MsoNormal>To rename the atoms, select all the atoms (double click in
2100the empty left upper square of the Atom table; the entries will turn blue or
2101grey. Then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
2102"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2103minor-latin'>Edit Atoms/On selected atoms…/Modify atom parameters</span></b>.
2104Select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2105mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Name</span></b>
2106from the popup window and press <b style='mso-bidi-font-weight:normal'><span
2107style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2108mso-hansi-theme-font:minor-latin'>OK</span></b>; you will be asked to confirm.
2109The atoms will be renamed. </p>
2110
2111<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2112 id="Picture_x0020_63" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:405pt;
2113 height:322.5pt;visibility:visible;mso-wrap-style:square'>
2114 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image090.png" o:title=""/>
2115</v:shape><![endif]--><![if !vml]><img width=540 height=430
2116src="Charge%20Flipping%20-%20sucrose_files/image091.png" v:shapes="Picture_x0020_63"><![endif]></span></p>
2117
2118<p class=MsoNormal>You can also reorder the atoms to make the connectivity
2119conform to usual chemical naming <span class=GramE>rules</span>; use the Alt
2120key to pick &amp; place each atom to be moved just as we did with the Map peak
2121results above.</p>
2122
2123<p class=MsoNormal>Save the project file; the next step is to complete the
2124structure by finding H-atoms and then do the final Rietveld refinements.</p>
2125
2126<h2>Step 5: Complete the structure</h2>
2127
2128<p class=MsoNormal>To complete the structure you will need to perform a
2129preliminary Rietveld refinement. This will make the atom positions more
2130accurate and prepare a set of calculated structure factors needed to generate a
2131difference Fourier map good enough to maybe reveal the H atoms. There are a
2132number of steps needed to set all the controls from the previous Pawley
2133refinement to get a successful start for the Rietveld refinement.</p>
2134
2135<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2136mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2137"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2138</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2139style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2140mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the
2141GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span
2142style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2143mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You don’t want to
2144start with these when the scale factor is unknown.</p>
2145
2146<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2147mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2148"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2149</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
2150style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2151mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b
2152style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2153mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2154scale factor</span></b> box. This is the scale factor for the data set. Uncheck
2155the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2156mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
2157class=SpellE>displ</span></span></b>.</p>
2158
2159<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2160mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2161"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2162</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
2163style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2164mso-hansi-theme-font:minor-latin'>Phases/sucrose General</span></b> tab and
2165uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2166mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
2167cell</span></b> and <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'>Do Pawley refinement</span></b> boxes. The
2170latter is most important; if you forget you will just get another Pawley
2171refinement!</p>
2172
2173<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
2174style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2175mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
2176GSAS-II data tree menu; only scale and background are refined. I got <span
2177class=SpellE>Rwp</span> ~25%. The plot shows clear intensity differences; the
2178atom positions obviously need refinement.</p>
2179
2180<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2181 id="Picture_x0020_64" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:440.25pt;
2182 height:377.25pt;visibility:visible;mso-wrap-style:square'>
2183 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image092.png" o:title=""/>
2184</v:shape><![endif]--><![if !vml]><img width=587 height=503
2185src="Charge%20Flipping%20-%20sucrose_files/image093.png" v:shapes="Picture_x0020_64"><![endif]></span></p>
2186
2187<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
2188obvious.</p>
2189
2190<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
2191style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2192mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and select the <b
2193style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2194mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2195tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub>
2196has an arbitrary location along the y-axis. Then double click the <b
2197style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2198mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
2199column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight:
2200normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2201minor-latin;mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and
2202press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2203mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2204The atoms table will show the refinement controls</p>
2205
2206<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2207 id="Picture_x0020_65" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
2208 height:213.75pt;visibility:visible;mso-wrap-style:square'>
2209 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image094.png" o:title=""/>
