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| 306 | <w:LsdException Locked="false" Priority="62" SemiHidden="false" |
|---|
| 307 | UnhideWhenUsed="false" Name="Light Grid Accent 6"/> |
|---|
| 308 | <w:LsdException Locked="false" Priority="63" SemiHidden="false" |
|---|
| 309 | UnhideWhenUsed="false" Name="Medium Shading 1 Accent 6"/> |
|---|
| 310 | <w:LsdException Locked="false" Priority="64" SemiHidden="false" |
|---|
| 311 | UnhideWhenUsed="false" Name="Medium Shading 2 Accent 6"/> |
|---|
| 312 | <w:LsdException Locked="false" Priority="65" SemiHidden="false" |
|---|
| 313 | UnhideWhenUsed="false" Name="Medium List 1 Accent 6"/> |
|---|
| 314 | <w:LsdException Locked="false" Priority="66" SemiHidden="false" |
|---|
| 315 | UnhideWhenUsed="false" Name="Medium List 2 Accent 6"/> |
|---|
| 316 | <w:LsdException Locked="false" Priority="67" SemiHidden="false" |
|---|
| 317 | UnhideWhenUsed="false" Name="Medium Grid 1 Accent 6"/> |
|---|
| 318 | <w:LsdException Locked="false" Priority="68" SemiHidden="false" |
|---|
| 319 | UnhideWhenUsed="false" Name="Medium Grid 2 Accent 6"/> |
|---|
| 320 | <w:LsdException Locked="false" Priority="69" SemiHidden="false" |
|---|
| 321 | UnhideWhenUsed="false" Name="Medium Grid 3 Accent 6"/> |
|---|
| 322 | <w:LsdException Locked="false" Priority="70" SemiHidden="false" |
|---|
| 323 | UnhideWhenUsed="false" Name="Dark List Accent 6"/> |
|---|
| 324 | <w:LsdException Locked="false" Priority="71" SemiHidden="false" |
|---|
| 325 | UnhideWhenUsed="false" Name="Colorful Shading Accent 6"/> |
|---|
| 326 | <w:LsdException Locked="false" Priority="72" SemiHidden="false" |
|---|
| 327 | UnhideWhenUsed="false" Name="Colorful List Accent 6"/> |
|---|
| 328 | <w:LsdException Locked="false" Priority="73" SemiHidden="false" |
|---|
| 329 | UnhideWhenUsed="false" Name="Colorful Grid Accent 6"/> |
|---|
| 330 | <w:LsdException Locked="false" Priority="19" SemiHidden="false" |
|---|
| 331 | UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis"/> |
|---|
| 332 | <w:LsdException Locked="false" Priority="21" SemiHidden="false" |
|---|
| 333 | UnhideWhenUsed="false" QFormat="true" Name="Intense Emphasis"/> |
|---|
| 334 | <w:LsdException Locked="false" Priority="31" SemiHidden="false" |
|---|
| 335 | UnhideWhenUsed="false" QFormat="true" Name="Subtle Reference"/> |
|---|
| 336 | <w:LsdException Locked="false" Priority="32" SemiHidden="false" |
|---|
| 337 | UnhideWhenUsed="false" QFormat="true" Name="Intense Reference"/> |
|---|
| 338 | <w:LsdException Locked="false" Priority="33" SemiHidden="false" |
|---|
| 339 | UnhideWhenUsed="false" QFormat="true" Name="Book Title"/> |
|---|
| 340 | <w:LsdException Locked="false" Priority="37" Name="Bibliography"/> |
|---|
| 341 | <w:LsdException Locked="false" Priority="39" QFormat="true" Name="TOC Heading"/> |
|---|
| 342 | </w:LatentStyles> |
|---|
| 343 | </xml><![endif]--> |
|---|
| 344 | <style> |
|---|
| 345 | <!-- |
|---|
| 346 | /* Font Definitions */ |
|---|
| 347 | @font-face |
|---|
| 348 | {font-family:Calibri; |
|---|
| 349 | panose-1:2 15 5 2 2 2 4 3 2 4; |
|---|
| 350 | mso-font-charset:0; |
|---|
| 351 | mso-generic-font-family:swiss; |
|---|
| 352 | mso-font-pitch:variable; |
|---|
| 353 | mso-font-signature:-536870145 1073786111 1 0 415 0;} |
|---|
| 354 | @font-face |
|---|
| 355 | {font-family:Tahoma; |
|---|
| 356 | panose-1:2 11 6 4 3 5 4 4 2 4; |
|---|
| 357 | mso-font-charset:0; |
|---|
| 358 | mso-generic-font-family:swiss; |
|---|
| 359 | mso-font-pitch:variable; |
|---|
| 360 | mso-font-signature:-520081665 -1073717157 41 0 66047 0;} |
|---|
| 361 | /* Style Definitions */ |
|---|
| 362 | p.MsoNormal, li.MsoNormal, div.MsoNormal |
|---|
| 363 | {mso-style-unhide:no; |
|---|
| 364 | mso-style-qformat:yes; |
|---|
| 365 | mso-style-parent:""; |
|---|
| 366 | margin:0in; |
|---|
| 367 | margin-bottom:.0001pt; |
|---|
| 368 | mso-pagination:widow-orphan; |
|---|
| 369 | font-size:12.0pt; |
|---|
| 370 | font-family:"Times New Roman","serif"; |
|---|
| 371 | mso-fareast-font-family:"Times New Roman"; |
