source: Tutorials/CFsucrose/Charge Flipping - sucrose.htm @ 1730

Last change on this file since 1730 was 1730, checked in by vondreele, 8 years ago

update sucrose charge flipping
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413  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
414  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
415  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
416  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
417  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
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425  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
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427  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
428  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
429  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
430  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
431  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
432  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
433  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
434  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
435  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
436  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
437  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
438  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
439  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
440  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
441  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
442  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
443  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
444  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
445  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
446  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
447  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
448  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
449  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
450  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
451  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
452  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
453  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
454  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
455  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
456  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
457  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
458  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
459  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
460  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
461  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
462  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
463  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
464  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
465  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
466  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
467  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
468  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
469  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
470  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
471  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
472  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
473  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
474  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
475  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
476  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
477  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
478  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
479  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
480  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
481  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
482  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
483  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
484  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
485  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
486  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
487  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
488  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
489  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
490  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
491  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
492  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
493  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
494  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
495  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
496  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
497  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
498  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
499  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
500  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
501  <w:LsdException Locked="false" Priority="19" QFormat="true"
502   Name="Subtle Emphasis"/>
503  <w:LsdException Locked="false" Priority="21" QFormat="true"
504   Name="Intense Emphasis"/>
505  <w:LsdException Locked="false" Priority="31" QFormat="true"
506   Name="Subtle Reference"/>
507  <w:LsdException Locked="false" Priority="32" QFormat="true"
508   Name="Intense Reference"/>
509  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
510  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
511   UnhideWhenUsed="true" Name="Bibliography"/>
512  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
513   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
514  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
515  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
516  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
517  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
518  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
519  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
520  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
521  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
522  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
523  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
524  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
525  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
526  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
527  <w:LsdException Locked="false" Priority="46"
528   Name="Grid Table 1 Light Accent 1"/>
529  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
530  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
531  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
532  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
533  <w:LsdException Locked="false" Priority="51"
534   Name="Grid Table 6 Colorful Accent 1"/>
535  <w:LsdException Locked="false" Priority="52"
536   Name="Grid Table 7 Colorful Accent 1"/>
537  <w:LsdException Locked="false" Priority="46"
538   Name="Grid Table 1 Light Accent 2"/>
539  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
540  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
541  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
542  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
543  <w:LsdException Locked="false" Priority="51"
544   Name="Grid Table 6 Colorful Accent 2"/>
545  <w:LsdException Locked="false" Priority="52"
546   Name="Grid Table 7 Colorful Accent 2"/>
547  <w:LsdException Locked="false" Priority="46"
548   Name="Grid Table 1 Light Accent 3"/>
549  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
550  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
551  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
552  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
553  <w:LsdException Locked="false" Priority="51"
554   Name="Grid Table 6 Colorful Accent 3"/>
555  <w:LsdException Locked="false" Priority="52"
556   Name="Grid Table 7 Colorful Accent 3"/>
557  <w:LsdException Locked="false" Priority="46"
558   Name="Grid Table 1 Light Accent 4"/>
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560  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
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562  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
563  <w:LsdException Locked="false" Priority="51"
564   Name="Grid Table 6 Colorful Accent 4"/>
565  <w:LsdException Locked="false" Priority="52"
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567  <w:LsdException Locked="false" Priority="46"
568   Name="Grid Table 1 Light Accent 5"/>
569  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
570  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
571  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
572  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
573  <w:LsdException Locked="false" Priority="51"
574   Name="Grid Table 6 Colorful Accent 5"/>
575  <w:LsdException Locked="false" Priority="52"
576   Name="Grid Table 7 Colorful Accent 5"/>
577  <w:LsdException Locked="false" Priority="46"
578   Name="Grid Table 1 Light Accent 6"/>
579  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
580  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
581  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
582  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
583  <w:LsdException Locked="false" Priority="51"
584   Name="Grid Table 6 Colorful Accent 6"/>
585  <w:LsdException Locked="false" Priority="52"
586   Name="Grid Table 7 Colorful Accent 6"/>
587  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
588  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
589  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
590  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
591  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
592  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
593  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
594  <w:LsdException Locked="false" Priority="46"
595   Name="List Table 1 Light Accent 1"/>
596  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
597  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
598  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
599  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
600  <w:LsdException Locked="false" Priority="51"
601   Name="List Table 6 Colorful Accent 1"/>
602  <w:LsdException Locked="false" Priority="52"
603   Name="List Table 7 Colorful Accent 1"/>
604  <w:LsdException Locked="false" Priority="46"
605   Name="List Table 1 Light Accent 2"/>
606  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
607  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
608  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
609  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
610  <w:LsdException Locked="false" Priority="51"
611   Name="List Table 6 Colorful Accent 2"/>
612  <w:LsdException Locked="false" Priority="52"
613   Name="List Table 7 Colorful Accent 2"/>
614  <w:LsdException Locked="false" Priority="46"
615   Name="List Table 1 Light Accent 3"/>
616  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
617  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
618  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
619  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
