source: Tutorials/CFsucrose/Charge Flipping - sucrose.htm @ 1937

Last change on this file since 1937 was 1937, checked in by vondreele, 6 years ago

revised sucrose charge flip tutorial

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413  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/>
414  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
415  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
416  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
417  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
418  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
419  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
420  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
421  <w:LsdException Locked="false" Priority="34" QFormat="true"
422   Name="List Paragraph"/>
423  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
424  <w:LsdException Locked="false" Priority="30" QFormat="true"
425   Name="Intense Quote"/>
426  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
427  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
428  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
429  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
430  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
431  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
432  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
433  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
434  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
435  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
436  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
437  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
438  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
439  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
440  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
441  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
442  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
443  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
444  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
445  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
446  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
447  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
448  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
449  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
450  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
451  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
452  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
453  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
454  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
455  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
456  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
457  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
458  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
459  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
460  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
461  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
462  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
463  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
464  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
465  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
466  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
467  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
468  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
469  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
470  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
471  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
472  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
473  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
474  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
475  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
476  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
477  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
478  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
479  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
480  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
481  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
482  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
483  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
484  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
485  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
486  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
487  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
488  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
489  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
490  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
491  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
492  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
493  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
494  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
495  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
496  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
497  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
498  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
499  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
500  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
501  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
502  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
503  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
504  <w:LsdException Locked="false" Priority="19" QFormat="true"
505   Name="Subtle Emphasis"/>
506  <w:LsdException Locked="false" Priority="21" QFormat="true"
507   Name="Intense Emphasis"/>
508  <w:LsdException Locked="false" Priority="31" QFormat="true"
509   Name="Subtle Reference"/>
510  <w:LsdException Locked="false" Priority="32" QFormat="true"
511   Name="Intense Reference"/>
512  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
513  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
514   UnhideWhenUsed="true" Name="Bibliography"/>
515  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
516   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
517  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
518  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
519  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
520  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
521  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
522  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
523  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
524  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
525  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
526  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
527  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
528  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
529  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
530  <w:LsdException Locked="false" Priority="46"
531   Name="Grid Table 1 Light Accent 1"/>
532  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
533  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
534  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
535  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
536  <w:LsdException Locked="false" Priority="51"
537   Name="Grid Table 6 Colorful Accent 1"/>
538  <w:LsdException Locked="false" Priority="52"
539   Name="Grid Table 7 Colorful Accent 1"/>
540  <w:LsdException Locked="false" Priority="46"
541   Name="Grid Table 1 Light Accent 2"/>
542  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
543  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
544  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
545  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
546  <w:LsdException Locked="false" Priority="51"
547   Name="Grid Table 6 Colorful Accent 2"/>
548  <w:LsdException Locked="false" Priority="52"
549   Name="Grid Table 7 Colorful Accent 2"/>
550  <w:LsdException Locked="false" Priority="46"
551   Name="Grid Table 1 Light Accent 3"/>
552  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
553  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
554  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
555  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
556  <w:LsdException Locked="false" Priority="51"
557   Name="Grid Table 6 Colorful Accent 3"/>
558  <w:LsdException Locked="false" Priority="52"
559   Name="Grid Table 7 Colorful Accent 3"/>
560  <w:LsdException Locked="false" Priority="46"
561   Name="Grid Table 1 Light Accent 4"/>
562  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
563  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
564  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
565  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
566  <w:LsdException Locked="false" Priority="51"
567   Name="Grid Table 6 Colorful Accent 4"/>
568  <w:LsdException Locked="false" Priority="52"
569   Name="Grid Table 7 Colorful Accent 4"/>
570  <w:LsdException Locked="false" Priority="46"
571   Name="Grid Table 1 Light Accent 5"/>
572  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
573  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
574  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
575  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
576  <w:LsdException Locked="false" Priority="51"
577   Name="Grid Table 6 Colorful Accent 5"/>
578  <w:LsdException Locked="false" Priority="52"
579   Name="Grid Table 7 Colorful Accent 5"/>
580  <w:LsdException Locked="false" Priority="46"
581   Name="Grid Table 1 Light Accent 6"/>
582  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
583  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
584  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
585  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
586  <w:LsdException Locked="false" Priority="51"
587   Name="Grid Table 6 Colorful Accent 6"/>
588  <w:LsdException Locked="false" Priority="52"
589   Name="Grid Table 7 Colorful Accent 6"/>
590  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
591  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
592  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
593  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
594  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
595  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
596  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
597  <w:LsdException Locked="false" Priority="46"
598   Name="List Table 1 Light Accent 1"/>
599  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
600  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
601  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
602  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
603  <w:LsdException Locked="false" Priority="51"
604   Name="List Table 6 Colorful Accent 1"/>
605  <w:LsdException Locked="false" Priority="52"
606   Name="List Table 7 Colorful Accent 1"/>
607  <w:LsdException Locked="false" Priority="46"
608   Name="List Table 1 Light Accent 2"/>
609  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
610  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
611  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
612  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
613  <w:LsdException Locked="false" Priority="51"