2210</v:shape><![endif]--><![if !vml]><img width=624 height=285
2211src="Charge%20Flipping%20-%20sucrose_files/image095.png" v:shapes="Picture_x0020_65"><![endif]></span></p>
2212
2213<p class=MsoNormal>To deal with the warning we need to set a “Hold” on one atom
2214y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span
2215style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2216mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II
2217data tree; the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2218"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2219minor-latin;mso-bidi-theme-font:minor-latin'>Phase</span></b> tab is the one we
2220want here.</p>
2221
2222<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2223 id="Picture_x0020_66" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
2224 height:213.75pt;visibility:visible;mso-wrap-style:square'>
2225 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image096.png" o:title=""/>
2226</v:shape><![endif]--><![if !vml]><img width=624 height=285
2227src="Charge%20Flipping%20-%20sucrose_files/image097.png" v:shapes="Picture_x0020_66"><![endif]></span></p>
2228
2229<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
2230style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2231mso-hansi-theme-font:minor-latin'>Edit Constr<span class=GramE>./</span>Add
2232hold</span></b> and select ‘<b style='mso-bidi-font-weight:normal'><span
2233style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2234mso-hansi-theme-font:minor-latin'>0::dAy:0 for O(1)</span></b>’ from the dialog
2235box. Notice the use of a filter to shorten the list. This will fix the shift
2236along y for the <span class=GramE>O(</span>1) atom.</p>
2237
2238<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2239 id="Picture_x0020_67" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
2240 height:248.25pt;visibility:visible;mso-wrap-style:square'>
2241 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image098.png" o:title=""/>
2242</v:shape><![endif]--><![if !vml]><img width=624 height=331
2243src="Charge%20Flipping%20-%20sucrose_files/image098.png" v:shapes="Picture_x0020_67"><![endif]></span></p>
2244
2245<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2246style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2247mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will
2248show the hold</p>
2249
2250<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2251 id="Picture_x0020_68" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
2252 height:213.75pt;visibility:visible;mso-wrap-style:square'>
2253 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image099.png" o:title=""/>
2254</v:shape><![endif]--><![if !vml]><img width=624 height=285
2255src="Charge%20Flipping%20-%20sucrose_files/image100.png" v:shapes="Picture_x0020_68"><![endif]></span></p>
2256
2257<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
2258style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2259mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
2260class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice
2261parameters (in the <b style='mso-bidi-font-weight:normal'><span
2262style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2263mso-hansi-theme-font:minor-latin'>General</span></b> tab for <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'>Phases/sucrose</span></b>),
2266the <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'>Instrument
2268parameters</span></b> <b style='mso-bidi-font-weight:normal'><span
2269style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2270mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
2271normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2272minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b
2273style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2274mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
2275<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2276mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2277&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2278mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2279and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2280mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
2281class=SpellE>displ</span></span></b>. You can also include refinement of atom
2282thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
2283refinement improved slightly to Rwp~10.0%. Next we should add the hydrogen
2284atoms that are on carbon as these can be located from the molecular geometry.
2285To do this do the following:</p>
2286
2287<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2288
2289<p class=MsoNormal>Go to the Atoms tab and select the <b style='mso-bidi-font-weight:
2290normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2291minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column; a popup
2292will appear. Select just the <b style='mso-bidi-font-weight:normal'><span
2293style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2294mso-hansi-theme-font:minor-latin'>C</span></b> atoms; these will be highlighted
2295in grey in the Atom table.</p>
2296
2297<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
2298style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2299mso-hansi-theme-font:minor-latin'>Edit Atoms/On selected atoms…/<span
2300class=SpellE>Calc</span> H atoms</span></b> from the menu; a Distance Angle
2301Controls popup will appear. You can change radii and Bond search factor if
2302needed (rarely). Press <b style='mso-bidi-font-weight:normal'><span
2303style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2304mso-hansi-theme-font:minor-latin'>Ok</span></b>. A new popup window will
2305appear.<br>
2306<span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_50"
2307 o:spid="_x0000_i1035" type="#_x0000_t75" style='width:300pt;height:363.75pt;
2308 visibility:visible;mso-wrap-style:square'>
2309 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""/>
2310</v:shape><![endif]--><![if !vml]><img width=400 height=485
2311src="Charge%20Flipping%20-%20sucrose_files/image035.png" v:shapes="Picture_x0020_50"><![endif]></span><br>
2312This offers the choice of how many H-atoms to be added for each atom in the
2313table; the maximum is chosen for each atom. If the bonds are sufficiently short
2314this may be fewer reflecting the possibility of sp<sup>2</sup> or <span
2315class=SpellE>sp</span> bonding on the atom. You can override the choices made