620  <w:LsdException Locked="false" Priority="51"
621   Name="List Table 6 Colorful Accent 3"/>
622  <w:LsdException Locked="false" Priority="52"
623   Name="List Table 7 Colorful Accent 3"/>
624  <w:LsdException Locked="false" Priority="46"
625   Name="List Table 1 Light Accent 4"/>
626  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
627  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
628  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
629  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
630  <w:LsdException Locked="false" Priority="51"
631   Name="List Table 6 Colorful Accent 4"/>
632  <w:LsdException Locked="false" Priority="52"
633   Name="List Table 7 Colorful Accent 4"/>
634  <w:LsdException Locked="false" Priority="46"
635   Name="List Table 1 Light Accent 5"/>
636  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
637  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
638  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
639  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
640  <w:LsdException Locked="false" Priority="51"
641   Name="List Table 6 Colorful Accent 5"/>
642  <w:LsdException Locked="false" Priority="52"
643   Name="List Table 7 Colorful Accent 5"/>
644  <w:LsdException Locked="false" Priority="46"
645   Name="List Table 1 Light Accent 6"/>
646  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
647  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
648  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
649  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
650  <w:LsdException Locked="false" Priority="51"
651   Name="List Table 6 Colorful Accent 6"/>
652  <w:LsdException Locked="false" Priority="52"
653   Name="List Table 7 Colorful Accent 6"/>
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783        mso-style-link:"Heading 2";
784        mso-ansi-font-size:18.0pt;
785        mso-bidi-font-size:18.0pt;
786        font-family:"Times New Roman",serif;
787        mso-ascii-font-family:"Times New Roman";
788        mso-fareast-font-family:"Times New Roman";
789        mso-fareast-theme-font:minor-fareast;
790        mso-hansi-font-family:"Times New Roman";
791        mso-bidi-font-family:"Times New Roman";
792        font-weight:bold;}
793span.BalloonTextChar
794        {mso-style-name:"Balloon Text Char";
795        mso-style-noshow:yes;
796        mso-style-priority:99;
797        mso-style-unhide:no;
798        mso-style-locked:yes;
799        mso-style-link:"Balloon Text";
800        mso-ansi-font-size:8.0pt;
801        mso-bidi-font-size:8.0pt;
802        font-family:"Tahoma",sans-serif;
803        mso-ascii-font-family:Tahoma;
804        mso-fareast-font-family:"Times New Roman";
805        mso-fareast-theme-font:minor-fareast;
806        mso-hansi-font-family:Tahoma;
807        mso-bidi-font-family:Tahoma;}
808span.SpellE
809        {mso-style-name:"";
810        mso-spl-e:yes;}
811span.GramE
812        {mso-style-name:"";
813        mso-gram-e:yes;}
814.MsoChpDefault
815        {mso-style-type:export-only;
816        mso-default-props:yes;
817        font-size:12.0pt;
818        mso-ansi-font-size:12.0pt;
819        mso-bidi-font-size:12.0pt;
820        mso-fareast-font-family:Calibri;
821        mso-fareast-theme-font:minor-latin;
822        mso-bidi-font-family:"Times New Roman";
823        mso-bidi-theme-font:minor-bidi;}
824@page WordSection1
825        {size:8.5in 11.0in;
826        margin:1.0in 1.0in 1.0in 1.0in;
827        mso-header-margin:.5in;
828        mso-footer-margin:.5in;
829        mso-paper-source:0;}
830div.WordSection1
831        {page:WordSection1;}
832 /* List Definitions */
833 @list l0
834        {mso-list-id:15232614;
835        mso-list-type:hybrid;
836        mso-list-template-ids:1768441438 -647724540 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
837@list l0:level1
838        {mso-level-tab-stop:none;
839        mso-level-number-position:left;
840        margin-left:.75in;
841        text-indent:-.25in;}
842@list l0:level2
843        {mso-level-number-format:alpha-lower;
844        mso-level-tab-stop:none;
845        mso-level-number-position:left;
846        margin-left:1.25in;
847        text-indent:-.25in;}
848@list l0:level3
849        {mso-level-number-format:roman-lower;
850        mso-level-tab-stop:none;
851        mso-level-number-position:right;
852        margin-left:1.75in;
853        text-indent:-9.0pt;}
854@list l0:level4
855        {mso-level-tab-stop:none;
856        mso-level-number-position:left;
857        margin-left:2.25in;
858        text-indent:-.25in;}
859@list l0:level5
860        {mso-level-number-format:alpha-lower;
861        mso-level-tab-stop:none;
862        mso-level-number-position:left;
863        margin-left:2.75in;
864        text-indent:-.25in;}
865@list l0:level6
866        {mso-level-number-format:roman-lower;
867        mso-level-tab-stop:none;
868        mso-level-number-position:right;
869        margin-left:3.25in;
870        text-indent:-9.0pt;}
871@list l0:level7
872        {mso-level-tab-stop:none;
873        mso-level-number-position:left;
874        margin-left:3.75in;
875        text-indent:-.25in;}
876@list l0:level8
877        {mso-level-number-format:alpha-lower;
878        mso-level-tab-stop:none;
879        mso-level-number-position:left;
880        margin-left:4.25in;
881        text-indent:-.25in;}
882@list l0:level9
883        {mso-level-number-format:roman-lower;
884        mso-level-tab-stop:none;
885        mso-level-number-position:right;
886        margin-left:4.75in;
887        text-indent:-9.0pt;}
888@list l1
889        {mso-list-id:82917343;
890        mso-list-type:hybrid;
891        mso-list-template-ids:-1527319822 -2100533712 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
892@list l1:level1
893        {mso-level-tab-stop:none;
894        mso-level-number-position:left;
895        margin-left:.75in;
896        text-indent:-.25in;}
897@list l1:level2
898        {mso-level-number-format:alpha-lower;
899        mso-level-tab-stop:none;
900        mso-level-number-position:left;
901        margin-left:1.25in;
902        text-indent:-.25in;}
903@list l1:level3
904        {mso-level-number-format:roman-lower;
905        mso-level-tab-stop:none;
906        mso-level-number-position:right;
907        margin-left:1.75in;
908        text-indent:-9.0pt;}
909@list l1:level4
910        {mso-level-tab-stop:none;
911        mso-level-number-position:left;
912        margin-left:2.25in;
913        text-indent:-.25in;}
914@list l1:level5
915        {mso-level-number-format:alpha-lower;
916        mso-level-tab-stop:none;
917        mso-level-number-position:left;
918        margin-left:2.75in;
919        text-indent:-.25in;}
920@list l1:level6
921        {mso-level-number-format:roman-lower;
922        mso-level-tab-stop:none;
923        mso-level-number-position:right;
924        margin-left:3.25in;
925        text-indent:-9.0pt;}
926@list l1:level7
927        {mso-level-tab-stop:none;
928        mso-level-number-position:left;
929        margin-left:3.75in;
930        text-indent:-.25in;}
931@list l1:level8
932        {mso-level-number-format:alpha-lower;
933        mso-level-tab-stop:none;
934        mso-level-number-position:left;
935        margin-left:4.25in;
936        text-indent:-.25in;}
937@list l1:level9
938        {mso-level-number-format:roman-lower;
939        mso-level-tab-stop:none;
940        mso-level-number-position:right;
941        margin-left:4.75in;
942        text-indent:-9.0pt;}
943@list l2
944        {mso-list-id:236667377;
945        mso-list-type:hybrid;
946        mso-list-template-ids:-513138304 1385070818 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
947@list l2:level1
948        {mso-level-tab-stop:none;
949        mso-level-number-position:left;
950        margin-left:.75in;
951        text-indent:-.25in;}
952@list l2:level2
953        {mso-level-number-format:alpha-lower;
954        mso-level-tab-stop:none;
955        mso-level-number-position:left;
956        margin-left:1.25in;
957        text-indent:-.25in;}
958@list l2:level3
959        {mso-level-number-format:roman-lower;
960        mso-level-tab-stop:none;
961        mso-level-number-position:right;
962        margin-left:1.75in;
963        text-indent:-9.0pt;}
964@list l2:level4
965        {mso-level-tab-stop:none;
966        mso-level-number-position:left;
967        margin-left:2.25in;
968        text-indent:-.25in;}
969@list l2:level5
970        {mso-level-number-format:alpha-lower;
971        mso-level-tab-stop:none;
972        mso-level-number-position:left;
973        margin-left:2.75in;
974        text-indent:-.25in;}
975@list l2:level6
976        {mso-level-number-format:roman-lower;
977        mso-level-tab-stop:none;
978        mso-level-number-position:right;
979        margin-left:3.25in;
980        text-indent:-9.0pt;}
981@list l2:level7
982        {mso-level-tab-stop:none;
983        mso-level-number-position:left;
984        margin-left:3.75in;
985        text-indent:-.25in;}
986@list l2:level8
987        {mso-level-number-format:alpha-lower;
988        mso-level-tab-stop:none;
989        mso-level-number-position:left;
990        margin-left:4.25in;
991        text-indent:-.25in;}
992@list l2:level9
993        {mso-level-number-format:roman-lower;
994        mso-level-tab-stop:none;
995        mso-level-number-position:right;
996        margin-left:4.75in;
997        text-indent:-9.0pt;}
998@list l3
999        {mso-list-id:533275380;
1000        mso-list-type:hybrid;
1001        mso-list-template-ids:-1319630076 -1606007952 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1002@list l3:level1
1003        {mso-level-tab-stop:none;
1004        mso-level-number-position:left;
1005        margin-left:.75in;
1006        text-indent:-.25in;}
1007@list l3:level2
1008        {mso-level-number-format:alpha-lower;
1009        mso-level-tab-stop:none;
1010        mso-level-number-position:left;
1011        margin-left:1.25in;
1012        text-indent:-.25in;}
1013@list l3:level3
1014        {mso-level-number-format:roman-lower;
1015        mso-level-tab-stop:none;
1016        mso-level-number-position:right;
1017        margin-left:1.75in;
1018        text-indent:-9.0pt;}
1019@list l3:level4
1020        {mso-level-tab-stop:none;
1021        mso-level-number-position:left;
1022        margin-left:2.25in;
1023        text-indent:-.25in;}
1024@list l3:level5
1025        {mso-level-number-format:alpha-lower;
1026        mso-level-tab-stop:none;
1027        mso-level-number-position:left;
1028        margin-left:2.75in;
1029        text-indent:-.25in;}
1030@list l3:level6
1031        {mso-level-number-format:roman-lower;
1032        mso-level-tab-stop:none;
1033        mso-level-number-position:right;
1034        margin-left:3.25in;
1035        text-indent:-9.0pt;}
1036@list l3:level7
1037        {mso-level-tab-stop:none;
1038        mso-level-number-position:left;
1039        margin-left:3.75in;
1040        text-indent:-.25in;}
1041@list l3:level8
1042        {mso-level-number-format:alpha-lower;
1043        mso-level-tab-stop:none;
1044        mso-level-number-position:left;
1045        margin-left:4.25in;
1046        text-indent:-.25in;}
1047@list l3:level9
1048        {mso-level-number-format:roman-lower;
1049        mso-level-tab-stop:none;
1050        mso-level-number-position:right;