614   Name="List Table 6 Colorful Accent 2"/>
615  <w:LsdException Locked="false" Priority="52"
616   Name="List Table 7 Colorful Accent 2"/>
617  <w:LsdException Locked="false" Priority="46"
618   Name="List Table 1 Light Accent 3"/>
619  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
620  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
621  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
622  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
623  <w:LsdException Locked="false" Priority="51"
624   Name="List Table 6 Colorful Accent 3"/>
625  <w:LsdException Locked="false" Priority="52"
626   Name="List Table 7 Colorful Accent 3"/>
627  <w:LsdException Locked="false" Priority="46"
628   Name="List Table 1 Light Accent 4"/>
629  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
630  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
631  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
632  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
633  <w:LsdException Locked="false" Priority="51"
634   Name="List Table 6 Colorful Accent 4"/>
635  <w:LsdException Locked="false" Priority="52"
636   Name="List Table 7 Colorful Accent 4"/>
637  <w:LsdException Locked="false" Priority="46"
638   Name="List Table 1 Light Accent 5"/>
639  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
640  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
641  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
642  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
643  <w:LsdException Locked="false" Priority="51"
644   Name="List Table 6 Colorful Accent 5"/>
645  <w:LsdException Locked="false" Priority="52"
646   Name="List Table 7 Colorful Accent 5"/>
647  <w:LsdException Locked="false" Priority="46"
648   Name="List Table 1 Light Accent 6"/>
649  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
650  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
651  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
652  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
653  <w:LsdException Locked="false" Priority="51"
654   Name="List Table 6 Colorful Accent 6"/>
655  <w:LsdException Locked="false" Priority="52"
656   Name="List Table 7 Colorful Accent 6"/>
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782        mso-style-priority:9;
783        mso-style-unhide:no;
784        mso-style-locked:yes;
785        mso-style-link:"Heading 2";
786        mso-ansi-font-size:18.0pt;
787        mso-bidi-font-size:18.0pt;
788        font-family:"Times New Roman",serif;
789        mso-ascii-font-family:"Times New Roman";
790        mso-fareast-font-family:"Times New Roman";
791        mso-fareast-theme-font:minor-fareast;
792        mso-hansi-font-family:"Times New Roman";
793        mso-bidi-font-family:"Times New Roman";
794        font-weight:bold;}
795span.BalloonTextChar
796        {mso-style-name:"Balloon Text Char";
797        mso-style-noshow:yes;
798        mso-style-priority:99;
799        mso-style-unhide:no;
800        mso-style-locked:yes;
801        mso-style-link:"Balloon Text";
802        mso-ansi-font-size:8.0pt;
803        mso-bidi-font-size:8.0pt;
804        font-family:"Tahoma",sans-serif;
805        mso-ascii-font-family:Tahoma;
806        mso-fareast-font-family:"Times New Roman";
807        mso-fareast-theme-font:minor-fareast;
808        mso-hansi-font-family:Tahoma;
809        mso-bidi-font-family:Tahoma;}
810span.SpellE
811        {mso-style-name:"";
812        mso-spl-e:yes;}
813span.GramE
814        {mso-style-name:"";
815        mso-gram-e:yes;}
816.MsoChpDefault
817        {mso-style-type:export-only;
818        mso-default-props:yes;
819        font-size:12.0pt;
820        mso-ansi-font-size:12.0pt;
821        mso-bidi-font-size:12.0pt;
822        mso-fareast-font-family:Calibri;
823        mso-fareast-theme-font:minor-latin;
824        mso-bidi-font-family:"Times New Roman";
825        mso-bidi-theme-font:minor-bidi;}
826@page WordSection1
827        {size:8.5in 11.0in;
828        margin:1.0in 1.0in 1.0in 1.0in;
829        mso-header-margin:.5in;
830        mso-footer-margin:.5in;
831        mso-paper-source:0;}
832div.WordSection1
833        {page:WordSection1;}
834 /* List Definitions */
835 @list l0
836        {mso-list-id:82917343;
837        mso-list-type:hybrid;
838        mso-list-template-ids:-1527319822 -2100533712 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
839@list l0:level1
840        {mso-level-tab-stop:none;
841        mso-level-number-position:left;
842        margin-left:.75in;
843        text-indent:-.25in;}
844@list l0:level2
845        {mso-level-number-format:alpha-lower;
846        mso-level-tab-stop:none;
847        mso-level-number-position:left;
848        margin-left:1.25in;
849        text-indent:-.25in;}
850@list l0:level3
851        {mso-level-number-format:roman-lower;
852        mso-level-tab-stop:none;
853        mso-level-number-position:right;
854        margin-left:1.75in;
855        text-indent:-9.0pt;}
856@list l0:level4
857        {mso-level-tab-stop:none;
858        mso-level-number-position:left;
859        margin-left:2.25in;
860        text-indent:-.25in;}
861@list l0:level5
862        {mso-level-number-format:alpha-lower;
863        mso-level-tab-stop:none;
864        mso-level-number-position:left;
865        margin-left:2.75in;
866        text-indent:-.25in;}
867@list l0:level6
868        {mso-level-number-format:roman-lower;
869        mso-level-tab-stop:none;
870        mso-level-number-position:right;
871        margin-left:3.25in;
872        text-indent:-9.0pt;}
873@list l0:level7
874        {mso-level-tab-stop:none;
875        mso-level-number-position:left;
876        margin-left:3.75in;
877        text-indent:-.25in;}
878@list l0:level8
879        {mso-level-number-format:alpha-lower;
880        mso-level-tab-stop:none;
881        mso-level-number-position:left;
882        margin-left:4.25in;
883        text-indent:-.25in;}
884@list l0:level9
885        {mso-level-number-format:roman-lower;
886        mso-level-tab-stop:none;
887        mso-level-number-position:right;
888        margin-left:4.75in;
889        text-indent:-9.0pt;}
890@list l1
891        {mso-list-id:236667377;
892        mso-list-type:hybrid;
893        mso-list-template-ids:-513138304 1385070818 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
894@list l1:level1
895        {mso-level-tab-stop:none;
896        mso-level-number-position:left;
897        margin-left:.75in;
898        text-indent:-.25in;}
899@list l1:level2
900        {mso-level-number-format:alpha-lower;
901        mso-level-tab-stop:none;
902        mso-level-number-position:left;
903        margin-left:1.25in;
904        text-indent:-.25in;}
905@list l1:level3
906        {mso-level-number-format:roman-lower;
907        mso-level-tab-stop:none;
908        mso-level-number-position:right;
909        margin-left:1.75in;
910        text-indent:-9.0pt;}
911@list l1:level4
912        {mso-level-tab-stop:none;
913        mso-level-number-position:left;
914        margin-left:2.25in;
915        text-indent:-.25in;}
916@list l1:level5
917        {mso-level-number-format:alpha-lower;
918        mso-level-tab-stop:none;
919        mso-level-number-position:left;
920        margin-left:2.75in;
921        text-indent:-.25in;}
922@list l1:level6
923        {mso-level-number-format:roman-lower;
924        mso-level-tab-stop:none;
925        mso-level-number-position:right;
926        margin-left:3.25in;
927        text-indent:-9.0pt;}
928@list l1:level7
929        {mso-level-tab-stop:none;
930        mso-level-number-position:left;
931        margin-left:3.75in;
932        text-indent:-.25in;}
933@list l1:level8
934        {mso-level-number-format:alpha-lower;
935        mso-level-tab-stop:none;
936        mso-level-number-position:left;
937        margin-left:4.25in;
938        text-indent:-.25in;}
939@list l1:level9
940        {mso-level-number-format:roman-lower;
941        mso-level-tab-stop:none;
942        mso-level-number-position:right;
943        margin-left:4.75in;
944        text-indent:-9.0pt;}
945@list l2
946        {mso-list-id:533275380;
947        mso-list-type:hybrid;
948        mso-list-template-ids:-1319630076 -1606007952 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
949@list l2:level1
950        {mso-level-tab-stop:none;
951        mso-level-number-position:left;
952        margin-left:.75in;
953        text-indent:-.25in;}
954@list l2:level2
955        {mso-level-number-format:alpha-lower;
956        mso-level-tab-stop:none;
957        mso-level-number-position:left;
958        margin-left:1.25in;
959        text-indent:-.25in;}
960@list l2:level3
961        {mso-level-number-format:roman-lower;
962        mso-level-tab-stop:none;
963        mso-level-number-position:right;
964        margin-left:1.75in;
965        text-indent:-9.0pt;}
966@list l2:level4
967        {mso-level-tab-stop:none;
968        mso-level-number-position:left;
969        margin-left:2.25in;
970        text-indent:-.25in;}
971@list l2:level5
972        {mso-level-number-format:alpha-lower;
973        mso-level-tab-stop:none;
974        mso-level-number-position:left;
975        margin-left:2.75in;
976        text-indent:-.25in;}
977@list l2:level6
978        {mso-level-number-format:roman-lower;
979        mso-level-tab-stop:none;
980        mso-level-number-position:right;
981        margin-left:3.25in;
982        text-indent:-9.0pt;}
983@list l2:level7
984        {mso-level-tab-stop:none;
985        mso-level-number-position:left;
986        margin-left:3.75in;
987        text-indent:-.25in;}
988@list l2:level8
989        {mso-level-number-format:alpha-lower;
990        mso-level-tab-stop:none;
991        mso-level-number-position:left;
992        margin-left:4.25in;
993        text-indent:-.25in;}
994@list l2:level9
995        {mso-level-number-format:roman-lower;
996        mso-level-tab-stop:none;
997        mso-level-number-position:right;
998        margin-left:4.75in;
999        text-indent:-9.0pt;}
1000@list l3
1001        {mso-list-id:588542776;
1002        mso-list-type:hybrid;
1003        mso-list-template-ids:477805396 -2056748102 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1004@list l3:level1
1005        {mso-level-tab-stop:none;
1006        mso-level-number-position:left;
1007        margin-left:.75in;
1008        text-indent:-.25in;}
1009@list l3:level2
1010        {mso-level-number-format:alpha-lower;
1011        mso-level-tab-stop:none;
1012        mso-level-number-position:left;
1013        margin-left:1.25in;
1014        text-indent:-.25in;}
1015@list l3:level3
1016        {mso-level-number-format:roman-lower;
1017        mso-level-tab-stop:none;
1018        mso-level-number-position:right;
1019        margin-left:1.75in;
1020        text-indent:-9.0pt;}
1021@list l3:level4
1022        {mso-level-tab-stop:none;
1023        mso-level-number-position:left;
1024        margin-left:2.25in;
1025        text-indent:-.25in;}
1026@list l3:level5
1027        {mso-level-number-format:alpha-lower;
1028        mso-level-tab-stop:none;
1029        mso-level-number-position:left;
1030        margin-left:2.75in;
1031        text-indent:-.25in;}
1032@list l3:level6
1033        {mso-level-number-format:roman-lower;
1034        mso-level-tab-stop:none;
1035        mso-level-number-position:right;
1036        margin-left:3.25in;