|---|
| 372 | mso-fareast-theme-font:minor-fareast;} |
|---|
| 373 | h1 |
|---|
| 374 | {mso-style-priority:9; |
|---|
| 375 | mso-style-unhide:no; |
|---|
| 376 | mso-style-qformat:yes; |
|---|
| 377 | mso-style-link:"Heading 1 Char"; |
|---|
| 378 | mso-margin-top-alt:auto; |
|---|
| 379 | margin-right:0in; |
|---|
| 380 | mso-margin-bottom-alt:auto; |
|---|
| 381 | margin-left:0in; |
|---|
| 382 | mso-pagination:widow-orphan; |
|---|
| 383 | mso-outline-level:1; |
|---|
| 384 | font-size:24.0pt; |
|---|
| 385 | font-family:"Times New Roman","serif"; |
|---|
| 386 | mso-fareast-font-family:"Times New Roman"; |
|---|
| 387 | mso-fareast-theme-font:minor-fareast;} |
|---|
| 388 | h2 |
|---|
| 389 | {mso-style-noshow:yes; |
|---|
| 390 | mso-style-priority:9; |
|---|
| 391 | mso-style-qformat:yes; |
|---|
| 392 | mso-style-link:"Heading 2 Char"; |
|---|
| 393 | mso-margin-top-alt:auto; |
|---|
| 394 | margin-right:0in; |
|---|
| 395 | mso-margin-bottom-alt:auto; |
|---|
| 396 | margin-left:0in; |
|---|
| 397 | mso-pagination:widow-orphan; |
|---|
| 398 | mso-outline-level:2; |
|---|
| 399 | font-size:18.0pt; |
|---|
| 400 | font-family:"Times New Roman","serif"; |
|---|
| 401 | mso-fareast-font-family:"Times New Roman"; |
|---|
| 402 | mso-fareast-theme-font:minor-fareast;} |
|---|
| 403 | a:link, span.MsoHyperlink |
|---|
| 404 | {mso-style-noshow:yes; |
|---|
| 405 | mso-style-priority:99; |
|---|
| 406 | color:blue; |
|---|
| 407 | text-decoration:underline; |
|---|
| 408 | text-underline:single;} |
|---|
| 409 | a:visited, span.MsoHyperlinkFollowed |
|---|
| 410 | {mso-style-noshow:yes; |
|---|
| 411 | mso-style-priority:99; |
|---|
| 412 | color:purple; |
|---|
| 413 | mso-themecolor:followedhyperlink; |
|---|
| 414 | text-decoration:underline; |
|---|
| 415 | text-underline:single;} |
|---|
| 416 | p.MsoAcetate, li.MsoAcetate, div.MsoAcetate |
|---|
| 417 | {mso-style-noshow:yes; |
|---|
| 418 | mso-style-priority:99; |
|---|
| 419 | mso-style-link:"Balloon Text Char"; |
|---|
| 420 | margin:0in; |
|---|
| 421 | margin-bottom:.0001pt; |
|---|
| 422 | mso-pagination:widow-orphan; |
|---|
| 423 | font-size:8.0pt; |
|---|
| 424 | font-family:"Tahoma","sans-serif"; |
|---|
| 425 | mso-fareast-font-family:"Times New Roman"; |
|---|
| 426 | mso-fareast-theme-font:minor-fareast;} |
|---|
| 427 | p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph |
|---|
| 428 | {mso-style-priority:34; |
|---|
| 429 | mso-style-unhide:no; |
|---|
| 430 | mso-style-qformat:yes; |
|---|
| 431 | margin-top:0in; |
|---|
| 432 | margin-right:0in; |
|---|
| 433 | margin-bottom:0in; |
|---|
| 434 | margin-left:.5in; |
|---|
| 435 | margin-bottom:.0001pt; |
|---|
| 436 | mso-pagination:widow-orphan; |
|---|
| 437 | font-size:12.0pt; |
|---|
| 438 | font-family:"Times New Roman","serif"; |
|---|
| 439 | mso-fareast-font-family:"Times New Roman"; |
|---|
| 440 | mso-fareast-theme-font:minor-fareast;} |
|---|
| 441 | span.Heading1Char |
|---|
| 442 | {mso-style-name:"Heading 1 Char"; |
|---|
| 443 | mso-style-priority:9; |
|---|
| 444 | mso-style-unhide:no; |
|---|
| 445 | mso-style-locked:yes; |
|---|
| 446 | mso-style-link:"Heading 1"; |
|---|
| 447 | mso-ansi-font-size:24.0pt; |
|---|
| 448 | mso-bidi-font-size:24.0pt; |
|---|
| 449 | font-family:"Times New Roman","serif"; |
|---|
| 450 | mso-ascii-font-family:"Times New Roman"; |
|---|
| 451 | mso-fareast-font-family:"Times New Roman"; |
|---|
| 452 | mso-fareast-theme-font:minor-fareast; |
|---|
| 453 | mso-hansi-font-family:"Times New Roman"; |
|---|
| 454 | mso-bidi-font-family:"Times New Roman"; |
|---|
| 455 | mso-font-kerning:18.0pt; |
|---|
| 456 | font-weight:bold;} |
|---|
| 457 | span.Heading2Char |
|---|
| 458 | {mso-style-name:"Heading 2 Char"; |
|---|
| 459 | mso-style-noshow:yes; |
|---|
| 460 | mso-style-priority:9; |
|---|
| 461 | mso-style-unhide:no; |
|---|
| 462 | mso-style-locked:yes; |
|---|
| 463 | mso-style-link:"Heading 2"; |
|---|
| 464 | mso-ansi-font-size:18.0pt; |
|---|
| 465 | mso-bidi-font-size:18.0pt; |