1051        margin-left:4.75in;
1052        text-indent:-9.0pt;}
1053@list l4
1054        {mso-list-id:588542776;
1055        mso-list-type:hybrid;
1056        mso-list-template-ids:477805396 -2056748102 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1057@list l4:level1
1058        {mso-level-tab-stop:none;
1059        mso-level-number-position:left;
1060        margin-left:.75in;
1061        text-indent:-.25in;}
1062@list l4:level2
1063        {mso-level-number-format:alpha-lower;
1064        mso-level-tab-stop:none;
1065        mso-level-number-position:left;
1066        margin-left:1.25in;
1067        text-indent:-.25in;}
1068@list l4:level3
1069        {mso-level-number-format:roman-lower;
1070        mso-level-tab-stop:none;
1071        mso-level-number-position:right;
1072        margin-left:1.75in;
1073        text-indent:-9.0pt;}
1074@list l4:level4
1075        {mso-level-tab-stop:none;
1076        mso-level-number-position:left;
1077        margin-left:2.25in;
1078        text-indent:-.25in;}
1079@list l4:level5
1080        {mso-level-number-format:alpha-lower;
1081        mso-level-tab-stop:none;
1082        mso-level-number-position:left;
1083        margin-left:2.75in;
1084        text-indent:-.25in;}
1085@list l4:level6
1086        {mso-level-number-format:roman-lower;
1087        mso-level-tab-stop:none;
1088        mso-level-number-position:right;
1089        margin-left:3.25in;
1090        text-indent:-9.0pt;}
1091@list l4:level7
1092        {mso-level-tab-stop:none;
1093        mso-level-number-position:left;
1094        margin-left:3.75in;
1095        text-indent:-.25in;}
1096@list l4:level8
1097        {mso-level-number-format:alpha-lower;
1098        mso-level-tab-stop:none;
1099        mso-level-number-position:left;
1100        margin-left:4.25in;
1101        text-indent:-.25in;}
1102@list l4:level9
1103        {mso-level-number-format:roman-lower;
1104        mso-level-tab-stop:none;
1105        mso-level-number-position:right;
1106        margin-left:4.75in;
1107        text-indent:-9.0pt;}
1108@list l5
1109        {mso-list-id:854225785;
1110        mso-list-type:hybrid;
1111        mso-list-template-ids:-2071413312 1417604178 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1112@list l5:level1
1113        {mso-level-tab-stop:none;
1114        mso-level-number-position:left;
1115        margin-left:.75in;
1116        text-indent:-.25in;}
1117@list l5:level2
1118        {mso-level-number-format:alpha-lower;
1119        mso-level-tab-stop:none;
1120        mso-level-number-position:left;
1121        margin-left:1.25in;
1122        text-indent:-.25in;}
1123@list l5:level3
1124        {mso-level-number-format:roman-lower;
1125        mso-level-tab-stop:none;
1126        mso-level-number-position:right;
1127        margin-left:1.75in;
1128        text-indent:-9.0pt;}
1129@list l5:level4
1130        {mso-level-tab-stop:none;
1131        mso-level-number-position:left;
1132        margin-left:2.25in;
1133        text-indent:-.25in;}
1134@list l5:level5
1135        {mso-level-number-format:alpha-lower;
1136        mso-level-tab-stop:none;
1137        mso-level-number-position:left;
1138        margin-left:2.75in;
1139        text-indent:-.25in;}
1140@list l5:level6
1141        {mso-level-number-format:roman-lower;
1142        mso-level-tab-stop:none;
1143        mso-level-number-position:right;
1144        margin-left:3.25in;
1145        text-indent:-9.0pt;}
1146@list l5:level7
1147        {mso-level-tab-stop:none;
1148        mso-level-number-position:left;
1149        margin-left:3.75in;
1150        text-indent:-.25in;}
1151@list l5:level8
1152        {mso-level-number-format:alpha-lower;
1153        mso-level-tab-stop:none;
1154        mso-level-number-position:left;
1155        margin-left:4.25in;
1156        text-indent:-.25in;}
1157@list l5:level9
1158        {mso-level-number-format:roman-lower;
1159        mso-level-tab-stop:none;
1160        mso-level-number-position:right;
1161        margin-left:4.75in;
1162        text-indent:-9.0pt;}
1163@list l6
1164        {mso-list-id:1022125565;
1165        mso-list-type:hybrid;
1166        mso-list-template-ids:-482838388 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1167@list l6:level1
1168        {mso-level-tab-stop:none;
1169        mso-level-number-position:left;
1170        margin-left:1.0in;
1171        text-indent:-.25in;}
1172@list l6:level2
1173        {mso-level-number-format:alpha-lower;
1174        mso-level-tab-stop:none;
1175        mso-level-number-position:left;
1176        margin-left:1.5in;
1177        text-indent:-.25in;}
1178@list l6:level3
1179        {mso-level-number-format:roman-lower;
1180        mso-level-tab-stop:none;
1181        mso-level-number-position:right;
1182        margin-left:2.0in;
1183        text-indent:-9.0pt;}
1184@list l6:level4
1185        {mso-level-tab-stop:none;
1186        mso-level-number-position:left;
1187        margin-left:2.5in;
1188        text-indent:-.25in;}
1189@list l6:level5
1190        {mso-level-number-format:alpha-lower;
1191        mso-level-tab-stop:none;
1192        mso-level-number-position:left;
1193        margin-left:3.0in;
1194        text-indent:-.25in;}
1195@list l6:level6
1196        {mso-level-number-format:roman-lower;
1197        mso-level-tab-stop:none;
1198        mso-level-number-position:right;
1199        margin-left:3.5in;
1200        text-indent:-9.0pt;}
1201@list l6:level7
1202        {mso-level-tab-stop:none;
1203        mso-level-number-position:left;
1204        margin-left:4.0in;
1205        text-indent:-.25in;}
1206@list l6:level8
1207        {mso-level-number-format:alpha-lower;
1208        mso-level-tab-stop:none;
1209        mso-level-number-position:left;
1210        margin-left:4.5in;
1211        text-indent:-.25in;}
1212@list l6:level9
1213        {mso-level-number-format:roman-lower;
1214        mso-level-tab-stop:none;
1215        mso-level-number-position:right;
1216        margin-left:5.0in;
1217        text-indent:-9.0pt;}
1218ol
1219        {margin-bottom:0in;}
1220ul
1221        {margin-bottom:0in;}
1222-->
1223</style>
1224<!--[if gte mso 10]>
1225<style>
1226 /* Style Definitions */
1227 table.MsoNormalTable
1228        {mso-style-name:"Table Normal";
1229        mso-tstyle-rowband-size:0;
1230        mso-tstyle-colband-size:0;
1231        mso-style-noshow:yes;
1232        mso-style-priority:99;
1233        mso-style-parent:"";
1234        mso-padding-alt:0in 5.4pt 0in 5.4pt;
1235        mso-para-margin:0in;
1236        mso-para-margin-bottom:.0001pt;
1237        mso-pagination:widow-orphan;
1238        font-size:12.0pt;
1239        font-family:"Times New Roman",serif;
1240        mso-bidi-font-family:"Times New Roman";
1241        mso-bidi-theme-font:minor-bidi;}
1242</style>
1243<![endif]--><!--[if gte mso 9]><xml>
1244 <o:shapedefaults v:ext="edit" spidmax="1029"/>
1245</xml><![endif]--><!--[if gte mso 9]><xml>
1246 <o:shapelayout v:ext="edit">
1247  <o:idmap v:ext="edit" data="1"/>
1248 </o:shapelayout></xml><![endif]-->
1249</head>
1250
1251<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1252
1253<div class=WordSection1>
1254
1255<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in
1256GSAS-II - sucrose<o:p></o:p></span></h1>
1257
1258<h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1>
1259
1260<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1261of sucrose from powder diffraction data via charge flipping. This structure was
1262originally solved from single crystal data in the space group P2<sub>1</sub>.
1263It is a difficult exercise to complete as the charge flipping does not always
1264yield a solution and to even have a chance the Pawley refinement must be done
1265with particular care. We have given a route that sometimes works.</p>
1266
1267<p class=MsoNormal>If you have not done so already, start GSAS-II and open the
1268GSAS-II project file (I called it <span class=SpellE><b style='mso-bidi-font-weight:
1269normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1270minor-latin;mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b></span>)
1271you saved from the third part of the peak fitting-indexing exercise. If you
1272didn’t do that exercise, do it now.</p>
1273
1274<h2>Step 1: Setup for Pawley refinement</h2>
1275
1276<p class=MsoNormal>There are a number of steps that must be done in preparation
1277for a Pawley refinement after having completed the unit cell indexing and new
1278phase creation. These cover two things: one is to prepare the powder pattern
1279(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1280
1281<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1282style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1283style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1284<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1285mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
1286in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1287region near d=1.0Å is readily seen. This is ~24deg 2<span style='font-family:
1288Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1289mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1290symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
1291relatively clear of peaks that makes a good place to end the calculations with
1292a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution
1293needed for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span
1294style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1295mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span class=SpellE><b
1296style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1297mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b></span>
1298as the upper limit and make a note of the exact d-spacing (1.0125Å) using the
1299mouse cursor on the plot.</p>
1300
1301<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1302style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1303style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1304<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1305mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1306Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1307style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1308mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1309style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1310mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1311profile</span></b> to recover the default values. The peak fitting done earlier
1312is over a much more limited range of 2<span style='font-family:Symbol;
1313mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1314mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1315symbol;mso-symbol-font-family:Symbol'>Q</span></span> giving values that might
1316not extrapolate well over the wider range to be used in the Pawley refinement.
1317We will refine them again later.</p>
1318
1319<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1320style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1321style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1322<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1323mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1324Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1325normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1326minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.