1037        text-indent:-9.0pt;}
1038@list l3:level7
1039        {mso-level-tab-stop:none;
1040        mso-level-number-position:left;
1041        margin-left:3.75in;
1042        text-indent:-.25in;}
1043@list l3:level8
1044        {mso-level-number-format:alpha-lower;
1045        mso-level-tab-stop:none;
1046        mso-level-number-position:left;
1047        margin-left:4.25in;
1048        text-indent:-.25in;}
1049@list l3:level9
1050        {mso-level-number-format:roman-lower;
1051        mso-level-tab-stop:none;
1052        mso-level-number-position:right;
1053        margin-left:4.75in;
1054        text-indent:-9.0pt;}
1055@list l4
1056        {mso-list-id:854225785;
1057        mso-list-type:hybrid;
1058        mso-list-template-ids:-2071413312 1417604178 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1059@list l4:level1
1060        {mso-level-tab-stop:none;
1061        mso-level-number-position:left;
1062        margin-left:.75in;
1063        text-indent:-.25in;}
1064@list l4:level2
1065        {mso-level-number-format:alpha-lower;
1066        mso-level-tab-stop:none;
1067        mso-level-number-position:left;
1068        margin-left:1.25in;
1069        text-indent:-.25in;}
1070@list l4:level3
1071        {mso-level-number-format:roman-lower;
1072        mso-level-tab-stop:none;
1073        mso-level-number-position:right;
1074        margin-left:1.75in;
1075        text-indent:-9.0pt;}
1076@list l4:level4
1077        {mso-level-tab-stop:none;
1078        mso-level-number-position:left;
1079        margin-left:2.25in;
1080        text-indent:-.25in;}
1081@list l4:level5
1082        {mso-level-number-format:alpha-lower;
1083        mso-level-tab-stop:none;
1084        mso-level-number-position:left;
1085        margin-left:2.75in;
1086        text-indent:-.25in;}
1087@list l4:level6
1088        {mso-level-number-format:roman-lower;
1089        mso-level-tab-stop:none;
1090        mso-level-number-position:right;
1091        margin-left:3.25in;
1092        text-indent:-9.0pt;}
1093@list l4:level7
1094        {mso-level-tab-stop:none;
1095        mso-level-number-position:left;
1096        margin-left:3.75in;
1097        text-indent:-.25in;}
1098@list l4:level8
1099        {mso-level-number-format:alpha-lower;
1100        mso-level-tab-stop:none;
1101        mso-level-number-position:left;
1102        margin-left:4.25in;
1103        text-indent:-.25in;}
1104@list l4:level9
1105        {mso-level-number-format:roman-lower;
1106        mso-level-tab-stop:none;
1107        mso-level-number-position:right;
1108        margin-left:4.75in;
1109        text-indent:-9.0pt;}
1110@list l5
1111        {mso-list-id:1022125565;
1112        mso-list-type:hybrid;
1113        mso-list-template-ids:-482838388 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1114@list l5:level1
1115        {mso-level-tab-stop:none;
1116        mso-level-number-position:left;
1117        margin-left:1.0in;
1118        text-indent:-.25in;}
1119@list l5:level2
1120        {mso-level-number-format:alpha-lower;
1121        mso-level-tab-stop:none;
1122        mso-level-number-position:left;
1123        margin-left:1.5in;
1124        text-indent:-.25in;}
1125@list l5:level3
1126        {mso-level-number-format:roman-lower;
1127        mso-level-tab-stop:none;
1128        mso-level-number-position:right;
1129        margin-left:2.0in;
1130        text-indent:-9.0pt;}
1131@list l5:level4
1132        {mso-level-tab-stop:none;
1133        mso-level-number-position:left;
1134        margin-left:2.5in;
1135        text-indent:-.25in;}
1136@list l5:level5
1137        {mso-level-number-format:alpha-lower;
1138        mso-level-tab-stop:none;
1139        mso-level-number-position:left;
1140        margin-left:3.0in;
1141        text-indent:-.25in;}
1142@list l5:level6
1143        {mso-level-number-format:roman-lower;
1144        mso-level-tab-stop:none;
1145        mso-level-number-position:right;
1146        margin-left:3.5in;
1147        text-indent:-9.0pt;}
1148@list l5:level7
1149        {mso-level-tab-stop:none;
1150        mso-level-number-position:left;
1151        margin-left:4.0in;
1152        text-indent:-.25in;}
1153@list l5:level8
1154        {mso-level-number-format:alpha-lower;
1155        mso-level-tab-stop:none;
1156        mso-level-number-position:left;
1157        margin-left:4.5in;
1158        text-indent:-.25in;}
1159@list l5:level9
1160        {mso-level-number-format:roman-lower;
1161        mso-level-tab-stop:none;
1162        mso-level-number-position:right;
1163        margin-left:5.0in;
1164        text-indent:-9.0pt;}
1165@list l6
1166        {mso-list-id:2020618629;
1167        mso-list-type:hybrid;
1168        mso-list-template-ids:-199700640 470186964 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1169@list l6:level1
1170        {mso-level-tab-stop:none;
1171        mso-level-number-position:left;
1172        margin-left:.75in;
1173        text-indent:-.25in;}
1174@list l6:level2
1175        {mso-level-number-format:alpha-lower;
1176        mso-level-tab-stop:none;
1177        mso-level-number-position:left;
1178        margin-left:1.25in;
1179        text-indent:-.25in;}
1180@list l6:level3
1181        {mso-level-number-format:roman-lower;
1182        mso-level-tab-stop:none;
1183        mso-level-number-position:right;
1184        margin-left:1.75in;
1185        text-indent:-9.0pt;}
1186@list l6:level4
1187        {mso-level-tab-stop:none;
1188        mso-level-number-position:left;
1189        margin-left:2.25in;
1190        text-indent:-.25in;}
1191@list l6:level5
1192        {mso-level-number-format:alpha-lower;
1193        mso-level-tab-stop:none;
1194        mso-level-number-position:left;
1195        margin-left:2.75in;
1196        text-indent:-.25in;}
1197@list l6:level6
1198        {mso-level-number-format:roman-lower;
1199        mso-level-tab-stop:none;
1200        mso-level-number-position:right;
1201        margin-left:3.25in;
1202        text-indent:-9.0pt;}
1203@list l6:level7
1204        {mso-level-tab-stop:none;
1205        mso-level-number-position:left;
1206        margin-left:3.75in;
1207        text-indent:-.25in;}
1208@list l6:level8
1209        {mso-level-number-format:alpha-lower;
1210        mso-level-tab-stop:none;
1211        mso-level-number-position:left;
1212        margin-left:4.25in;
1213        text-indent:-.25in;}
1214@list l6:level9
1215        {mso-level-number-format:roman-lower;
1216        mso-level-tab-stop:none;
1217        mso-level-number-position:right;
1218        margin-left:4.75in;
1219        text-indent:-9.0pt;}
1220ol
1221        {margin-bottom:0in;}
1222ul
1223        {margin-bottom:0in;}
1224-->
1225</style>
1226<!--[if gte mso 10]>
1227<style>
1228 /* Style Definitions */
1229 table.MsoNormalTable
1230        {mso-style-name:"Table Normal";
1231        mso-tstyle-rowband-size:0;
1232        mso-tstyle-colband-size:0;
1233        mso-style-noshow:yes;
1234        mso-style-priority:99;
1235        mso-style-parent:"";
1236        mso-padding-alt:0in 5.4pt 0in 5.4pt;
1237        mso-para-margin:0in;
1238        mso-para-margin-bottom:.0001pt;
1239        mso-pagination:widow-orphan;
1240        font-size:12.0pt;
1241        font-family:"Times New Roman",serif;
1242        mso-bidi-font-family:"Times New Roman";
1243        mso-bidi-theme-font:minor-bidi;}
1244</style>
1245<![endif]--><!--[if gte mso 9]><xml>
1246 <o:shapedefaults v:ext="edit" spidmax="1029"/>
1247</xml><![endif]--><!--[if gte mso 9]><xml>
1248 <o:shapelayout v:ext="edit">
1249  <o:idmap v:ext="edit" data="1"/>
1250 </o:shapelayout></xml><![endif]-->
1251</head>
1252
1253<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1254
1255<div class=WordSection1>
1256
1257<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in
1258GSAS-II - sucrose<o:p></o:p></span></h1>
1259
1260<h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1>
1261
1262<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1263of sucrose from powder diffraction data via charge flipping. This structure was
1264originally solved from single crystal data in the space group P2<sub>1</sub>.
1265It is a difficult exercise to complete as the charge flipping does not always
1266yield a solution and to even have a chance the Pawley refinement must be done
1267with particular care. We have given a route that sometimes works.</p>
1268
1269<p class=MsoNormal>If you have not done so already, start GSAS-II and open the
1270GSAS-II project file (I called it <span class=SpellE><b style='mso-bidi-font-weight:
1271normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1272minor-latin;mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b></span>)
1273you saved from the third part of the peak fitting-indexing exercise. If you
1274didn’t do that exercise, do it now.</p>
1275
1276<h2>Step 1: Setup for Pawley refinement</h2>
1277
1278<p class=MsoNormal>There are a number of steps that must be done in preparation
1279for a Pawley refinement after having completed the unit cell indexing and new
1280phase creation. These cover two things: one is to prepare the powder pattern
1281(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1282
1283<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1284style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1285style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1286<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1287mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
1288in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1289region near d=1.0Å is readily seen. This is ~24deg 2<span style='font-family:
1290Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1291mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1292symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
1293relatively clear of peaks that makes a good place to end the calculations with
1294a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution
1295needed for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span
1296style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1297mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span class=SpellE><b
1298style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1299mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b></span>
1300as the upper limit and make a note of the exact d-spacing (1.0125Å) using the
1301mouse cursor on the plot.</p>
1302
1303<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1304style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1305style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1306<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1307mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1308Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1309style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1310mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1311style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1312mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1313profile</span></b> to recover the default values. The peak fitting done earlier
1314is over a much more limited range of 2<span style='font-family:Symbol;
1315mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1316mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1317symbol;mso-symbol-font-family:Symbol'>Q</span></span> giving values that might
1318not extrapolate well over the wider range to be used in the Pawley refinement.