2316by default. You also can deselect some of the other attached atoms so they will
2317not be used in the geometry calculations for H-atom placement (e.g. a metal
2318atom in certain organometallics). When you are satisfied with the choices
2319(actually no changes are needed in this case), press <b style='mso-bidi-font-weight:
2320normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2321minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>. The structure will
2322be redrawn with H-atoms shown as van der Waals spheres; they are inserted in
2323the Atom list immediately after the C-atom they are bound to and they are named
2324accordingly. </p>
2325
2326<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2327 id="Picture_x0020_69" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:400.5pt;
2328 height:346.5pt;visibility:visible;mso-wrap-style:square'>
2329 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image101.png" o:title=""/>
2330</v:shape><![endif]--><![if !vml]><img width=534 height=462
2331src="Charge%20Flipping%20-%20sucrose_files/image102.png" v:shapes="Picture_x0020_69"><![endif]></span></p>
2332
2333<p class=MsoNormal>These hydrogen atoms will better describe the scattering
2334density in the vicinity of the carbon atoms; their positions need to be refined
2335to find their better locations. Do <b style='mso-bidi-font-weight:normal'><span
2336style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2337mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (the refinement
2338flags are already set for this – NB: don’t be tempted to refine the H-atom
2339positions as they are likely to move erratically). My result was Rwp~9.2% and
2340the drawing is updated with the new atom positions (as van der Waals spheres).</p>
2341
2342<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2343 id="Picture_x0020_70" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:369.75pt;
2344 height:319.5pt;visibility:visible;mso-wrap-style:square'>
2345 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image103.png" o:title=""/>
2346</v:shape><![endif]--><![if !vml]><img width=493 height=426
2347src="Charge%20Flipping%20-%20sucrose_files/image104.png" v:shapes="Picture_x0020_70"><![endif]></span></p>
2348
2349<p class=MsoNormal>Because the C-atoms have probably moved; the H-atoms (which
2350were fixed) are now no longer in their optimal locations. From the menu, do <span
2351class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2352"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2353minor-latin'>Edit</span></b></span><b style='mso-bidi-font-weight:normal'><span
2354style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2355mso-hansi-theme-font:minor-latin'> Atoms/ <span class=SpellE>pdate</span> H
2356atoms</span></b>. This will shift their positions slightly. Repeat <b
2357style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2358mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
2359and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2360mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Update
2361H atoms</span></b>; you should see no shift this time. (<span class=SpellE>Rwp</span>
2362may be slightly higher; I got ~9.3%).</p>
2363
2364<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2365
2366<p class=MsoNormal>Now we have to find the hydrogens that are on oxygen; these
2367cannot be geometrically located except that they are somewhere on a circle at
2368the bonding distance from the O-atom. We need a difference Fourier map. Go to
2369the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2370mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose
2371General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
2372style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2373mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway
2374down the window.</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'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2379</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
2380normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2381minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
2382style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2383mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
2384for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2385mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</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'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2390</span></span></span><![endif]>Select <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'>PWDR 11bmb_8716.fxye Bank 1</span></b> for
2393the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2394mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
2395set from</span></b> item (the only choice). The Fourier calculation will use
2396the structure factors shown in the Reflection list item for this PWDR data set.</p>
2397
2398<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2399mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2400"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2401</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2402style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2403mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b
2404style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2405mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2406tab window. The map will be computed via fast Fourier techniques and is very
2407fast. A few lines summarizing the map is printed on the console, the structure
2408plot may show a single green dot somewhere (it could be hidden beneath an
2409atom!), this is the highest point in the map.</p>
2410
2411<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2412mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2413"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2414</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2415style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2416mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b
2417style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2418mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
2419level</span></b> slider until something appears on the map. You can also reduce
2420the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2421mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
2422and shift the View Point (use right mouse button) to help clarify the view.