1327While you are here set <b style='mso-bidi-font-weight:normal'><span
1328style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1329mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> to <b
1330style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1331mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>.</p>
1332
1333<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span
1334style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1335style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1336to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1337mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1338to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1339"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1340minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1341normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1342minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
1343box and enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
1344style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1345mso-hansi-theme-font:minor-latin'>1.0125</span></b>) into the <b
1346style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1347mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1348class=SpellE>dmin</span></span></b> box.</p>
1349
1350<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1351style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1352mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1353
1354<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1355 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1356 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1357 <v:stroke joinstyle="miter"/>
1358 <v:formulas>
1359  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1360  <v:f eqn="sum @0 1 0"/>
1361  <v:f eqn="sum 0 0 @1"/>
1362  <v:f eqn="prod @2 1 2"/>
1363  <v:f eqn="prod @3 21600 pixelWidth"/>
1364  <v:f eqn="prod @3 21600 pixelHeight"/>
1365  <v:f eqn="sum @0 0 1"/>
1366  <v:f eqn="prod @6 1 2"/>
1367  <v:f eqn="prod @7 21600 pixelWidth"/>
1368  <v:f eqn="sum @8 21600 0"/>
1369  <v:f eqn="prod @7 21600 pixelHeight"/>
1370  <v:f eqn="sum @10 21600 0"/>
1371 </v:formulas>
1372 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1373 <o:lock v:ext="edit" aspectratio="t"/>
1374</v:shapetype><v:shape id="_x0000_i1064" type="#_x0000_t75" style='width:542.25pt;
1375 height:375pt;visibility:visible;mso-wrap-style:square'>
1376 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image001.png" o:title=""/>
1377</v:shape><![endif]--><![if !vml]><img width=723 height=500
1378src="Charge%20Flipping%20-%20sucrose_files/image001.png" v:shapes="_x0000_i1064"><![endif]></span></p>
1379
1380<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1381style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1382mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1383for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
1384style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1385mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
1386dialog box will appear</p>
1387
1388<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1389 id="Picture_x0020_2" o:spid="_x0000_i1063" type="#_x0000_t75" style='width:259.5pt;
1390 height:252pt;visibility:visible;mso-wrap-style:square'>
1391 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image002.png" o:title=""/>
1392</v:shape><![endif]--><![if !vml]><img width=346 height=336
1393src="Charge%20Flipping%20-%20sucrose_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1394
1395<p class=MsoNormal>Select either choice; the desired data set will be added to
1396this phase for analysis. The data tab now shows the new data set.</p>
1397
1398<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1399 id="_x0000_i1062" type="#_x0000_t75" style='width:359.25pt;height:375pt;
1400 visibility:visible;mso-wrap-style:square'>
1401 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image003.png" o:title=""/>
1402</v:shape><![endif]--><![if !vml]><img width=479 height=500
1403src="Charge%20Flipping%20-%20sucrose_files/image003.png" v:shapes="_x0000_i1062"><![endif]></span></p>
1404
1405<p class=MsoNormal>I’ve stretched the window slightly to see the entire
1406contents. This is the location for all the phase dependent parameters for this
1407histogram. Notice that it includes phase fraction, size &amp; <span
1408class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1409and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1410intended for protein work where a significant region of the structure is
1411disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1412surfaces</p>
1413
1414<p class=MsoNormal><span class=GramE>as</span> well as preferred orientation
1415correction curves.</p>
1416
1417<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1418style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1419mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1420empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
1421style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1422mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
1423makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
1424normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1425minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>.
1426The table should list reflections 0-780. Select and check the refine column
1427using the same technique you used for the peak list. </p>
1428
1429<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1430 id="Picture_x0020_4" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:375pt;
1431 height:225pt;visibility:visible;mso-wrap-style:square'>
1432 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image004.png" o:title=""/>
1433</v:shape><![endif]--><![if !vml]><img width=500 height=300
1434src="Charge%20Flipping%20-%20sucrose_files/image004.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
1435
1436<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1437you didn’t skip a step as it might not work correctly if you did.</p>
1438
1439<h2>Step 2: Pawley refinement</h2>
1440
1441<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1442normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1443minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1444the main GSAS-II data tree window. Before it begins a backup of the project
1445file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
1446style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1447mso-hansi-theme-font:minor-latin'>sucrose.bck0.gpx</span></b>. It can be used
1448to recover from a bad refinement. A progress dialog box will appear showing the
1449residual as the refinement proceeds. Notice that there was a singular matrix
1450warning on the console window and the last reflection (781) was removed from
1451the refinement because it was off the end of the used part of the pattern. This
1452is the GSAS-II singular matrix recovery mechanism; you can go to the <b
1453style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1454mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1455reflections</span></b> tab and uncheck the last reflection. Then repeat <b
1456style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1457mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
1458to make sure it has essentially minimized. My refinement completed with <span
1459class=SpellE>Rwp</span> ~26.3%; a dialog box appears asking if you wish to load
1460the result. Press <b style='mso-bidi-font-weight:normal'><span
1461style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1462mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
1463PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
1464
1465<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1466 id="Picture_x0020_46" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:525pt;
1467 height:450pt;visibility:visible;mso-wrap-style:square'>
1468 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image005.png" o:title=""/>
1469</v:shape><![endif]--><![if !vml]><img width=700 height=600
1470src="Charge%20Flipping%20-%20sucrose_files/image005.png" v:shapes="Picture_x0020_46"><![endif]></span></p>
1471
1472<p class=MsoNormal>It is evident from examining the plot that some improvement
1473can be had by refining the lattice and profile parameters and perhaps the
1474sample X position. Go to <b style='mso-bidi-font-weight:normal'><span
1475style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1476mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> in the GSAS-II data
1477tree and check the <b style='mso-bidi-font-weight:normal'><span
1478style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1479mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> box. Now select <b
1480style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1481mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1482parameters</span></b> for the PWDR data set in the GSAS-II data tree and check <b
1483style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1484mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>,
1485<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1486mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>V</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'>W</span></b>,<b
1489style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1490mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
1491class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
1492style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1493mso-hansi-theme-font:minor-latin'> Y</span></b>. The go to <b style='mso-bidi-font-weight:
1494normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1495minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and
1496check <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1497mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
1498class=SpellE>displ</span></span></b>.; make the <b style='mso-bidi-font-weight:
1499normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1500minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> <b
1501style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1502mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1503if you didn’t do this earlier. Repeat <b style='mso-bidi-font-weight:normal'><span
1504style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1505mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged;
1506I obtained an improved residual of ~9.05% with a much better fit at the high
1507angle part of the pattern but still not fit well for the lower part.</p>
1508
1509<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1510 id="Picture_x0020_26" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:504.75pt;
1511 height:432.75pt;visibility:visible;mso-wrap-style:square'>
1512 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image006.png" o:title=""/>
1513</v:shape><![endif]--><![if !vml]><img width=673 height=577
1514src="Charge%20Flipping%20-%20sucrose_files/image006.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
1515
1516<p class=MsoNormal>What you see is that the background has a substantial
1517diffuse scattering feature at ~5deg and there are some peak shape issues (which
1518may be a consequence of the poor background fit). We’d like the fit to be
1519better before trying charge flipping. First select <b style='mso-bidi-font-weight:
1520normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1521minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>, set <b
1522style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1523mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peaks in
1524background: No. peaks</span></b> to <b style='mso-bidi-font-weight:normal'><span
1525style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1526mso-hansi-theme-font:minor-latin'>1</span></b> from the pull down box; the
1527window changes to </p>
1528
1529<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1530 id="Picture_x0020_27" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:366.75pt;
1531 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1532 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image007.png" o:title=""/>
1533</v:shape><![endif]--><![if !vml]><img width=489 height=263
1534src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span><span
1535style='mso-spacerun:yes'> </span></p>
1536
1537<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
1538style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1539mso-hansi-theme-font:minor-latin'>5.0</span></b> for <span class=SpellE><b
1540style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1541mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span>,
1542<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1543mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
1544for <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1545style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1546mso-hansi-theme-font:minor-latin'>int</span></b></span> and <b
1547style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1548mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
1549for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1550mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
1551(as appropriate for broad diffuse peaks) and then check all three refine boxes.
1552Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1553mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
1554class=SpellE>coeff</span>.</span></b> <span class=GramE>pulldown</span> to <b
1555style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1556mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>
1557for the <span class=SpellE>chebyschev</span> part of the background. The window
1558should look like</p>
1559
1560<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1561 id="Picture_x0020_28" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:402pt;
1562 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1563 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image008.png" o:title=""/>
1564</v:shape><![endif]--><![if !vml]><img width=536 height=263
1565src="Charge%20Flipping%20-%20sucrose_files/image008.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1566
1567<p class=MsoNormal>Go to the <b style='mso-bidi-font-weight:normal'><span
1568style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1569mso-hansi-theme-font:minor-latin'>Controls</span></b> item in the GSAS-II data
1570tree and set the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1571"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1572minor-latin'>Max cycles</span></b> to <b style='mso-bidi-font-weight:normal'><span
1573style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1574mso-hansi-theme-font:minor-latin'>5</span></b>. Now do <b style='mso-bidi-font-weight:
1575normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1576minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until
1577the refinement converges. After a set of refinement cycles go to the <b
1578style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1579mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
1580reflections</span></b> tab and check the intensities. If there are many
1581negatives amongst the highest angle reflections do <b style='mso-bidi-font-weight:
1582normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1583minor-latin;mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this
1584replaces all the values with those in the extracted from the profile as listed
1585in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1586mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1587list</span></b> for the PWDR data set each multiplied by 0.5. Additionally
1588their refinement flags are turned off. Do <b style='mso-bidi-font-weight:normal'><span
1589style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1590mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b><span
1591style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1592mso-hansi-theme-font:minor-latin'>; this will adjust all the reflections in the
1593vicinity of the reset ones</span>. You may repeat this process to suppress any
1594new negatives that may appear. Then set all the Pawley refinement flags back on
1595(excluding any that lead to a singular matrix) and repeat the refinement. After
1596refinement, mine converged to ~5.3% with very few negatives and <span
1597class=SpellE>and</span> the plot looked like</p>
1598
1599<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1600 id="_x0000_i1056" type="#_x0000_t75" style='width:525pt;height:450pt;
1601 visibility:visible;mso-wrap-style:square'>
1602 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image009.png" o:title=""/>
1603</v:shape><![endif]--><![if !vml]><img width=700 height=600
1604src="Charge%20Flipping%20-%20sucrose_files/image009.png" v:shapes="_x0000_i1056"><![endif]></span></p>
1605
1606<p class=MsoNormal>Let’s see if this is good enough for charge flipping.</p>
1607
1608<h2>Step 3: Charge flipping</h2>
1609
1610<p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
1611Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1612mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
1613and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1614"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1615minor-latin'>Charge flip controls</span></b> in the middle of the <b
1616style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1617mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1618tab.</p>
1619
1620<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1621mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1622"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1623</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
1624style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1625mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b
1626style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1627mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
162811bmb_8716.fxye Bank 1</span></b> (the only choice!). This makes the reflection
1629set to be used those in <b style='mso-bidi-font-weight:normal'><span
1630style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1631mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
1632data set; these should match the <b style='mso-bidi-font-weight:normal'><span
1633style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1634mso-hansi-theme-font:minor-latin'>Pawley reflection</span></b> set.</p>
1635
1636<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1637mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1638"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1639</span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span
1640style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1641mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b
1642style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1643mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map
1644controls</span></b>) to <b style='mso-bidi-font-weight:normal'><span
1645style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1646mso-hansi-theme-font:minor-latin'>20%</span></b>. This controls the map search
1647routine.</p>
1648
1649<p class=MsoNormal>For powder data it is not usually advisable to select a <b
1650style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1651mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing
1652element</span></b>; if selected a periodic table appears – select an element or
1653‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1654mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None’</span></b>.