|---|
| 466 | font-family:"Times New Roman","serif"; |
|---|
| 467 | mso-ascii-font-family:"Times New Roman"; |
|---|
| 468 | mso-fareast-font-family:"Times New Roman"; |
|---|
| 469 | mso-fareast-theme-font:minor-fareast; |
|---|
| 470 | mso-hansi-font-family:"Times New Roman"; |
|---|
| 471 | mso-bidi-font-family:"Times New Roman"; |
|---|
| 472 | font-weight:bold;} |
|---|
| 473 | span.BalloonTextChar |
|---|
| 474 | {mso-style-name:"Balloon Text Char"; |
|---|
| 475 | mso-style-noshow:yes; |
|---|
| 476 | mso-style-priority:99; |
|---|
| 477 | mso-style-unhide:no; |
|---|
| 478 | mso-style-locked:yes; |
|---|
| 479 | mso-style-link:"Balloon Text"; |
|---|
| 480 | mso-ansi-font-size:8.0pt; |
|---|
| 481 | mso-bidi-font-size:8.0pt; |
|---|
| 482 | font-family:"Tahoma","sans-serif"; |
|---|
| 483 | mso-ascii-font-family:Tahoma; |
|---|
| 484 | mso-fareast-font-family:"Times New Roman"; |
|---|
| 485 | mso-fareast-theme-font:minor-fareast; |
|---|
| 486 | mso-hansi-font-family:Tahoma; |
|---|
| 487 | mso-bidi-font-family:Tahoma;} |
|---|
| 488 | span.SpellE |
|---|
| 489 | {mso-style-name:""; |
|---|
| 490 | mso-spl-e:yes;} |
|---|
| 491 | span.GramE |
|---|
| 492 | {mso-style-name:""; |
|---|
| 493 | mso-gram-e:yes;} |
|---|
| 494 | .MsoChpDefault |
|---|
| 495 | {mso-style-type:export-only; |
|---|
| 496 | mso-default-props:yes; |
|---|
| 497 | font-size:12.0pt; |
|---|
| 498 | mso-ansi-font-size:12.0pt; |
|---|
| 499 | mso-bidi-font-size:12.0pt; |
|---|
| 500 | mso-fareast-font-family:Calibri; |
|---|
| 501 | mso-fareast-theme-font:minor-latin; |
|---|
| 502 | mso-bidi-font-family:"Times New Roman"; |
|---|
| 503 | mso-bidi-theme-font:minor-bidi;} |
|---|
| 504 | @page WordSection1 |
|---|
| 505 | {size:8.5in 11.0in; |
|---|
| 506 | margin:1.0in 1.0in 1.0in 1.0in; |
|---|
| 507 | mso-header-margin:.5in; |
|---|
| 508 | mso-footer-margin:.5in; |
|---|
| 509 | mso-paper-source:0;} |
|---|
| 510 | div.WordSection1 |
|---|
| 511 | {page:WordSection1;} |
|---|
| 512 | /* List Definitions */ |
|---|
| 513 | @list l0 |
|---|
| 514 | {mso-list-id:15232614; |
|---|
| 515 | mso-list-type:hybrid; |
|---|
| 516 | mso-list-template-ids:1768441438 -647724540 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} |
|---|
| 517 | @list l0:level1 |
|---|
| 518 | {mso-level-tab-stop:none; |
|---|
| 519 | mso-level-number-position:left; |
|---|
| 520 | margin-left:.75in; |
|---|
| 521 | text-indent:-.25in;} |
|---|
| 522 | @list l0:level2 |
|---|
| 523 | {mso-level-number-format:alpha-lower; |
|---|
| 524 | mso-level-tab-stop:none; |
|---|
| 525 | mso-level-number-position:left; |
|---|
| 526 | margin-left:1.25in; |
|---|
| 527 | text-indent:-.25in;} |
|---|
| 528 | @list l0:level3 |
|---|
| 529 | {mso-level-number-format:roman-lower; |
|---|
| 530 | mso-level-tab-stop:none; |
|---|
| 531 | mso-level-number-position:right; |
|---|
| 532 | margin-left:1.75in; |
|---|
| 533 | text-indent:-9.0pt;} |
|---|
| 534 | @list l0:level4 |
|---|
| 535 | {mso-level-tab-stop:none; |
|---|
| 536 | mso-level-number-position:left; |
|---|
| 537 | margin-left:2.25in; |
|---|
| 538 | text-indent:-.25in;} |
|---|
| 539 | @list l0:level5 |
|---|
| 540 | {mso-level-number-format:alpha-lower; |
|---|
| 541 | mso-level-tab-stop:none; |
|---|
| 542 | mso-level-number-position:left; |
|---|
| 543 | margin-left:2.75in; |
|---|
| 544 | text-indent:-.25in;} |
|---|
| 545 | @list l0:level6 |
|---|
| 546 | {mso-level-number-format:roman-lower; |
|---|
| 547 | mso-level-tab-stop:none; |
|---|
| 548 | mso-level-number-position:right; |
|---|
| 549 | margin-left:3.25in; |
|---|
| 550 | text-indent:-9.0pt;} |
|---|
| 551 | @list l0:level7 |
|---|
| 552 | {mso-level-tab-stop:none; |
|---|
| 553 | mso-level-number-position:left; |
|---|
| 554 | margin-left:3.75in; |
|---|
| 555 | text-indent:-.25in;} |
|---|
| 556 | @list l0:level8 |
|---|
| 557 | {mso-level-number-format:alpha-lower; |
|---|
| 558 | mso-level-tab-stop:none; |
|---|
| 559 | mso-level-number-position:left; |
|---|
| 560 | margin-left:4.25in; |
|---|