2423Note that the map continues to show the density around the View Point even if
2424it is outside the unit cell box.</p>
2425
2426<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2427 id="Picture_x0020_31" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:362.25pt;
2428 height:308.25pt;visibility:visible;mso-wrap-style:square'>
2429 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image040.png" o:title=""
2430  croptop="10982f" cropbottom="17558f" cropleft="37484f" cropright="13065f"/>
2431</v:shape><![endif]--><![if !vml]><img width=483 height=411
2432src="Charge%20Flipping%20-%20sucrose_files/image105.jpg" v:shapes="Picture_x0020_31"><![endif]></span></p>
2433
2434<p class=MsoNormal>What is drawn here are green (&amp; red for negative) dots
2435whose size are proportional to the electron density. There are peaks that might
2436be H-atom positions as well as features that suggest O-atoms out of position.
2437Recall that the refinement was just done without any H-atoms on the oxygen
2438atoms; it will make the best fit compensating for the missing H-atoms by
2439displacing the O atoms in the direction of the missing H-atoms. To add the OH
2440atoms do the following:</p>
2441
2442<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2443mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2444"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2445</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2446style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2447mso-hansi-theme-font:minor-latin'>Phases/sucrose Atoms</span></b> tab.</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'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2452</span></span></span><![endif]>Select all O-atoms in the table (double click
2453the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2454mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b>
2455column heading &amp; select <b style='mso-bidi-font-weight:normal'><span
2456style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2457mso-hansi-theme-font:minor-latin'>O</span></b> atoms from the popup); all will
2458turn grey.</p>
2459
2460<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2461mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2462"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2463</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2464style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2465mso-hansi-theme-font:minor-latin'>Edit Atoms/On selected atoms…/<span
2466class=SpellE>Calc</span> H atoms</span></b> from the menu; a Distance Angle
2467Controls popup will appear. You can change radii and Bond search factor if
2468needed (rarely). Press <b style='mso-bidi-font-weight:normal'><span
2469style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2470mso-hansi-theme-font:minor-latin'>Ok</span></b>. A new popup window will appear</p>
2471
2472<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2473 id="Picture_x0020_32" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:300pt;
2474 height:363.75pt;visibility:visible;mso-wrap-style:square'>
2475 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/>
2476</v:shape><![endif]--><![if !vml]><img width=400 height=485
2477src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
2478
2479<p class=MsoNormal style='margin-left:.5in'>This offers the choice of how many
2480H-atoms to be added for each O-atom in the table; one is chosen in this case
2481for each atom. Press <b style='mso-bidi-font-weight:normal'><span
2482style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2483mso-hansi-theme-font:minor-latin'>Ok</span></b>. The structure will be redrawn
2484showing the added H-atoms.</p>
2485
2486<p class=MsoNormal style='margin-left:.5in'><o:p>&nbsp;</o:p></p>
2487
2488<p class=MsoNormal style='margin-left:.5in'>These OH hydrogens are found by finding
2489the highest point in the delta-F map for all possible orientations of this bond
2490at a fixed angle (109.5°). The new hydrogen atoms are inserted in the Atom list
2491immediately after the O-atom they are bound to and they are named accordingly</p>
2492
2493<p class=MsoNormal>Do the set of <b style='mso-bidi-font-weight:normal'><span
2494style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2495mso-hansi-theme-font:minor-latin'>Calculate/Refine, Edit Atoms/Update H atoms</span></b>
2496at least twice to finish this stage in the structure analysis; end with a <b
2497style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2498mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>.