1655The <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'>Resolution</span></b>
1657defines the map spacing and thus the extent of the reflection set; the observed
1658reflection set is zero filled to this limit for charge flipping. The <b
1659style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1660mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b>
1661and <b style='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-Max</span></b>
1663determine the lower threshold and upper limit for charge flipping,
1664respectively. The latter is used to avoid “Uranium solutions” in the result.
1665Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1666"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1667minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
1668ones. For sucrose set it to <b style='mso-bidi-font-weight:normal'><span
1669style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1670mso-hansi-theme-font:minor-latin'>12.</span></b> When ready select <b
1671style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1672mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
1673flipping</span></b>; a progress bar dialog will appear that tracks the residual
1674found in each charge flipping cycle. It will quickly drop to some level
1675(42-44%) and then for a successful charge flipping run perhaps drop again into
1676the 20-25% range after a considerable length of time. You should save the
1677project if you get an apparently good solution. Many times it will not drop
1678below ~40%; just try <b style='mso-bidi-font-weight:normal'><span
1679style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1680mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b> again. If
1681several tries fail to yield a solution, go back to the last step of the Pawley
1682refinement and just repeat it (that is do <b style='mso-bidi-font-weight:normal'><span
1683style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1684mso-hansi-theme-font:minor-latin'>Pawley update</span></b> and <b
1685style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1686mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>).
1687This will generate a different set of intensities for the highly overlapped
1688part of the powder pattern; perhaps they will give a successful charge flip
1689solution. Unless otherwise interrupted, GSAS-II will try 10000 times for a
1690charge flip solution (for sucrose this takes 5-10min on my laptop). Press <b
1691style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1692mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b>
1693to stop the charge flipping; a peak list and a drawing of the solution will
1694appear. One of my runs gave</p>
1695
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1701src="Charge%20Flipping%20-%20sucrose_files/image010.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1702
1703<p class=MsoNormal><o:p>&nbsp;</o:p></p>
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1802   o:connectangles="0,0"/>
1803 </v:shape></v:group><![endif]--><![if !vml]><span style='mso-ignore:vglayout;
1804position:absolute;z-index:251662336;margin-left:315px;margin-top:308px;
1805width:16px;height:35px'><img width=16 height=35
1806src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
1807style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
1808 o:spid="_x0000_i1054" type="#_x0000_t75" style='width:502.5pt;height:431.25pt;
1809 visibility:visible;mso-wrap-style:square'>
1810 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image012.png" o:title=""
1811  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
1812</v:shape><![endif]--><![if !vml]><img width=670 height=575
1813src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
1814
1815<p class=MsoNormal>The result looks very promising! Charge flipping operates
1816without regard to symmetry and GSAS-II attempts to locate the map with respect
1817to the symmetry elements from the computed reflection phases. (NB: charge
1818flipping also will give a solution without regard to handedness; this solution
1819may be either the correct one for sucrose or its inverse.) Errors in these
1820phases can disrupt this process so that the map and peak positions are offset
1821from their true positions. To discover this and fix it, rotate the drawing
1822around to check that atom positions are related via the 2<sub>1</sub> screw
1823axis (through the multicolored cross in the center of the cell and parallel to
1824the y-axis – the green cell edge). Avoid motions with the right mouse button
1825pressed, this moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:
1826normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1827minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the
1828cross to the cell center. I’ve placed the symbol for a 2<sub>1</sub> axis on my
1829drawing above to show where I think it should be. If you find an offset to the
1830map, orient it so the offset is horizontal or vertical and then press the <b
1831style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1832mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>,
1833<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1834mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>,
1835<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1836mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
1837or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1838mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
1839keys to shift the map and peaks as needed. The shift is in resolution units
1840(0.5Å) so the fix can only be approximate. Repeat as needed. Notice that the
1841peak positions in the table are updated as the offset is changed. In this case,
1842I needed just a few steps to correct the map offset. NB: you can use these keys
1843to move the result anywhere you wish, e.g. to select a different origin for the
1844structure but pay attention to the location of symmetry elements. After
1845adjustment, my solution looked like</p>
1846
1847<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1848 id="Picture_x0020_12" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:500.25pt;
1849 height:424.5pt;visibility:visible;mso-wrap-style:square'>
1850 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image014.png" o:title=""
1851  croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/>
1852</v:shape><![endif]--><![if !vml]><img width=667 height=566
1853src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
1854
1855<h2>Step 4: Obtain solution from charge flip result</h2>
1856
1857<p class=MsoNormal>The next step is to extract the unique peak positions from
1858the map and make atoms out of them. The map peak list is initially sorted by
1859peak magnitude; you can change the sorting to be along any of the column
1860headings in the table by a single click on the desired heading. The <span
1861class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1862"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1863minor-latin'>dzero</span></b></span> column gives the distance of each peak
1864from the origin. The menu items under Map peaks give you several tools to aid
1865in the peak selection process; we will just use a couple in this example. I
1866have chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:
1867normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1868minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and
1869then finding the unique ones. </p>
1870
1871<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1872mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1873"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1874</span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight:
1875normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1876minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> column heading. This
1877will sort the peaks in increasing z-axis coordinate.</p>
1878
1879<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1880mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1881"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1882</span></span></span><![endif]>Do a single click on the upper left (empty) box
1883of the table. All entries will be colored grey indicating their selection.</p>
1884
1885<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1886mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1887"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1888</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1889style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1890mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That
1891should select (grey) 23 out of 46 peak positions in the table and all should be
1892near the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub>
1893that would be all the C &amp; O atoms! They will be colored green in the plot.
1894If more are selected then check the map offset – it may need a slight
1895correction.</p>
1896
1897<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1898 id="Picture_x0020_13" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:337.5pt;
1899 height:411.75pt;visibility:visible;mso-wrap-style:square'>
1900 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image016.png" o:title=""/>
1901</v:shape><![endif]--><![if !vml]><img width=450 height=549
1902src="Charge%20Flipping%20-%20sucrose_files/image016.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1903
1904<p class=MsoNormal>The drawing shows the selected atoms in green.</p>
1905
1906<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1907 id="Picture_x0020_14" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:7in;
1908 height:429pt;visibility:visible;mso-wrap-style:square'>
1909 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image017.png" o:title=""
1910  croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/>
1911</v:shape><![endif]--><![if !vml]><img width=672 height=572
1912src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
1913
1914<p class=MsoNormal>Notice that in my case one atom is in a neighboring
1915molecule, one can deselect it and then pick the desired equivalent. Hold the <b
1916style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1917mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b>
1918key down and use the right mouse button to pick/unpick atoms in the drawing.