1319We will refine them again later.</p>
1320
1321<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1322style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1323style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1324<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1325mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1326Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1327normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1328minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.
1329While you are here set <b style='mso-bidi-font-weight:normal'><span
1330style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1331mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> to <b
1332style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1333mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>.</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'>4.<span
1337style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1338to <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'>Phases/sucrose</span></b>
1340to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1341"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1342minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1343normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1344minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
1345box and enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
1346style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1347mso-hansi-theme-font:minor-latin'>1.0125</span></b>) into the <b
1348style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1349mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1350class=SpellE>dmin</span></span></b> box.</p>
1351
1352<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1353style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1354mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1355
1356<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1357 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1358 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1359 <v:stroke joinstyle="miter"/>
1360 <v:formulas>
1361  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1362  <v:f eqn="sum @0 1 0"/>
1363  <v:f eqn="sum 0 0 @1"/>
1364  <v:f eqn="prod @2 1 2"/>
1365  <v:f eqn="prod @3 21600 pixelWidth"/>
1366  <v:f eqn="prod @3 21600 pixelHeight"/>
1367  <v:f eqn="sum @0 0 1"/>
1368  <v:f eqn="prod @6 1 2"/>
1369  <v:f eqn="prod @7 21600 pixelWidth"/>
1370  <v:f eqn="sum @8 21600 0"/>
1371  <v:f eqn="prod @7 21600 pixelHeight"/>
1372  <v:f eqn="sum @10 21600 0"/>
1373 </v:formulas>
1374 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1375 <o:lock v:ext="edit" aspectratio="t"/>
1376</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1062" type="#_x0000_t75"
1377 style='width:542.25pt;height:375pt;visibility:visible;mso-wrap-style:square'>
1378 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image001.png" o:title=""/>
1379</v:shape><![endif]--><![if !vml]><img width=723 height=500
1380src="Charge%20Flipping%20-%20sucrose_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
1381
1382<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1383style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1384mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1385for some text. Do <b style='mso-bidi-font-weight:normal'><span
1386style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1387mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
1388dialog box will appear</p>
1389
1390<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1391 id="Picture_x0020_2" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:240pt;
1392 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1393 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image002.png" o:title=""/>
1394</v:shape><![endif]--><![if !vml]><img width=320 height=310
1395src="Charge%20Flipping%20-%20sucrose_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1396
1397<p class=MsoNormal>Select the only choice and press <b style='mso-bidi-font-weight:
1398normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1399minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>; the desired data
1400set will be added to this phase for analysis. The data tab now shows the new
1401data set.</p>
1402
1403<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1404 id="Picture_x0020_3" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:359.25pt;
1405 height:375pt;visibility:visible;mso-wrap-style:square'>
1406 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image003.png" o:title=""/>
1407</v:shape><![endif]--><![if !vml]><img width=479 height=500
1408src="Charge%20Flipping%20-%20sucrose_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
1409
1410<p class=MsoNormal>I’ve stretched the window slightly to see the entire
1411contents. This is the location for all the phase dependent parameters for this
1412histogram. Notice that it includes phase fraction, size &amp; <span
1413class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1414and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1415intended for protein work where a significant region of the structure is disordered
1416solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1417surfaces as well as preferred orientation correction curves.</p>
1418
1419<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1420style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1421mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1422empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
1423style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1424mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
1425makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
1426normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1427minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>.
1428The table should list reflections 0~780. Select and check the refine column
1429using the same technique you used for the peak list. </p>
1430
1431<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1432 id="Picture_x0020_4" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:375pt;
1433 height:225pt;visibility:visible;mso-wrap-style:square'>
1434 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image004.png" o:title=""/>
1435</v:shape><![endif]--><![if !vml]><img width=500 height=300
1436src="Charge%20Flipping%20-%20sucrose_files/image004.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
1437
1438<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1439you didn’t skip a step as it might not work correctly if you did.</p>
1440
1441<h2>Step 2: Pawley refinement</h2>
1442
1443<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1444normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1445minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1446the main GSAS-II data tree window. Before it begins a backup of the project
1447file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
1448style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1449mso-hansi-theme-font:minor-latin'>sucrose.bck0.gpx</span></b>. It can be used
1450to recover from a bad refinement. A progress dialog box will appear showing the
1451residual as the refinement proceeds. Notice that there was a singular matrix
1452warning on the console window and perhaps the last reflection (781) was removed
1453from the refinement because it was off the end of the used part of the pattern.
1454This is the GSAS-II singular matrix recovery mechanism; you can go to the <b
1455style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1456mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1457reflections</span></b> tab and uncheck the last reflection. Then repeat <b
1458style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1459mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1460to make sure it has essentially minimized. My refinement completed with <span
1461class=SpellE>Rwp</span> ~25%; a dialog box appears asking if you wish to load
1462the result. Press <b style='mso-bidi-font-weight:normal'><span
1463style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1464mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
1465PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
1466
1467<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1468 id="Picture_x0020_5" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:525pt;
1469 height:450pt;visibility:visible;mso-wrap-style:square'>
1470 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image005.png" o:title=""/>
1471</v:shape><![endif]--><![if !vml]><img width=700 height=600
1472src="Charge%20Flipping%20-%20sucrose_files/image005.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
1473
1474<p class=MsoNormal>It is evident from examining the plot that some improvement
1475can be had by refining the lattice and profile parameters and perhaps the
1476sample X position. Go to <b style='mso-bidi-font-weight:normal'><span
1477style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1478mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> in the GSAS-II data
1479tree and check the <b style='mso-bidi-font-weight:normal'><span
1480style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1481mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> box. Now select <b
1482style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1483mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1484parameters</span></b> for the PWDR data set in the GSAS-II data tree and check <b
1485style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1486mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>,
1487<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1488mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>,
1489<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1490mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,<b
1491style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1492mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
1493class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
1494style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1495mso-hansi-theme-font:minor-latin'> Y</span></b>. The go to <b style='mso-bidi-font-weight:
1496normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1497minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and
1498check <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1499mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1500class=SpellE>displ</span></span></b>.; make the <b style='mso-bidi-font-weight:
1501normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1502minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> <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'>1000</span></b>
1505if you didn’t do this earlier. Repeat <b style='mso-bidi-font-weight:normal'><span
1506style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1507mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged;
1508I obtained an improved residual of ~7.3% with a much better fit at the high
1509angle part of the pattern but still not fit well for the lower part.</p>
1510
1511<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1512 id="Picture_x0020_6" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:504.75pt;
1513 height:432.75pt;visibility:visible;mso-wrap-style:square'>
1514 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image006.png" o:title=""/>
1515</v:shape><![endif]--><![if !vml]><img width=673 height=577
1516src="Charge%20Flipping%20-%20sucrose_files/image006.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
1517
1518<p class=MsoNormal>What you see is that the background has a substantial
1519diffuse scattering feature at ~5deg and there are some peak shape issues (which
1520may be a consequence of the poor background fit). We’d like the fit to be
1521better before trying charge flipping. First select <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'>Background</span></b>, set <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'>Peaks in
1526background: No. peaks</span></b> to <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'>1</span></b> from the pull down box; the
1529window changes to </p>
1530
1531<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1532 id="Picture_x0020_7" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:366.75pt;
1533 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1534 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image007.png" o:title=""/>
1535</v:shape><![endif]--><![if !vml]><img width=489 height=263
1536src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_7"><![endif]></span><span
1537style='mso-spacerun:yes'> </span></p>
1538
1539<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
1540style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1541mso-hansi-theme-font:minor-latin'>5.0</span></b> for <span class=SpellE><b
1542style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1543mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span>,
1544<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1545mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
1546for <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1547style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1548mso-hansi-theme-font:minor-latin'>int</span></b></span> and <b
1549style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1550mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1551for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1552mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
1553(as appropriate for broad diffuse peaks) and then check all three refine boxes.