2499My <span class=SpellE>Rwp</span> was ~8.14% with all the H-atoms included (but
2500not refined). The fit looks pretty good</p>
2501
2502<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2503 id="Picture_x0020_71" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:407.25pt;
2504 height:348.75pt;visibility:visible;mso-wrap-style:square'>
2505 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image106.png" o:title=""/>
2506</v:shape><![endif]--><![if !vml]><img width=543 height=465
2507src="Charge%20Flipping%20-%20sucrose_files/image107.png" v:shapes="Picture_x0020_71"><![endif]></span></p>
2508
2509<h2>Step 6: Final refinement</h2>
2510
2511<p class=MsoNormal>Looking at the fit, there may be room for improvement. First
2512we need to change the profile model to include crystallite size and <span
2513class=SpellE>mustrain</span> broadening. Go to <b style='mso-bidi-font-weight:
2514normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2515minor-latin;mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>,
2516set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2517mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2518and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2519mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2520to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2521mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>zero</span></b>
2522and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2523"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2524minor-latin'>Refine</span></b> flags for them.</p>
2525
2526<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
2527style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2528mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and look at the <b
2529style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2530mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
2531tab. Check the boxes for both <span class=SpellE><b style='mso-bidi-font-weight:
2532normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2533minor-latin;mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b
2534style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2535mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span
2536class=GramE>size</span></span></b> and <span class=SpellE><b style='mso-bidi-font-weight:
2537normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2538minor-latin;mso-hansi-theme-font:minor-latin'>microstrain</span></b></span>.</p>
2539
2540<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2541 id="Picture_x0020_72" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
2542 height:279.75pt;visibility:visible;mso-wrap-style:square'>
2543 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image108.png" o:title=""/>
2544</v:shape><![endif]--><![if !vml]><img width=624 height=373
2545src="Charge%20Flipping%20-%20sucrose_files/image109.png" v:shapes="Picture_x0020_72"><![endif]></span></p>
2546
2547<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2548style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2549mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2550class=SpellE>Rwp</span> will start out high but should converge to where it was
2551before this change. I got 8.09% and the <b style='mso-bidi-font-weight:normal'><span
2552style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2553mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>
2554
2555<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2556 id="Picture_x0020_73" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
2557 height:279.75pt;visibility:visible;mso-wrap-style:square'>
2558 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image110.png" o:title=""/>
2559</v:shape><![endif]--><![if !vml]><img width=624 height=373
2560src="Charge%20Flipping%20-%20sucrose_files/image111.png" v:shapes="Picture_x0020_73"><![endif]></span></p>
2561
2562<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
2563style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2564mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span
2565class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2566"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2567minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span
2568style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2569mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
2570phenomenological model for <span class=SpellE>microstrain</span> which has 9
2571terms for monoclinic structures. Check all the boxes for it and press <b
2572style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2573mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reset</span></b>.
2574This will convert the isotropic strain value to the equivalent generalized
2575values.</p>
2576
2577<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2578 id="Picture_x0020_74" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
2579 height:305.25pt;visibility:visible;mso-wrap-style:square'>
2580 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image112.png" o:title=""/>
2581</v:shape><![endif]--><![if !vml]><img width=624 height=407
2582src="Charge%20Flipping%20-%20sucrose_files/image113.png" v:shapes="Picture_x0020_74"><![endif]></span></p>
2583
2584<p class=MsoNormal>Do a <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'>Calculate/Refine</span></b>; the <span
2587class=SpellE>Rwp</span> will start out high but should converge lower than
2588where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight:
2589normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2590minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like.
2591If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2592style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2593mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b
2594style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2595mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot
2596type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span>
2597surface plot for ground sucrose.</p>
2598
2599<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2600 id="Picture_x0020_75" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
2601 height:305.25pt;visibility:visible;mso-wrap-style:square'>
2602 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image114.png" o:title=""/>
2603</v:shape><![endif]--><![if !vml]><img width=624 height=407
2604src="Charge%20Flipping%20-%20sucrose_files/image115.png" v:shapes="Picture_x0020_75"><![endif]></span></p>
2605
2606<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2607 id="Picture_x0020_76" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:357pt;
2608 height:378.75pt;visibility:visible;mso-wrap-style:square'>
2609 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image116.png" o:title=""/>
2610</v:shape><![endif]--><![if !vml]><img width=476 height=505
2611src="Charge%20Flipping%20-%20sucrose_files/image117.png" v:shapes="Picture_x0020_76"><![endif]></span></p>
2612
2613<p class=MsoNormal>This completes the exercise.</p>
2614
2615</div>
2616
2617</body>
2618
2619</html>
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