1919NB: the left mouse button will clear all the selections. The other two “lone”
1920atoms belong to molecules in neighboring unit cells; we’ll deal with them
1921later.</p>
1922
1923<p class=MsoNormal>These are now ready to turn into atoms. Do <b
1924style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1925mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1926peaks/Move peaks</span></b>. The drawing will show white balls for each of the
1927selected positions and the <b style='mso-bidi-font-weight:normal'><span
1928style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1929mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 23 new H
1930atoms. </p>
1931
1932<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1933 id="Picture_x0020_15" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:7in;
1934 height:433.5pt;visibility:visible;mso-wrap-style:square'>
1935 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image019.png" o:title=""
1936  croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/>
1937</v:shape><![endif]--><![if !vml]><img width=672 height=578
1938src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
1939
1940<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1941 id="Picture_x0020_44" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
1942 height:414.75pt;visibility:visible;mso-wrap-style:square'>
1943 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image021.png" o:title=""/>
1944</v:shape><![endif]--><![if !vml]><img width=700 height=553
1945src="Charge%20Flipping%20-%20sucrose_files/image021.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
1946
1947<p class=MsoNormal>The atom names indicate the peak magnitude to aid
1948identification (M100 for the largest in the <b style='mso-bidi-font-weight:
1949normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1950minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
1951may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
1952style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1953mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
1954them by selecting a row with 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'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
1957normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1958minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down and
1959then selecting a position in the table with the <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'>Alt</span></b> key still down. On
1962Linux machines the <b style='mso-bidi-font-weight:normal'><span
1963style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1964mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by
1965the operating system; use <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'>Shift/Ctrl</span></b> instead to move atoms.
1968After sorting by magnitude, my list is now </p>
1969
1970<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1971 id="Picture_x0020_17" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:525pt;
1972 height:417pt;visibility:visible;mso-wrap-style:square'>
1973 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image022.png" o:title=""/>
1974</v:shape><![endif]--><![if !vml]><img width=700 height=556
1975src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1976
1977<p class=MsoNormal>Notice that in this case the atom list is neatly sorted out
1978into two groups with a clear gap between M79 and M64. The higher ones are
1979likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit
1980of ambiguity in the middle, but just assign the top 11 as O and the rest as C
1981and see what happens. You can do this by selecting a block of atoms, go to <b
1982style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1983mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify
1984atom parameters</span></b> and select <b style='mso-bidi-font-weight:normal'><span
1985style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1986mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a periodic
1987table will appear. Select the desired element and they will be changed in the
1988list and drawing.</p>
1989
1990<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1991 id="Picture_x0020_18" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:7in;
1992 height:405.75pt;visibility:visible;mso-wrap-style:square'>
1993 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image023.png" o:title=""
1994  croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/>
1995</v:shape><![endif]--><![if !vml]><img width=672 height=541
1996src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
1997
1998<p class=MsoNormal>The original charge flipping solution is still visible and
1999the atoms are now identified, I’ve changed the drawing to show balls and sticks
2000and labeled the atoms with their names, this is done in the <b
2001style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2002mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b>
2003tab. Double click the appropriate column heading and make the selection from
2004the dialog box.<span style='mso-spacerun:yes'>  </span></p>
2005
2006<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2007 id="Picture_x0020_19" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:450pt;
2008 height:415.5pt;visibility:visible;mso-wrap-style:square'>
2009 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image025.png" o:title=""/>
2010</v:shape><![endif]--><![if !vml]><img width=600 height=554
2011src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
2012
2013<p class=MsoNormal>Now one can safely remove the map peaks (do <b
2014style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2015mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
2016peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span
2017style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2018mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
2019charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
2020style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2021mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
2022normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2023minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
2024style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2025mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2026tab). The atom positions I obtained have two atoms (O3 &amp; O4) not connected
2027to the sucrose molecule because they belong to neighboring molecules. We need
2028to discover the equivalent ones that belong to this molecule. Follow the steps:</p>
2029
2030<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2031mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2032"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2033</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2034style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2035mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> tab and select them
2036(hold the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2037mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ctrl</span></b>
2038key down and select the appropriate rows). </p>
2039
2040<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2041mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2042"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2043</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2044style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2045mso-hansi-theme-font:minor-latin'>Edit/Fill unit cell</span></b>; new atoms
2046will appear at end of list and in the drawing. </p>
2047
2048<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2049mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2050"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2051</span></span></span><![endif]>Select all the atoms in the <b style='mso-bidi-font-weight:
2052normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2053minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table by a
2054double click on upper left corner box of the table.</p>
2055
2056<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2057mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2058"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2059</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2060style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2061mso-hansi-theme-font:minor-latin'>Edit/Fill CN-sphere</span></b>; new atoms
2062will appear that are bonded to the molecule.</p>
2063
2064<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2065mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2066"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2067</span></span></span><![endif]>Select these new atoms that are in the molecule;
2068they will probably be outside the unit cell box. Do this on the drawing with <b
2069style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2070mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift left</span></b>
2071for the first one &amp; <b style='mso-bidi-font-weight:normal'><span
2072style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2073mso-hansi-theme-font:minor-latin'>Shift right</span></b> for the rest, they
2074will show in green. </p>
2075
2076<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2077mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2078"Times New Roman"'><span style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2079</span></span></span><![endif]>Look at the <b style='mso-bidi-font-weight:normal'><span
2080style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2081mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the
2082selections and make note of the <span class=SpellE><b style='mso-bidi-font-weight:
2083normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2084minor-latin;mso-hansi-theme-font:minor-latin'>Sym</span></b></span><b
2085style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2086mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Op</span></b>
2087for each one. In my case they were “<b style='mso-bidi-font-weight:normal'><span
2088style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2089mso-hansi-theme-font:minor-latin'>2+1<span class=GramE>,0,0</span></span></b>”
2090for O(4) and “<b style='mso-bidi-font-weight:normal'><span style='font-family:
2091"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2092minor-latin'>2+2,-1,1</span></b>” for O(3). The first number is the symmetry
2093operator number and the 3 numbers after the ‘<b style='mso-bidi-font-weight:
2094normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2095minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’ are unit cell
2096translations.</p>
2097
2098<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2099mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2100"Times New Roman"'><span style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2101</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2102style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2103mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab.</p>
2104
2105<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2106mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2107"Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2108</span></span></span><![endif]>Select an atom in turn that needs to be moved,
2109e.g. in my case <span class=GramE>O(</span>3) or O(4). </p>
2110
2111<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2112mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2113"Times New Roman"'><span style='mso-list:Ignore'>9.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2114</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2115style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2116mso-hansi-theme-font:minor-latin'>Edit/Transform atoms</span></b>, select the
2117operator and unit cell translations, then press <b style='mso-bidi-font-weight:
2118normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2119minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom
2120coordinates will be transformed.</p>
2121
2122<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2123mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
2124"Times New Roman"'><span style='mso-list:Ignore'>10.<span style='font:7.0pt "Times New Roman"'>&nbsp;
2125</span></span></span><![endif]>Repeat 8 &amp; 9 for any other atoms to be
2126moved.</p>
2127
2128<p class=MsoNormal style='margin-left:.5in'>This will complete the molecule
2129with the extra atoms. Do <b style='mso-bidi-font-weight:normal'><span
2130style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2131mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b> to see the
2132completed <span class=GramE>molecule.</span> I’ve made it a balls &amp; sticks
2133with names as labels.</p>
2134
2135<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2136 id="Picture_x0020_20" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:7in;
2137 height:6in;visibility:visible;mso-wrap-style:square'>
2138 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image026.png" o:title=""
2139  cropbottom="28348f" cropleft="41090f" cropright="9483f"/>
2140</v:shape><![endif]--><![if !vml]><img width=672 height=576
2141src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
2142
2143<p class=MsoNormal>Save the project file; the next step is to complete the
2144structure by finding H-atoms and then do the final Rietveld refinements.</p>
2145
2146<h2>Step 5: Complete the structure</h2>
2147
2148<p class=MsoNormal>To complete the structure you will need to perform a
2149preliminary Rietveld refinement. This will make the atom positions more
2150accurate and prepare a set of calculated structure factors needed to generate a
2151difference Fourier map good enough to maybe reveal the H atoms. There are a
2152number of steps needed to set all the controls from the previous Pawley refinement
2153to get a successful start for the Rietveld refinement.</p>
2154
2155<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2156mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2157"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2158</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2159style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2160mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the
2161GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span
2162style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2163mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You don’t want to
2164start with these when the scale factor is unknown.</p>
2165
2166<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2167mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2168"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2169</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
2170style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2171mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b
2172style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2173mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
2174scale factor</span></b> box. This is the scale factor for the data set. Uncheck
2175the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2176mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
2177class=SpellE>displ</span></span></b>.</p>
2178
2179<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2180mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
2181"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2182</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
2183style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2184mso-hansi-theme-font:minor-latin'>Phases/sucrose General</span></b> tab and
2185uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2186mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
2187cell</span></b> and <b style='mso-bidi-font-weight:normal'><span
2188style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2189mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The
2190latter is most important; if you forget you will just get another Pawley
2191refinement!</p>
2192
2193<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
2194style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2195mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
2196GSAS-II data tree menu; only scale and background are refined. I got <span
2197class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear
2198intensity differences; the atom positions obviously need refinement.</p>
2199
2200<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2201 id="_x0000_i1044" type="#_x0000_t75" style='width:525pt;height:450pt;
2202 visibility:visible;mso-wrap-style:square'>
2203 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/>
2204</v:shape><![endif]--><![if !vml]><img width=700 height=600
2205src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="_x0000_i1044"><![endif]></span></p>
2206
2207<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
2208obvious.</p>
2209
2210<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
2211style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2212mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and select the <b
2213style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2214mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2215tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub>
2216has an arbitrary location along the y-axis. Then double click the <b
2217style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2218mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
2219column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight:
2220normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2221minor-latin;mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and
2222press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2223mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2224The atoms table will show the refinement controls</p>
2225
2226<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2227 id="Picture_x0020_22" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
2228 height:225pt;visibility:visible;mso-wrap-style:square'>
2229 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/>
2230</v:shape><![endif]--><![if !vml]><img width=700 height=300
2231src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
2232
2233<p class=MsoNormal>To deal with the warning we need to set a “Hold” on one atom
2234y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span
2235style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2236mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II
2237data tree.</p>
2238
2239<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2240 id="Picture_x0020_23" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:225pt;
2241 height:187.5pt;visibility:visible;mso-wrap-style:square'>
2242 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image030.png" o:title=""/>
2243</v:shape><![endif]--><![if !vml]><img width=300 height=250