| 561 | text-indent:-.25in;} |
|---|
| 562 | @list l0:level9 |
|---|
| 563 | {mso-level-number-format:roman-lower; |
|---|
| 564 | mso-level-tab-stop:none; |
|---|
| 565 | mso-level-number-position:right; |
|---|
| 566 | margin-left:4.75in; |
|---|
| 567 | text-indent:-9.0pt;} |
|---|
| 568 | @list l1 |
|---|
| 569 | {mso-list-id:82917343; |
|---|
| 570 | mso-list-type:hybrid; |
|---|
| 571 | mso-list-template-ids:-1527319822 -2100533712 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} |
|---|
| 572 | @list l1:level1 |
|---|
| 573 | {mso-level-tab-stop:none; |
|---|
| 574 | mso-level-number-position:left; |
|---|
| 575 | margin-left:.75in; |
|---|
| 576 | text-indent:-.25in;} |
|---|
| 577 | @list l1:level2 |
|---|
| 578 | {mso-level-number-format:alpha-lower; |
|---|
| 579 | mso-level-tab-stop:none; |
|---|
| 580 | mso-level-number-position:left; |
|---|
| 581 | margin-left:1.25in; |
|---|
| 582 | text-indent:-.25in;} |
|---|
| 583 | @list l1:level3 |
|---|
| 584 | {mso-level-number-format:roman-lower; |
|---|
| 585 | mso-level-tab-stop:none; |
|---|
| 586 | mso-level-number-position:right; |
|---|
| 587 | margin-left:1.75in; |
|---|
| 588 | text-indent:-9.0pt;} |
|---|
| 589 | @list l1:level4 |
|---|
| 590 | {mso-level-tab-stop:none; |
|---|
| 591 | mso-level-number-position:left; |
|---|
| 592 | margin-left:2.25in; |
|---|
| 593 | text-indent:-.25in;} |
|---|
| 594 | @list l1:level5 |
|---|
| 595 | {mso-level-number-format:alpha-lower; |
|---|
| 596 | mso-level-tab-stop:none; |
|---|
| 597 | mso-level-number-position:left; |
|---|
| 598 | margin-left:2.75in; |
|---|
| 599 | text-indent:-.25in;} |
|---|
| 600 | @list l1:level6 |
|---|
| 601 | {mso-level-number-format:roman-lower; |
|---|
| 602 | mso-level-tab-stop:none; |
|---|
| 603 | mso-level-number-position:right; |
|---|
| 604 | margin-left:3.25in; |
|---|
| 605 | text-indent:-9.0pt;} |
|---|
| 606 | @list l1:level7 |
|---|
| 607 | {mso-level-tab-stop:none; |
|---|
| 608 | mso-level-number-position:left; |
|---|
| 609 | margin-left:3.75in; |
|---|
| 610 | text-indent:-.25in;} |
|---|
| 611 | @list l1:level8 |
|---|
| 612 | {mso-level-number-format:alpha-lower; |
|---|
| 613 | mso-level-tab-stop:none; |
|---|
| 614 | mso-level-number-position:left; |
|---|
| 615 | margin-left:4.25in; |
|---|
| 616 | text-indent:-.25in;} |
|---|
| 617 | @list l1:level9 |
|---|
| 618 | {mso-level-number-format:roman-lower; |
|---|
| 619 | mso-level-tab-stop:none; |
|---|
| 620 | mso-level-number-position:right; |
|---|
| 621 | margin-left:4.75in; |
|---|
| 622 | text-indent:-9.0pt;} |
|---|
| 623 | @list l2 |
|---|
| 624 | {mso-list-id:236667377; |
|---|
| 625 | mso-list-type:hybrid; |
|---|
| 626 | mso-list-template-ids:-513138304 1385070818 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} |
|---|
| 627 | @list l2:level1 |
|---|
| 628 | {mso-level-tab-stop:none; |
|---|
| 629 | mso-level-number-position:left; |
|---|
| 630 | margin-left:.75in; |
|---|
| 631 | text-indent:-.25in;} |
|---|
| 632 | @list l2:level2 |
|---|
| 633 | {mso-level-number-format:alpha-lower; |
|---|
| 634 | mso-level-tab-stop:none; |
|---|
| 635 | mso-level-number-position:left; |
|---|
| 636 | margin-left:1.25in; |
|---|
| 637 | text-indent:-.25in;} |
|---|
| 638 | @list l2:level3 |
|---|
| 639 | {mso-level-number-format:roman-lower; |
|---|
| 640 | mso-level-tab-stop:none; |
|---|
| 641 | mso-level-number-position:right; |
|---|
| 642 | margin-left:1.75in; |
|---|
| 643 | text-indent:-9.0pt;} |
|---|
| 644 | @list l2:level4 |
|---|
| 645 | {mso-level-tab-stop:none; |
|---|
| 646 | mso-level-number-position:left; |
|---|
| 647 | margin-left:2.25in; |
|---|
| 648 | text-indent:-.25in;} |
|---|
| 649 | @list l2:level5 |
|---|
| 650 | {mso-level-number-format:alpha-lower; |
|---|
| 651 | mso-level-tab-stop:none; |
|---|
| 652 | mso-level-number-position:left; |
|---|
| 653 | margin-left:2.75in; |
|---|
| 654 | text-indent:-.25in;} |
|---|
| 655 | @list l2:level6 |
|---|
| 656 | {mso-level-number-format:roman-lower; |
|---|
| 657 | mso-level-tab-stop:none; |
|---|