1554Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1555mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
1556class=SpellE>coeff</span>.</span></b> <span class=GramE>pulldown</span> to <b
1557style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1558mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>
1559for the <span class=SpellE>Chebyschev</span> part of the background. The window
1560should look like</p>
1561
1562<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1563 id="Picture_x0020_8" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:439.5pt;
1564 height:199.5pt;visibility:visible;mso-wrap-style:square'>
1565 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image008.png" o:title=""/>
1566</v:shape><![endif]--><![if !vml]><img width=586 height=266
1567src="Charge%20Flipping%20-%20sucrose_files/image008.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1568
1569<p class=MsoNormal>Go to the <b style='mso-bidi-font-weight:normal'><span
1570style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1571mso-hansi-theme-font:minor-latin'>Controls</span></b> item in the GSAS-II data
1572tree and set the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1573"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1574minor-latin'>Max cycles</span></b> to <b style='mso-bidi-font-weight:normal'><span
1575style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1576mso-hansi-theme-font:minor-latin'>5</span></b>. Now do <b style='mso-bidi-font-weight:
1577normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1578minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until
1579the refinement converges. After a set of refinement cycles go to the <b
1580style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1581mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1582reflections</span></b> tab and check the intensities. If there are many
1583negatives amongst the highest angle reflections do <b style='mso-bidi-font-weight:
1584normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1585minor-latin;mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this
1586replaces all the values with those in the extracted from the profile as listed
1587in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1588mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1589list</span></b> for the PWDR data set each multiplied by 0.5. Additionally
1590their refinement flags are turned off. Do <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'>Calculate/Refine</span></b><span
1593style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1594mso-hansi-theme-font:minor-latin'>; this will adjust all the reflections in the
1595vicinity of the reset ones</span>. You may repeat this process to suppress any
1596new negatives that may appear. Then set all the Pawley refinement flags back on
1597(excluding any that lead to a singular matrix) and repeat the refinement. After
1598refinement, mine converged to ~5.3% with very few negatives and the plot looked
1599like</p>
1600
1601<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1602 id="Picture_x0020_9" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:525pt;
1603 height:450pt;visibility:visible;mso-wrap-style:square'>
1604 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image009.png" o:title=""/>
1605</v:shape><![endif]--><![if !vml]><img width=700 height=600
1606src="Charge%20Flipping%20-%20sucrose_files/image009.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
1607
1608<p class=MsoNormal>Let’s see if this is good enough for charge flipping.</p>
1609
1610<h2>Step 3: Charge flipping</h2>
1611
1612<p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
1613Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1614mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1615and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1616"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1617minor-latin'>Charge flip controls</span></b> in the middle of the <b
1618style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1619mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1620tab.</p>
1621
1622<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1623mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1624"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1625</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
1626style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1627mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b
1628style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1629mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
163011bmb_8716.fxye Bank 1</span></b> (the only choice!). This makes the reflection
1631set to be used those in <b style='mso-bidi-font-weight:normal'><span
1632style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1633mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
1634data set; these should match the <b style='mso-bidi-font-weight:normal'><span
1635style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1636mso-hansi-theme-font:minor-latin'>Pawley reflection</span></b> set.</p>
1637
1638<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1639mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1640"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1641</span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span
1642style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1643mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b
1644style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1645mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map
1646controls</span></b>) to <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'>20%</span></b>. This controls the map search
1649routine.</p>
1650
1651<p class=MsoNormal>For powder data it is not usually advisable to select a <b
1652style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1653mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing
1654element</span></b>; if selected a periodic table appears – select an element or
1655‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1656mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None’</span></b>.
1657The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1658mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1659defines the map spacing and thus the extent of the reflection set; the observed
1660reflection set is zero filled to this limit for charge flipping. The <b
1661style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1662mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b>
1663and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1664mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b>
1665determine the lower threshold and upper limit for charge flipping,
1666respectively. The latter is used to avoid “Uranium solutions” in the result.
1667Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1668"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1669minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
1670ones. For sucrose set it to <b style='mso-bidi-font-weight:normal'><span
1671style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1672mso-hansi-theme-font:minor-latin'>12.</span></b> When ready select <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'>Compute/Charge
1675flipping</span></b>; a progress bar dialog will appear that tracks the residual
1676found in each charge flipping cycle. It will quickly drop to some level
1677(42-44%) and then for a successful charge flipping run perhaps drop again into
1678the 20-25% range after a considerable length of time. You should save the
1679project if you get an apparently good solution. Many times it will not drop
1680below ~40%; just try <b style='mso-bidi-font-weight:normal'><span
1681style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1682mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b> again. If
1683several tries fail to yield a solution, go back to the last step of the Pawley
1684refinement and just repeat it (that is do <b style='mso-bidi-font-weight:normal'><span
1685style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1686mso-hansi-theme-font:minor-latin'>Pawley update</span></b> and <b
1687style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1688mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>).
1689This will generate a different set of intensities for the highly overlapped
1690part of the powder pattern; perhaps they will give a successful charge flip
1691solution. Unless otherwise interrupted, GSAS-II will try 10000 times for a
1692charge flip solution (for sucrose this takes 5-10min on my laptop). Press <b
1693style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1694mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b>
1695to stop the charge flipping; a peak list and a drawing of the solution will
1696appear. One of my runs gave</p>
1697
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1704
1705<p class=MsoNormal><o:p>&nbsp;</o:p></p>
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1805 </v:shape></v:group><![endif]--><![if !vml]><span style='mso-ignore:vglayout;
1806position:absolute;z-index:251662336;margin-left:315px;margin-top:308px;
1807width:16px;height:35px'><img width=16 height=35
1808src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
1809style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1052" type="#_x0000_t75"
1810 style='width:502.5pt;height:431.25pt;visibility:visible;mso-wrap-style:square'>
1811 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image012.png" o:title=""
1812  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
1813</v:shape><![endif]--><![if !vml]><img width=670 height=575
1814src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="_x0000_i1052"><![endif]></span></p>
1815
1816<p class=MsoNormal>The result looks very promising! Charge flipping operates
1817without regard to symmetry and GSAS-II attempts to locate the map with respect
1818to the symmetry elements from the computed reflection phases. (NB: charge
1819flipping also will give a solution without regard to handedness; this solution
1820may be either the correct one for sucrose or its inverse.) Errors in these
1821phases can disrupt this process so that the map and peak positions are offset
1822from their true positions. To discover this and fix it, rotate the drawing
1823around to check that atom positions are related via the 2<sub>1</sub> screw
1824axis (through the multicolored cross in the center of the cell and parallel to
1825the y-axis – the green cell edge). Avoid motions with the right mouse button
1826pressed, this moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:
1827normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1828minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the
1829cross to the cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my
1830drawing above to show where I think it should be. If you find an offset to the
1831map, orient it so the offset is horizontal or vertical and then press the <b
1832style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1833mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>,
1834<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1835mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>,
1836<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1837mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
1838or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1839mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
1840keys to shift the map and peaks as needed. The shift is in resolution units
1841(0.5Å) so the fix can only be approximate. Repeat as needed. Notice that the
1842peak positions in the table are updated as the offset is changed. In this case,
1843I needed just a few steps to correct the map offset. NB: you can use these keys
1844to move the result anywhere you wish, e.g. to select a different origin for the
1845structure but pay attention to the location of symmetry elements. After
1846adjustment, my solution looked like</p>
1847
1848<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1849 id="Picture_x0020_12" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:500.25pt;
1850 height:424.5pt;visibility:visible;mso-wrap-style:square'>
1851 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image014.png" o:title=""
1852  croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/>
1853</v:shape><![endif]--><![if !vml]><img width=667 height=566
1854src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
1855
1856<h2>Step 4: Obtain solution from charge flip result</h2>
1857
1858<p class=MsoNormal>The next step is to extract the unique peak positions from
1859the map and make atoms out of them. The map peak list is initially sorted by
1860peak magnitude; you can change the sorting to be along any of the column
1861headings in the table by a single click on the desired heading. The <span
1862class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1863"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1864minor-latin'>dzero</span></b></span> column gives the distance of each peak
1865from the origin. The menu items under Map peaks give you several tools to aid
1866in the peak selection process; we will just use a couple in this example. I have
1867chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:normal'><span
1868style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1869mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and then finding
1870the unique ones. </p>
1871
1872<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1873mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1874"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1875</span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight:
1876normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1877minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> column heading. This
1878will sort the peaks in increasing z-axis coordinate.</p>
1879
1880<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1881mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1882"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1883</span></span></span><![endif]>Do a single click on the upper left (empty) box
1884of the table. All entries will be colored grey indicating their selection.</p>
1885
1886<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1887mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1888"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1889</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1890style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1891mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That
1892should select (grey) 23 out of 46 peak positions in the table and all should be
1893near the top of the list. The console displays this as both the number of unique
1894peaks and the fraction found (the ideal value for the latter is easily inferred
1895from the space group). Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
1896that would be all the C &amp; O atoms! They will be colored green in the plot.