2244src="Charge%20Flipping%20-%20sucrose_files/image030.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
2245
2246<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
2247style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2248mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
2249style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2250mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
2251class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will
2252fix the shift along y for the <span class=GramE>O(</span>1) atom.</p>
2253
2254<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2255 id="Picture_x0020_53" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:259.5pt;
2256 height:271.5pt;visibility:visible;mso-wrap-style:square'>
2257 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/>
2258</v:shape><![endif]--><![if !vml]><img width=346 height=362
2259src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_53"><![endif]></span></p>
2260
2261<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
2262style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2263mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will
2264show the hold</p>
2265
2266<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2267 id="Picture_x0020_54" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:225pt;
2268 height:187.5pt;visibility:visible;mso-wrap-style:square'>
2269 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image032.png" o:title=""/>
2270</v:shape><![endif]--><![if !vml]><img width=300 height=250
2271src="Charge%20Flipping%20-%20sucrose_files/image032.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
2272
2273<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
2274style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2275mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
2276class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice
2277parameters (in the <b style='mso-bidi-font-weight:normal'><span
2278style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2279mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
2280style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2281mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>),
2282the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2283mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
2284parameters</span></b> <b style='mso-bidi-font-weight:normal'><span
2285style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2286mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
2287normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2288minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b
2289style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2290mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
2291<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2292mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2293&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2294mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2295and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2296mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
2297class=SpellE>displ</span></span></b>. You can also include refinement of atom
2298thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
2299refinement improved slightly to Rwp~10.0%. Let’s see if a difference Fourier
2300map will show anything.<br>
2301Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2302mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose
2303General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
2304style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2305mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway down
2306the window.</p>
2307
2308<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2309mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2310"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2311</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
2312normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2313minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
2314style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2315mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
2316for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2317mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
2318
2319<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2320mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2321"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2322</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
2323style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2324mso-hansi-theme-font:minor-latin'>PWDR 11bmb_8716.fxye Bank 1</span></b> for
2325the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2326mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
2327set from</span></b> item (the only choice). The Fourier calculation will use
2328the structure factors shown in the <b style='mso-bidi-font-weight:normal'><span
2329style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2330mso-hansi-theme-font:minor-latin'>Reflection list</span></b> item for this PWDR
2331data set.</p>
2332
2333<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2334mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2335"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2336</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2337style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2338mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b
2339style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2340mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2341tab window. The map will be computed via fast Fourier techniques and is very
2342fast. A few lines summarizing the map is printed on the console, the structure
2343plot may show a single green dot somewhere (it could be hidden beneath an
2344atom!), this is the highest point in the map.</p>
2345
2346<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2347mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
2348"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2349</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2350style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2351mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b
2352style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2353mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
2354level</span></b> slider until something appears on the map. You can also reduce
2355the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2356mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b>
2357to help clarify the view.</p>
2358
2359<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2360 id="Picture_x0020_35" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:502.5pt;
2361 height:435.75pt;visibility:visible;mso-wrap-style:square'>
2362 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title=""
2363  croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/>
2364</v:shape><![endif]--><![if !vml]><img width=670 height=581
2365src="Charge%20Flipping%20-%20sucrose_files/image034.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
2366
2367<p class=MsoNormal>What is drawn here are green dots whose size are
2368proportional to the electron density. There are peaks that might be H-atom
2369positions as well as features that suggest C &amp; O-atoms out of position.
2370Recall that the refinement was just done without any H-atoms; it will make the
2371best fit compensating for the missing H-atoms by displacing the C &amp; O atoms
2372in the direction of the missing H-atoms. </p>
2373
2374<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2375mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2376"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2377</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
2378style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2379mso-hansi-theme-font:minor-latin'>Phases/sucrose Draw Atoms</span></b> tab.</p>
2380
2381<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2382mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2383"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2384</span></span></span><![endif]>Select a C or O atom with possible H-atom
2385density nearby. It will appear green. Do <b style='mso-bidi-font-weight:normal'><span
2386style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2387mso-hansi-theme-font:minor-latin'>Edit/View point</span></b>; this will
2388position the cross on the selected atom.</p>
2389
2390<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2391mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2392"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2393</span></span></span><![endif]>Using the mouse, position the multicolored cross
2394directly in the center of the nearby H atom peak. Rotate the drawing around
2395with the left mouse button and shift the cross with the right mouse button. You
2396can zoom in using the roll wheel on the mouse (or else use the <b
2397style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2398mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Camera
2399distance</span></b> slider in the <b style='mso-bidi-font-weight:normal'><span
2400style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2401mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab if your mouse
2402lacks a wheel).</p>
2403
2404<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2405 id="Picture_x0020_36" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:7in;
2406 height:435.75pt;visibility:visible;mso-wrap-style:square'>
2407 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title=""
2408  croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/>
2409</v:shape><![endif]--><![if !vml]><img width=672 height=581
2410src="Charge%20Flipping%20-%20sucrose_files/image036.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
2411
2412<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2413mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2414"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2415</span></span></span><![endif]>Go to the Atoms tab and do <b style='mso-bidi-font-weight:
2416normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2417minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>,
2418a white ball will appear at the selected position and an H-atom (name = <b
2419style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2420mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>)
2421will be appended to the end of the atom list. Repeat steps 1-4 for as many
2422recognizable H-atom positions you can find; the goal is to find all 22 of them
2423(you probably will find less than that, but you could guess many of the rest).
2424I easily found all but 5 of them.</p>
2425
2426<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2427 id="Picture_x0020_38" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:7in;
2428 height:427.5pt;visibility:visible;mso-wrap-style:square'>
2429 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image037.png" o:title=""
2430  croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/>
2431</v:shape><![endif]--><![if !vml]><img width=672 height=570
2432src="Charge%20Flipping%20-%20sucrose_files/image038.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
2433
2434<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2435mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2436"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2437</span></span></span><![endif]>Change their <b style='mso-bidi-font-weight:
2438normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2439minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> to <b
2440style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2441mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>,
2442they will be renamed and make then all ball &amp; stick. Do a <b
2443style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2444mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
2445there should be a drop in <span class=SpellE>Rwp</span>. Then repeat the <b
2446style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2447mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier
2448map</span></b> in the <b style='mso-bidi-font-weight:normal'><span
2449style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2450mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust the <b
2451style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2452mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
2453level</span></b> and <b style='mso-bidi-font-weight:normal'><span
2454style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2455mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for
2456the remaining H-atoms; you may have to guess positions for some of them using
2457known stereochemistry rules. My model looked like</p>
2458
2459<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2460 id="Picture_x0020_39" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:502.5pt;
2461 height:421.5pt;visibility:visible;mso-wrap-style:square'>
2462 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image039.png" o:title=""
2463  croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/>
2464</v:shape><![endif]--><![if !vml]><img width=670 height=562
2465src="Charge%20Flipping%20-%20sucrose_files/image040.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
2466
2467<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2468style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2469mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> to finish this
2470stage in the structure analysis. My <span class=SpellE>Rwp</span> was ~8.02%
2471with all the H-atoms included (but not refined). The fit looks pretty good</p>
2472
2473<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2474 id="Picture_x0020_40" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
2475 height:450pt;visibility:visible;mso-wrap-style:square'>
2476 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image041.png" o:title=""/>
2477</v:shape><![endif]--><![if !vml]><img width=700 height=600
2478src="Charge%20Flipping%20-%20sucrose_files/image041.png" v:shapes="Picture_x0020_40"><![endif]></span></p>
2479
2480<h2>Step 6: Final refinement</h2>
2481
2482<p class=MsoNormal>Looking at the fit, there may be room for improvement and
2483we’d like to refine the H-atom positions. First we need to change the profile
2484model to include crystallite size and <span class=SpellE>mustrain</span>
2485broadening. Go to <b style='mso-bidi-font-weight:normal'><span
2486style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2487mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>, set <b
2488style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2489mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2490and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2491mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
2492to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2493mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>zero</span></b>
2494and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2495"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2496minor-latin'>Refine</span></b> flags for them.</p>
2497
2498<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
2499style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2500mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and look at the <b
2501style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2502mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
2503tab; make sure the <b style='mso-bidi-font-weight:normal'><span
2504style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2505mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the
2506boxes for both <span class=SpellE><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'>Cryst</span></b></span><b style='mso-bidi-font-weight:
2509normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2510minor-latin;mso-hansi-theme-font:minor-latin'>. <span class=GramE>size</span></span></b>
2511and <span class=SpellE><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'>microstrain</span></b></span>.</p>
2514
2515<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2516 id="Picture_x0020_41" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:480pt;
2517 height:339pt;visibility:visible;mso-wrap-style:square'>
2518 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/>
2519</v:shape><![endif]--><![if !vml]><img width=640 height=452
2520src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
2521
2522<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2523style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2524mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2525class=SpellE>Rwp</span> will start out high but should converge to where it was
2526before this change. I got 8.08% and the <b style='mso-bidi-font-weight:normal'><span
2527style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2528mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>
2529
2530<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2531 id="Picture_x0020_42" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:480pt;
2532 height:334.5pt;visibility:visible;mso-wrap-style:square'>
2533 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image043.png" o:title=""/>
2534</v:shape><![endif]--><![if !vml]><img width=640 height=446
2535src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
2536
2537<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
2538style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2539mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span
2540class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2541"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2542minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span
2543style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2544mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
2545phenomenological model for <span class=SpellE>microstrain</span> which has 9
2546terms for monoclinic structures. Check all the boxes for it.</p>
2547
2548<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2549 id="Picture_x0020_43" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:480pt;
2550 height:303.75pt;visibility:visible;mso-wrap-style:square'>
2551 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image044.png" o:title=""/>
2552</v:shape><![endif]--><![if !vml]><img width=640 height=405
2553src="Charge%20Flipping%20-%20sucrose_files/image044.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
2554
2555<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
2556style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2557mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
2558class=SpellE>Rwp</span> will start out high but should converge lower than
2559where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight:
2560normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2561minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like.