| 658 | mso-level-number-position:right; |
|---|
| 659 | margin-left:3.25in; |
|---|
| 660 | text-indent:-9.0pt;} |
|---|
| 661 | @list l2:level7 |
|---|
| 662 | {mso-level-tab-stop:none; |
|---|
| 663 | mso-level-number-position:left; |
|---|
| 664 | margin-left:3.75in; |
|---|
| 665 | text-indent:-.25in;} |
|---|
| 666 | @list l2:level8 |
|---|
| 667 | {mso-level-number-format:alpha-lower; |
|---|
| 668 | mso-level-tab-stop:none; |
|---|
| 669 | mso-level-number-position:left; |
|---|
| 670 | margin-left:4.25in; |
|---|
| 671 | text-indent:-.25in;} |
|---|
| 672 | @list l2:level9 |
|---|
| 673 | {mso-level-number-format:roman-lower; |
|---|
| 674 | mso-level-tab-stop:none; |
|---|
| 675 | mso-level-number-position:right; |
|---|
| 676 | margin-left:4.75in; |
|---|
| 677 | text-indent:-9.0pt;} |
|---|
| 678 | @list l3 |
|---|
| 679 | {mso-list-id:533275380; |
|---|
| 680 | mso-list-type:hybrid; |
|---|
| 681 | mso-list-template-ids:-1319630076 -1606007952 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} |
|---|
| 682 | @list l3:level1 |
|---|
| 683 | {mso-level-tab-stop:none; |
|---|
| 684 | mso-level-number-position:left; |
|---|
| 685 | margin-left:.75in; |
|---|
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| 930 | |
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| 931 | <body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'> |
|---|
| 932 | |
|---|
| 933 | <div class=WordSection1> |
|---|
| 934 | |
|---|
| 935 | <h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in |
|---|
| 936 | GSAS-II - sucrose<o:p></o:p></span></h1> |
|---|
| 937 | |
|---|
| 938 | <h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1> |
|---|
| 939 | |
|---|
| 940 | <p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure |
|---|
| 941 | of sucrose from powder diffraction data via charge flipping. This structure was |
|---|
| 942 | originally solved from single crystal data in the space group P2<sub>1</sub>. |
|---|
| 943 | It is a difficult exercise to complete as the charge flipping does not always |
|---|
| 944 | yield a solution and to even have a chance the Pawley refinement must be done |
|---|
| 945 | with particular care. We have given a route that sometimes works.</p> |
|---|
| 946 | |
|---|
| 947 | <p class=MsoNormal>If you have not done so already, <a |
|---|
| 948 | href="Starting%20GSAS.htm">start GSAS-II</a> and open the GSAS-II project file |
|---|
| 949 | (I called it <span class=SpellE><b style='mso-bidi-font-weight:normal'><span |
|---|
| 950 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 951 | mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b></span>) you saved from |
|---|
| 952 | the third part of the <a href="Fit%20Peaks.htm#sucrose_peak_fit">peak |
|---|
| 953 | fitting-indexing exercise</a>. If you didnt do that exercise, do it now.</p> |
|---|
| 954 | |
|---|
| 955 | <h2>Step 1: Setup for Pawley refinement</h2> |
|---|
| 956 | |
|---|
| 957 | <p class=MsoNormal>There are a number of steps that must be done in preparation |
|---|
| 958 | for a Pawley refinement after having completed the unit cell indexing and new |
|---|
| 959 | phase creation. These cover two things: one is to prepare the powder pattern |
|---|
| 960 | (reset limits, etc.) and the other is to prepare the phase for the refinement.</p> |
|---|
| 961 | |
|---|
| 962 | <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span |
|---|
| 963 | style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span |
|---|
| 964 | style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Select |
|---|
| 965 | <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 966 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b> |
|---|
| 967 | in the GSAS-II data tree for the PWDR data set and expand the plot so that the |
|---|
| 968 | region near d=1.0Å is readily seen. This is ~24deg 2<span style='font-family: |
|---|
| 969 | Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman"; |
|---|
| 970 | mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type: |
|---|