1897If more are selected then check the map offset – it may need a slight
1898correction.</p>
1899
1900<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1901 id="Picture_x0020_13" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:337.5pt;
1902 height:411.75pt;visibility:visible;mso-wrap-style:square'>
1903 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image016.png" o:title=""/>
1904</v:shape><![endif]--><![if !vml]><img width=450 height=549
1905src="Charge%20Flipping%20-%20sucrose_files/image016.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1906
1907<p class=MsoNormal>The drawing shows the selected atoms in green.</p>
1908
1909<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1910 id="Picture_x0020_14" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:7in;
1911 height:429pt;visibility:visible;mso-wrap-style:square'>
1912 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image017.png" o:title=""
1913  croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/>
1914</v:shape><![endif]--><![if !vml]><img width=672 height=572
1915src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
1916
1917<p class=MsoNormal>Notice that in my case one atom is in a neighboring
1918molecule, one can deselect it and then pick the desired equivalent. Hold the <b
1919style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1920mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1921key down and use the right mouse button to pick/unpick atoms in the drawing.
1922NB: the left mouse button will clear all the selections. The other two “lone”
1923atoms belong to molecules in neighboring unit cells; we’ll deal with them
1924later.</p>
1925
1926<p class=MsoNormal>These are now ready to turn into atoms. Do <b
1927style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1928mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1929peaks/Move peaks</span></b>. The drawing will show white balls for each of the
1930selected positions and the <b style='mso-bidi-font-weight:normal'><span
1931style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1932mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 23 new H
1933atoms. </p>
1934
1935<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1936 id="Picture_x0020_15" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:7in;
1937 height:433.5pt;visibility:visible;mso-wrap-style:square'>
1938 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image019.png" o:title=""
1939  croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/>
1940</v:shape><![endif]--><![if !vml]><img width=672 height=578
1941src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
1942
1943<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1944 id="Picture_x0020_44" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;
1945 height:414.75pt;visibility:visible;mso-wrap-style:square'>
1946 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image021.png" o:title=""/>
1947</v:shape><![endif]--><![if !vml]><img width=700 height=553
1948src="Charge%20Flipping%20-%20sucrose_files/image021.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
1949
1950<p class=MsoNormal>The atom names indicate the peak magnitude to aid
1951identification (M100 for the largest in the <b style='mso-bidi-font-weight:
1952normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1953minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
1954may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
1955style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1956mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
1957them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
1958style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1959mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
1960normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1961minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
1962and then selecting a position in the table with the <b style='mso-bidi-font-weight:
1963normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1964minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
1965Linux machines the <b style='mso-bidi-font-weight:normal'><span
1966style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1967mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by
1968the operating system; use <b style='mso-bidi-font-weight:normal'><span
1969style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1970mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms.
1971After sorting by magnitude, my list is now </p>
1972
1973<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1974 id="Picture_x0020_17" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
1975 height:417pt;visibility:visible;mso-wrap-style:square'>
1976 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image022.png" o:title=""/>
1977</v:shape><![endif]--><![if !vml]><img width=700 height=556
1978src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1979
1980<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out
1981into two groups with a clear gap between M79 and M64. The higher ones are likely
1982to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of
1983ambiguity in the middle, but just assign the top 11 as O and the rest as C and
1984see what happens. You can do this by selecting a block of atoms, go to <b
1985style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1986mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1987atom parameters</span></b> and select <b style='mso-bidi-font-weight:normal'><span
1988style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1989mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a
1990periodic table will appear. Select the desired element and they will be changed
1991in the list and drawing. (NB: I show below the result from a different charge
1992flipping run which had a different origin choice so the sucrose molecule is
1993more fragmented).</p>
1994
1995<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1996 id="Picture_x0020_18" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:364.5pt;
1997 height:311.25pt;visibility:visible;mso-wrap-style:square'>
1998 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image023.png" o:title=""
1999  croptop="10802f" cropbottom="17378f" cropleft="37546f" cropright="12910f"/>
2000</v:shape><![endif]--><![if !vml]><img width=486 height=415
2001src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
2002
2003<p class=MsoNormal>The original charge flipping solution is still visible and
2004the atoms are now identified, I’ve changed the drawing to show balls and sticks
2005and labeled the atoms with their names, this is done in the <b
2006style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2007mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b>
2008tab. Double click the appropriate column heading and make the selection from
2009the dialog box.<span style='mso-spacerun:yes'>  </span></p>
2010
2011<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2012 id="Picture_x0020_19" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:525pt;
2013 height:449.25pt;visibility:visible;mso-wrap-style:square'>
2014 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image025.png" o:title=""/>
2015</v:shape><![endif]--><![if !vml]><img width=700 height=599
2016src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
2017
2018<p class=MsoNormal>Now one can safely remove the map peaks (do <b
2019style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2020mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
2021peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span
2022style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2023mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
2024charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
2025style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2026mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
2027normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2028minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
2029style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2030mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2031tab). The atom positions I obtained in this charge flipping run have the
2032sucrose molecule fragmented over several neighboring molecules. We need
2033assemble these into a single molecule. Follow the steps:</p>
2034
2035<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2036mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2037"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2038</span></span></span><![endif]>In the Atoms tab of the Data window do <b
2039style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2040mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload
2041draw <span class=GramE>atoms<span style='font-family:"Times New Roman",serif;
2042font-weight:normal'>.</span></span></span></b> This ensures the drawing is
2043up-to-date with the Atom list.</p>
2044
2045<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2046mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2047"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2048</span></span></span><![endif]>Select one atom in one of the fragments (perhaps
2049<span class=GramE>O(</span>1) in the drawing above as that is likely to be the
2050bridging O-atom between the two rings of sucrose. With the Atoms table showing
2051on the data window, use Shift-Left mouse button on the desired atom; it will
2052turn green indicating selection.</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'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2057</span></span></span><![endif]>Then in the Atoms menu do <b style='mso-bidi-font-weight:
2058normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2059minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b>;
2060a popup dialog offering choices of distances (&amp; angles – not used). Press <b
2061style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2062mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>.</p>
2063
2064<p class=MsoNormal style='margin-left:.5in'>The atoms will automatically be
2065reorganized into a single molecule and are ordered in the table according to
2066connectivity.</p>
2067
2068<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2069 id="Picture_x0020_20" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:360.75pt;
2070 height:312pt;visibility:visible;mso-wrap-style:square'>
2071 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image026.png" o:title=""
2072  croptop="14042f" cropbottom="14048f" cropleft="39221f" cropright="11359f"/>
2073</v:shape><![endif]--><![if !vml]><img width=481 height=416
2074src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
2075
2076<p class=MsoNormal>I’ve changed the style to balls &amp; sticks and added the
2077atom names as labels.</p>
2078
2079<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2080 id="_x0000_i1042" type="#_x0000_t75" style='width:525pt;height:448.5pt;
2081 visibility:visible;mso-wrap-style:square'>
2082 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/>
2083</v:shape><![endif]--><![if !vml]><img width=700 height=598
2084src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="_x0000_i1042"><![endif]></span></p>
2085
2086<p class=MsoNormal>To rename the atoms, select all the atoms (double click in
2087the empty left upper square of the Atom table; the entries will turn blue or
2088grey. Then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
2089"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2090minor-latin'>Edit/Modify atom parameters</span></b>. Select <b
2091style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2092mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Name</span></b>
2093from the popup window and press <b style='mso-bidi-font-weight:normal'><span
2094style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2095mso-hansi-theme-font:minor-latin'>OK</span></b>; you will be asked to confirm.