2562If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2563style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2564mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b
2565style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2566mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot
2567type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span>
2568surface plot for ground sucrose.</p>
2569
2570<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2571 id="Picture_x0020_45" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:480pt;
2572 height:305.25pt;visibility:visible;mso-wrap-style:square'>
2573 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image045.png" o:title=""/>
2574</v:shape><![endif]--><![if !vml]><img width=640 height=407
2575src="Charge%20Flipping%20-%20sucrose_files/image045.png" v:shapes="Picture_x0020_45"><![endif]></span></p>
2576
2577<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2578style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2579mso-hansi-theme-font:minor-latin;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2580 id="Picture_x0020_47" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
2581 height:450pt;visibility:visible;mso-wrap-style:square'>
2582 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image046.png" o:title=""/>
2583</v:shape><![endif]--><![if !vml]><img width=700 height=600
2584src="Charge%20Flipping%20-%20sucrose_files/image046.png" v:shapes="Picture_x0020_47"><![endif]></span></b></p>
2585
2586<p class=MsoNormal>Before refining H-atom positions it would be wise to create
2587restraints on their bond distances and angles. Locate <b style='mso-bidi-font-weight:
2588normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2589minor-latin;mso-hansi-theme-font:minor-latin'>Restraints</span></b> in the main
2590GSAS-II data tree; there will be an almost blank window telling you there are
2591no bond restraints for sucrose. Do <b style='mso-bidi-font-weight:normal'><span
2592style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2593mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
2594will appear asking for the origin atom for the bond. </p>
2595
2596<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2597 id="Picture_x0020_48" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:259.5pt;
2598 height:252pt;visibility:visible;mso-wrap-style:square'>
2599 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image047.png" o:title=""/>
2600</v:shape><![endif]--><![if !vml]><img width=346 height=336
2601src="Charge%20Flipping%20-%20sucrose_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span></p>
2602
2603<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2604style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2605mso-hansi-theme-font:minor-latin'>all H</span></b> and press <b
2606style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2607mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2608A new dialog box will appear asking for the target atoms for the bonds.</p>
2609
2610<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2611 id="Picture_x0020_49" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:259.5pt;
2612 height:252pt;visibility:visible;mso-wrap-style:square'>
2613 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image048.png" o:title=""/>
2614</v:shape><![endif]--><![if !vml]><img width=346 height=336
2615src="Charge%20Flipping%20-%20sucrose_files/image048.png" v:shapes="Picture_x0020_49"><![endif]></span></p>
2616
2617<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2618style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2619mso-hansi-theme-font:minor-latin'>all C</span></b> and <b style='mso-bidi-font-weight:
2620normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2621minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b> and a third
2622dialog box appears asking for the bond length</p>
2623
2624<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2625 id="Picture_x0020_50" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:147pt;
2626 height:78.75pt;visibility:visible;mso-wrap-style:square'>
2627 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image049.png" o:title=""/>
2628</v:shape><![endif]--><![if !vml]><img width=196 height=105
2629src="Charge%20Flipping%20-%20sucrose_files/image049.png" v:shapes="Picture_x0020_50"><![endif]></span><span
2630style='mso-spacerun:yes'> </span></p>
2631
2632<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
2633style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2634mso-hansi-theme-font:minor-latin'>1.09</span></b> and press <b
2635style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2636mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
2637I got a short list of 8 H-C and H-O restraints, but I expect 22 of them. Change
2638the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2639mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Search range</span></b>
2640to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2641mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.5</span></b>
2642and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
2643"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2644minor-latin'>Edit/Add restraints</span></b>. There are now 22 restraints on H-C
2645and H-O bond lengths.</p>
2646
2647<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2648 id="Picture_x0020_51" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:450pt;
2649 height:423pt;visibility:visible;mso-wrap-style:square'>
2650 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image050.png" o:title=""/>
2651</v:shape><![endif]--><![if !vml]><img width=600 height=564
2652src="Charge%20Flipping%20-%20sucrose_files/image050.png" v:shapes="Picture_x0020_51"><![endif]></span></p>
2653
2654<p class=MsoNormal>Next select the <b style='mso-bidi-font-weight:normal'><span
2655style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2656mso-hansi-theme-font:minor-latin'>Angle restraints</span></b> tab and again
2657there aren’t any. Do <b style='mso-bidi-font-weight:normal'><span
2658style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2659mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
2660will appear asking for the A atom in the angle A-B-C. Select <b
2661style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2662mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all H</span></b>.
2663The next dialog asks for the B atom in the A-B-C angle, select <b
2664style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2665mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all C</span></b>
2666and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2667mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b>.
2668The third dialog asks for the angle and has a default of <b style='mso-bidi-font-weight:
2669normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2670minor-latin;mso-hansi-theme-font:minor-latin'>109.54</span></b>. This is the
2671tetrahedral angle so just press <b style='mso-bidi-font-weight:normal'><span
2672style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2673mso-hansi-theme-font:minor-latin'>OK</span></b>. 36 restraints will be listed;
2674they are listed in order of the B atom. O-atoms should have one angle apiece;
2675C-atoms will have more. </p>
2676
2677<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2678 id="Picture_x0020_52" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:450pt;
2679 height:365.25pt;visibility:visible;mso-wrap-style:square'>
2680 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image051.png" o:title=""/>
2681</v:shape><![endif]--><![if !vml]><img width=600 height=487
2682src="Charge%20Flipping%20-%20sucrose_files/image051.png" v:shapes="Picture_x0020_52"><![endif]></span></p>
2683
2684<p class=MsoNormal>Now go back the <b style='mso-bidi-font-weight:normal'><span
2685style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2686mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab in <b style='mso-bidi-font-weight:
2687normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2688minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>, select
2689<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2690mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>
2691from the dialog box by double clicking on the <b style='mso-bidi-font-weight:
2692normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2693minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column. Then do <b
2694style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2695mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Set
2696atom refinement flags</span></b>. Select <b style='mso-bidi-font-weight:normal'><span
2697style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2698mso-hansi-theme-font:minor-latin'>X-coordinates</span></b>; this will set those
2699for all H-atoms. Now do <b style='mso-bidi-font-weight:normal'><span
2700style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2701mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>, the console will
2702list progress on the “Penalty function” (i.e. the restraints) and the <span
2703class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase the <b
2704style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2705mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Restraint
2706weight factors</span></b> to tighten them up at some expense in <span
2707class=SpellE>Rwp</span>. In the end I chose <b style='mso-bidi-font-weight:
2708normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2709minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b> for both <b
2710style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2711mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond</span></b>
2712and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2713mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b>
2714restraints to give a final <span class=SpellE>Rwp</span> ~7.1%. NB: the H-atom
2715positions may not be correct even though the refinement apparently succeeded.
2716You should check that the OH ones all give reasonable H-bonds to neighboring O-atoms.
2717As this is powder data such changes will hardly affect the fit but will be more
2718satisfying. At present such checking is outside the scope of GSAS-II.</p>
2719
2720<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2721
2722<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2723
2724</div>
2725
2726</body>
2727
2728</html>
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