| 971 | symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area |
|---|
| 972 | relatively clear of peaks that makes a good place to end the calculations with |
|---|
| 973 | a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution |
|---|
| 974 | needed for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span |
|---|
| 975 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 976 | mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span class=SpellE><b |
|---|
| 977 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 978 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b></span> |
|---|
| 979 | as the upper limit and make a note of the exact d-spacing (1.0125Å) using the |
|---|
| 980 | mouse cursor on the plot.</p> |
|---|
| 981 | |
|---|
| 982 | <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span |
|---|
| 983 | style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span |
|---|
| 984 | style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Select |
|---|
| 985 | <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 986 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument |
|---|
| 987 | Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span |
|---|
| 988 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 989 | mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b |
|---|
| 990 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 991 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset |
|---|
| 992 | profile</span></b> to recover the default values. The peak fitting done earlier |
|---|
| 993 | is over a much more limited range of 2<span style='font-family:Symbol; |
|---|
| 994 | mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman"; |
|---|
| 995 | mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type: |
|---|
| 996 | symbol;mso-symbol-font-family:Symbol'>Q</span></span> giving values that might |
|---|
| 997 | not extrapolate well over the wider range to be used in the Pawley refinement. |
|---|
| 998 | We will refine them again later.</p> |
|---|
| 999 | |
|---|
| 1000 | <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span |
|---|
| 1001 | style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span |
|---|
| 1002 | style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Select |
|---|
| 1003 | <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1004 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample |
|---|
| 1005 | Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight: |
|---|
| 1006 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1007 | minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>. |
|---|
| 1008 | While you are here set <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1009 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1010 | mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> to <b |
|---|
| 1011 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1012 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>.</p> |
|---|
| 1013 | |
|---|
| 1014 | <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo2'><![if !supportLists]><span |
|---|
| 1015 | style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span |
|---|
| 1016 | style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Go |
|---|
| 1017 | to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1018 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> |
|---|
| 1019 | to find the <b style='mso-bidi-font-weight:normal'><span style='font-family: |
|---|
| 1020 | "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: |
|---|
| 1021 | minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight: |
|---|
| 1022 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1023 | minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> |
|---|
| 1024 | box and enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span |
|---|
| 1025 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1026 | mso-hansi-theme-font:minor-latin'>1.0125</span></b>) into the <b |
|---|