2096The atoms will be renamed. </p>
2097
2098<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2099 id="Picture_x0020_22" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;
2100 height:448.5pt;visibility:visible;mso-wrap-style:square'>
2101 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/>
2102</v:shape><![endif]--><![if !vml]><img width=700 height=598
2103src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
2104
2105<p class=MsoNormal>You can also reorder the atoms to make the connectivity
2106conform to usual chemical naming rules; use the Alt key to pick &amp; place
2107each atom to be moved just as we did with the Map peak results above.</p>
2108
2109<p class=MsoNormal>Save the project file; the next step is to complete the
2110structure by finding H-atoms and then do the final Rietveld refinements.</p>
2111
2112<h2>Step 5: Complete the structure</h2>
2113
2114<p class=MsoNormal>To complete the structure you will need to perform a
2115preliminary Rietveld refinement. This will make the atom positions more
2116accurate and prepare a set of calculated structure factors needed to generate a
2117difference Fourier map good enough to maybe reveal the H atoms. There are a
2118number of steps needed to set all the controls from the previous Pawley
2119refinement to get a successful start for the Rietveld refinement.</p>
2120
2121<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2122mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2123"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2124</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2125style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2126mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the
2127GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span
2128style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2129mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You don’t want to
2130start with these when the scale factor is unknown.</p>
2131
2132<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2133mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2134"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2135</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
2136style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2137mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b
2138style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2139mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2140scale factor</span></b> box. This is the scale factor for the data set. Uncheck
2141the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2142mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
2143class=SpellE>displ</span></span></b>.</p>
2144
2145<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2146mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2147"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2148</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
2149style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2150mso-hansi-theme-font:minor-latin'>Phases/sucrose General</span></b> tab and
2151uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2152mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
2153cell</span></b> and <b style='mso-bidi-font-weight:normal'><span
2154style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2155mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The
2156latter is most important; if you forget you will just get another Pawley
2157refinement!</p>
2158
2159<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
2160style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2161mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
2162GSAS-II data tree menu; only scale and background are refined. I got <span
2163class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear
2164intensity differences; the atom positions obviously need refinement.</p>
2165
2166<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2167 id="Picture_x0020_21" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
2168 height:450pt;visibility:visible;mso-wrap-style:square'>
2169 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image030.png" o:title=""/>
2170</v:shape><![endif]--><![if !vml]><img width=700 height=600
2171src="Charge%20Flipping%20-%20sucrose_files/image030.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
2172
2173<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
2174obvious.</p>
2175
2176<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
2177style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2178mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and select the <b
2179style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2180mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2181tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub>
2182has an arbitrary location along the y-axis. Then double click the <b
2183style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2184mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
2185column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight:
2186normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2187minor-latin;mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and
2188press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2189mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2190The atoms table will show the refinement controls</p>
2191
2192<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2193 id="Picture_x0020_24" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
2194 height:225pt;visibility:visible;mso-wrap-style:square'>
2195 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/>
2196</v:shape><![endif]--><![if !vml]><img width=700 height=300
2197src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
2198
2199<p class=MsoNormal>To deal with the warning we need to set a “Hold” on one atom
2200y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span
2201style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2202mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II
2203data tree.</p>
2204
2205<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2206 id="Picture_x0020_23" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:225pt;
2207 height:187.5pt;visibility:visible;mso-wrap-style:square'>
2208 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image032.png" o:title=""/>
2209</v:shape><![endif]--><![if !vml]><img width=300 height=250
2210src="Charge%20Flipping%20-%20sucrose_files/image032.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
2211
2212<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
2213style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2214mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
2215style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2216mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
2217class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will fix
2218the shift along y for the <span class=GramE>O(</span>1) atom.</p>
2219
2220<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2221 id="Picture_x0020_26" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:259.5pt;
2222 height:271.5pt;visibility:visible;mso-wrap-style:square'>
2223 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title=""/>
2224</v:shape><![endif]--><![if !vml]><img width=346 height=362
2225src="Charge%20Flipping%20-%20sucrose_files/image033.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
2226
2227<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2228style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2229mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will
2230show the hold</p>
2231
2232<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2233 id="Picture_x0020_27" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:225pt;
2234 height:187.5pt;visibility:visible;mso-wrap-style:square'>
2235 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image034.png" o:title=""/>
2236</v:shape><![endif]--><![if !vml]><img width=300 height=250
2237src="Charge%20Flipping%20-%20sucrose_files/image034.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
2238
2239<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
2240style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2241mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
2242class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice
2243parameters (in the <b style='mso-bidi-font-weight:normal'><span
2244style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2245mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
2246style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2247mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>),
2248the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2249mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
2250parameters</span></b> <b style='mso-bidi-font-weight:normal'><span
2251style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2252mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
2253normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2254minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b
2255style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2256mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
2257<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2258mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2259&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2260mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2261and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2262mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
2263class=SpellE>displ</span></span></b>. You can also include refinement of atom
2264thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
2265refinement improved slightly to Rwp~10.0%. Next we should add the hydrogen
2266atoms that are on carbon as these can be located from the molecular geometry.
2267To do this do the following:</p>
2268
2269<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2270
2271<p class=MsoNormal>Go to the Atoms tab and select the <b style='mso-bidi-font-weight:
2272normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2273minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column; a popup
2274will appear. Select just the <b style='mso-bidi-font-weight:normal'><span
2275style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2276mso-hansi-theme-font:minor-latin'>C</span></b> atoms; these will be highlighted
2277in grey in the Atom table.</p>
2278
2279<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
2280style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2281mso-hansi-theme-font:minor-latin'>Edit/Insert H atoms</span></b> from the Atoms
2282menu; a Distance Angle Controls popup will appear. You can change radii and
2283Bond search factor if needed (rarely). Press <b style='mso-bidi-font-weight:
2284normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2285minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>. A new popup window
2286will appear.<br>
2287<span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_45"
2288 o:spid="_x0000_i1035" type="#_x0000_t75" style='width:300pt;height:363.75pt;
2289 visibility:visible;mso-wrap-style:square'>
2290 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""/>
2291</v:shape><![endif]--><![if !vml]><img width=400 height=485
2292src="Charge%20Flipping%20-%20sucrose_files/image035.png" v:shapes="Picture_x0020_45"><![endif]></span><br>
2293This offers the choice of how many H-atoms to be added for each atom in the
2294table; the maximum is chosen for each atom. If the bonds are sufficiently short
2295this may be fewer reflecting the possibility of sp<sup>2</sup> or <span
2296class=SpellE>sp</span> bonding on the atom. You can override the choices made
2297by default. You also can deselect some of the other attached atoms so they will
2298not be used in the geometry calculations for H-atom placement (e.g. a metal
2299atom in certain organometallics). When you are satisfied with the choices
2300(actually no changes are needed in this case), press <b style='mso-bidi-font-weight:
2301normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2302minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>. The structure will
2303be redrawn with H-atoms shown as van der Waals spheres; they are appended to
2304the end of the Atom list.</p>
2305
2306<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2307 id="Picture_x0020_46" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:360.75pt;
2308 height:312.75pt;visibility:visible;mso-wrap-style:square'>
2309 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image036.png" o:title=""
2310  croptop="12872f" cropbottom="15128f" cropleft="40027f" cropright="10552f"/>
2311</v:shape><![endif]--><![if !vml]><img width=481 height=417
2312src="Charge%20Flipping%20-%20sucrose_files/image037.jpg" v:shapes="Picture_x0020_46"><![endif]></span></p>
2313
2314<p class=MsoNormal>These hydrogen atoms will better describe the scattering
2315density in the vicinity of the carbon atoms; their positions need to be refined
2316to find their better locations. Do <b style='mso-bidi-font-weight:normal'><span
2317style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2318mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (the refinement
2319flags are already set for this – NB: don’t be tempted to refine the H-atom
2320positions as they are likely to move erratically). My result was Rwp~9.2% and
2321the drawing is updated with the new atom positions (as van der Waals spheres).</p>
2322
2323<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2324 id="Picture_x0020_47" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:363pt;
2325 height:312pt;visibility:visible;mso-wrap-style:square'>
2326 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image038.png" o:title=""
2327  croptop="12872f" cropbottom="15218f" cropleft="40028f" cropright="10490f"/>
2328</v:shape><![endif]--><![if !vml]><img width=484 height=416
2329src="Charge%20Flipping%20-%20sucrose_files/image039.jpg" v:shapes="Picture_x0020_47"><![endif]></span></p>
2330
2331<p class=MsoNormal>Because the C-atoms have probably moved; the H-atoms (which
2332were fixed) are now no longer in their optimal locations. From the Atom tab
2333menu, do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2334mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/ Update
2335H atoms</span></b>. This will shift their positions slightly. Repeat <b
2336style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2337mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
2338and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2339mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Update
2340H atoms</span></b>; you should see no shift this time. (<span class=SpellE>Rwp</span>
2341may be slightly higher; I got ~9.3%).</p>
2342
2343<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2344
2345<p class=MsoNormal>Now we have to find the hydrogens that are on oxygen; these
2346cannot be geometrically located except that they are somewhere on a circle at
2347the bonding distance from the O-atom. We need a difference Fourier map. Go to
2348the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2349mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose
2350General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
2351style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2352mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway
2353down the window.</p>
2354
2355<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2356mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2357"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2358</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
2359normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2360minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
2361style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2362mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
2363for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2364mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
2365
2366<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2367mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2368"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2369</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
2370style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2371mso-hansi-theme-font:minor-latin'>PWDR 11bmb_8716.fxye Bank 1</span></b> for
2372the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2373mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
2374set from</span></b> item (the only choice). The Fourier calculation will use
2375the structure factors shown in the Reflection list item for this PWDR data set.</p>
2376
2377<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2378mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2379"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2380</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2381style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2382mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b
2383style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2384mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2385tab window. The map will be computed via fast Fourier techniques and is very
2386fast. A few lines summarizing the map is printed on the console, the structure
2387plot may show a single green dot somewhere (it could be hidden beneath an
2388atom!), this is the highest point in the map.</p>
2389
2390<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2391mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2392"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2393</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2394style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2395mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b
2396style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2397mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
2398level</span></b> slider until something appears on the map. You can also reduce
2399the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2400mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
2401and shift the View Point (use right mouse button) to help clarify the view.
2402Note that the map continues to show the density around the View Point even if
2403it is outside the unit cell box.</p>
2404
2405<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2406 id="Picture_x0020_31" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:362.25pt;
2407 height:308.25pt;visibility:visible;mso-wrap-style:square'>
2408 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image040.png" o:title=""
2409  croptop="10982f" cropbottom="17558f" cropleft="37484f" cropright="13065f"/>
2410</v:shape><![endif]--><![if !vml]><img width=483 height=411
2411src="Charge%20Flipping%20-%20sucrose_files/image041.jpg" v:shapes="Picture_x0020_31"><![endif]></span></p>
2412
2413<p class=MsoNormal>What is drawn here are green (&amp; red for negative) dots
2414whose size are proportional to the electron density. There are peaks that might
2415be H-atom positions as well as features that suggest O-atoms out of position.
2416Recall that the refinement was just done without any H-atoms on the oxygen
2417atoms; it will make the best fit compensating for the missing H-atoms by
2418displacing the O atoms in the direction of the missing H-atoms. To add the OH
2419atoms do the following:</p>
2420
2421<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2422mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2423"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2424</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2425style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2426mso-hansi-theme-font:minor-latin'>Phases/sucrose Atoms</span></b> tab.</p>
2427
2428<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2429mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2430"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2431</span></span></span><![endif]>Select all O-atoms in the table (double click the
2432<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2433mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b>
2434column heading &amp; select <b style='mso-bidi-font-weight:normal'><span
2435style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2436mso-hansi-theme-font:minor-latin'>O</span></b> atoms from the popup); all will
2437turn grey.</p>
2438
2439<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2440mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2441"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2442</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2443style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2444mso-hansi-theme-font:minor-latin'>Edit/Insert H atoms</span></b> from the menu;
2445a Distance Angle Controls popup will appear. You can change radii and Bond
2446search factor if needed (rarely). Press <b style='mso-bidi-font-weight:normal'><span
2447style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2448mso-hansi-theme-font:minor-latin'>Ok</span></b>. A new popup window will appear</p>
2449
2450<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2451 id="Picture_x0020_32" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:300pt;
2452 height:363.75pt;visibility:visible;mso-wrap-style:square'>
2453 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/>
2454</v:shape><![endif]--><![if !vml]><img width=400 height=485
2455src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
2456
2457<p class=MsoNormal style='margin-left:.5in'>This offers the choice of how many
2458H-atoms to be added for each O-atom in the table; one is chosen in this case
2459for each atom. Press <b style='mso-bidi-font-weight:normal'><span
2460style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2461mso-hansi-theme-font:minor-latin'>Ok</span></b>. The structure will be redrawn
2462showing the added H-atoms.</p>
2463
2464<p class=MsoNormal style='margin-left:.5in'><o:p>&nbsp;</o:p></p>
2465
2466<p class=MsoNormal style='margin-left:.5in'>These OH hydrogens are found by
2467finding the highest point in the delta-F map for all possible orientations of
2468this bond at a fixed angle (109.5°). The new hydrogen atoms are named in
2469sequence and are appended to the end of the Atom list.</p>
2470
2471<p class=MsoNormal style='margin-left:.5in'><o:p>&nbsp;</o:p></p>
2472
2473<p class=MsoNormal>Do the set of <b style='mso-bidi-font-weight:normal'><span
2474style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2475mso-hansi-theme-font:minor-latin'>Calculate/Refine, Edit/Update H atoms</span></b>
2476at least twice to finish this stage in the structure analysis; end with a <b
2477style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2478mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>.
2479My <span class=SpellE>Rwp</span> was ~8.14% with all the H-atoms included (but
2480not refined). The fit looks pretty good</p>
2481
2482<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2483 id="Picture_x0020_40" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
2484 height:450pt;visibility:visible;mso-wrap-style:square'>
2485 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image043.png" o:title=""/>
2486</v:shape><![endif]--><![if !vml]><img width=700 height=600
2487src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
2488
2489<h2>Step 6: Final refinement</h2>
2490
2491<p class=MsoNormal>Looking at the fit, there may be room for improvement. First
2492we need to change the profile model to include crystallite size and <span
2493class=SpellE>mustrain</span> broadening. Go to <b style='mso-bidi-font-weight:
2494normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2495minor-latin;mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>,
2496set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2497mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2498and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2499mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2500to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2501mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>zero</span></b>
2502and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2503"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2504minor-latin'>Refine</span></b> flags for them.</p>
2505
2506<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
2507style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2508mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and look at the <b
2509style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2510mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
2511tab; make sure the <b style='mso-bidi-font-weight:normal'><span
2512style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2513mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the
2514boxes for both <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2515style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2516mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b style='mso-bidi-font-weight:
2517normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2518minor-latin;mso-hansi-theme-font:minor-latin'>. <span class=GramE>size</span></span></b>
2519and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2520style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2521mso-hansi-theme-font:minor-latin'>microstrain</span></b></span>.</p>
2522
2523<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2524 id="Picture_x0020_41" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:480pt;
2525 height:339pt;visibility:visible;mso-wrap-style:square'>
2526 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image044.png" o:title=""/>
2527</v:shape><![endif]--><![if !vml]><img width=640 height=452
2528src="Charge%20Flipping%20-%20sucrose_files/image044.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
2529
2530<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2531style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2532mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2533class=SpellE>Rwp</span> will start out high but should converge to where it was
2534before this change. I got 8.09% and the <b style='mso-bidi-font-weight:normal'><span
2535style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2536mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>
2537
2538<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2539 id="Picture_x0020_42" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:480pt;
2540 height:334.5pt;visibility:visible;mso-wrap-style:square'>
2541 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image045.png" o:title=""/>
2542</v:shape><![endif]--><![if !vml]><img width=640 height=446
2543src="Charge%20Flipping%20-%20sucrose_files/image045.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
2544
2545<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
2546style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2547mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span
2548class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2549"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2550minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span
2551style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2552mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
2553phenomenological model for <span class=SpellE>microstrain</span> which has 9
2554terms for monoclinic structures. Check all the boxes for it and press <b
2555style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2556mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reset</span></b>.
2557This will convert the isotropic strain value to the equivalent generalized
2558values.</p>
2559
2560<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2561 id="Picture_x0020_55" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:402pt;
2562 height:375pt;visibility:visible;mso-wrap-style:square'>
2563 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image046.png" o:title=""/>
2564</v:shape><![endif]--><![if !vml]><img width=536 height=500
2565src="Charge%20Flipping%20-%20sucrose_files/image046.png" v:shapes="Picture_x0020_55"><![endif]></span></p>
2566
2567<p class=MsoNormal>Do a <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'>Calculate/Refine</span></b>; the <span
2570class=SpellE>Rwp</span> will start out high but should converge lower than
2571where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight:
2572normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2573minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like.
2574If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2575style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2576mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b
2577style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2578mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot
2579type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span>
2580surface plot for ground sucrose.</p>
2581
2582<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2583 id="Picture_x0020_56" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:402pt;
2584 height:375pt;visibility:visible;mso-wrap-style:square'>
2585 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image047.png" o:title=""/>
2586</v:shape><![endif]--><![if !vml]><img width=536 height=500
2587src="Charge%20Flipping%20-%20sucrose_files/image047.png" v:shapes="Picture_x0020_56"><![endif]></span></p>
2588
2589<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2590 id="Picture_x0020_58" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
2591 height:450pt;visibility:visible;mso-wrap-style:square'>
2592 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image048.png" o:title=""/>
2593</v:shape><![endif]--><![if !vml]><img width=700 height=600
2594src="Charge%20Flipping%20-%20sucrose_files/image048.png" v:shapes="Picture_x0020_58"><![endif]></span></p>
2595
2596<p class=MsoNormal>This completes the exercise.</p>
2597
2598</div>
2599
2600</body>
2601
2602</html>
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