| 1027 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1028 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span |
|---|
| 1029 | class=SpellE>dmin</span></span></b> box.</p> |
|---|
| 1030 | |
|---|
| 1031 | <p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1032 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1033 | mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p> |
|---|
| 1034 | |
|---|
| 1035 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype |
|---|
| 1036 | id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t" |
|---|
| 1037 | path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f"> |
|---|
| 1038 | <v:stroke joinstyle="miter"/> |
|---|
| 1039 | <v:formulas> |
|---|
| 1040 | <v:f eqn="if lineDrawn pixelLineWidth 0"/> |
|---|
| 1041 | <v:f eqn="sum @0 1 0"/> |
|---|
| 1042 | <v:f eqn="sum 0 0 @1"/> |
|---|
| 1043 | <v:f eqn="prod @2 1 2"/> |
|---|
| 1044 | <v:f eqn="prod @3 21600 pixelWidth"/> |
|---|
| 1045 | <v:f eqn="prod @3 21600 pixelHeight"/> |
|---|
| 1046 | <v:f eqn="sum @0 0 1"/> |
|---|
| 1047 | <v:f eqn="prod @6 1 2"/> |
|---|
| 1048 | <v:f eqn="prod @7 21600 pixelWidth"/> |
|---|
| 1049 | <v:f eqn="sum @8 21600 0"/> |
|---|
| 1050 | <v:f eqn="prod @7 21600 pixelHeight"/> |
|---|
| 1051 | <v:f eqn="sum @10 21600 0"/> |
|---|
| 1052 | </v:formulas> |
|---|
| 1053 | <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/> |
|---|
| 1054 | <o:lock v:ext="edit" aspectratio="t"/> |
|---|
| 1055 | </v:shapetype><v:shape id="Picture_x0020_25" o:spid="_x0000_i1064" type="#_x0000_t75" |
|---|
| 1056 | style='width:545.25pt;height:303.75pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1057 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image001.png" o:title=""/> |
|---|
| 1058 | </v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405 |
|---|
| 1059 | src="Charge%20Flipping%20-%20sucrose_files/image001.png" v:shapes="Picture_x0020_25"><![endif]></span></p> |
|---|
| 1060 | |
|---|
| 1061 | <p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1062 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1063 | mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except |
|---|
| 1064 | for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1065 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1066 | mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a |
|---|
| 1067 | dialog box will appear</p> |
|---|
| 1068 | |
|---|
| 1069 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1070 | id="Picture_x0020_2" o:spid="_x0000_i1063" type="#_x0000_t75" style='width:259.5pt; |
|---|
| 1071 | height:252pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1072 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image002.png" o:title=""/> |
|---|
| 1073 | </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336 |
|---|
| 1074 | src="Charge%20Flipping%20-%20sucrose_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p> |
|---|
| 1075 | |
|---|
| 1076 | <p class=MsoNormal>Select either choice; the desired data set will be added to |
|---|
| 1077 | this phase for analysis. The data tab now shows the new data set; check the <b |
|---|
| 1078 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1079 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b> |
|---|
| 1080 | button to see the full information</p> |
|---|
| 1081 | |
|---|
| 1082 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1083 | id="Picture_x0020_3" o:spid="_x0000_i1062" type="#_x0000_t75" style='width:480pt; |
|---|
| 1084 | height:393pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1085 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image003.png" o:title=""/> |
|---|
| 1086 | </v:shape><![endif]--><![if !vml]><img border=0 width=640 height=524 |
|---|
| 1087 | src="Charge%20Flipping%20-%20sucrose_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p> |
|---|
| 1088 | |
|---|
| 1089 | <p class=MsoNormal>Ive stretched the window slightly to see the entire |
|---|
| 1090 | contents. This is the location for all the phase dependent parameters for this |
|---|
| 1091 | histogram. Notice that it includes phase fraction, size & <span |
|---|
| 1092 | class=SpellE>mustrain</span> as well as preferred orientation, elastic strain |
|---|
| 1093 | and extinction corrections. The <span class=SpellE>Babinet</span> correction is |
|---|
| 1094 | intended for protein work where a significant region of the structure is |
|---|
| 1095 | disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span> |
|---|
| 1096 | surfaces</p> |
|---|
| 1097 | |
|---|
| 1098 | <p class=MsoNormal><span class=GramE>as</span> well as preferred orientation |
|---|
| 1099 | correction curves.</p> |
|---|
| 1100 | |
|---|
| 1101 | <p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1102 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1103 | mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be |
|---|
| 1104 | empty except for column headings. <span class=GramE>Do</span> <b |
|---|
| 1105 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1106 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley |
|---|
| 1107 | create</span></b>; this makes the reflection set over the range covered by |
|---|
| 1108 | setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1109 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span |
|---|
| 1110 | class=SpellE>dmin</span></span></b>. The table should list reflections 0-781. |
|---|
| 1111 | Select and check the refine column using the same technique you used for the |
|---|
| 1112 | peak list. </p> |
|---|
| 1113 | |
|---|
| 1114 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1115 | id="Picture_x0020_4" o:spid="_x0000_i1061" type="#_x0000_t75" style='width:375pt; |
|---|
| 1116 | height:225pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1117 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image004.png" o:title=""/> |
|---|
| 1118 | </v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300 |
|---|
| 1119 | src="Charge%20Flipping%20-%20sucrose_files/image004.png" v:shapes="Picture_x0020_4"><![endif]></span></p> |
|---|
| 1120 | |
|---|
| 1121 | <p class=MsoNormal>This completes the Pawley refinement setup; be careful that |
|---|
| 1122 | you didnt skip a step as it might not work correctly if you did.</p> |
|---|
| 1123 | |
|---|
| 1124 | <h2>Step 2: Pawley refinement</h2> |
|---|
| 1125 | |
|---|
| 1126 | <p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight: |
|---|
| 1127 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1128 | minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on |
|---|
| 1129 | the main GSAS-II data tree window. Before it begins a backup of the project |
|---|
| 1130 | file is made; the name will be <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1131 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1132 | mso-hansi-theme-font:minor-latin'>sucrose.bck0.gpx</span></b>. It can be used |
|---|
| 1133 | to recover from a bad refinement. A progress dialog box will appear showing the |
|---|
| 1134 | residual as the refinement proceeds. Notice that there was a singular matrix |
|---|
| 1135 | warning on the console window and the last reflection (781) was removed from |
|---|
| 1136 | the refinement because it was off the end of the used part of the pattern. This |
|---|
| 1137 | is the GSAS-II singular matrix recovery mechanism; you can go to the <b |
|---|
| 1138 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1139 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley |
|---|
| 1140 | reflections</span></b> tab and uncheck the last reflection. Then repeat <b |
|---|
| 1141 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1142 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> |
|---|
| 1143 | to make sure it has essentially minimized. My refinement completed with <span |
|---|
| 1144 | class=SpellE>Rwp</span> ~26.3%; a dialog box appears asking if you wish to load |
|---|
| 1145 | the result. Press <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1146 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1147 | mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the |
|---|
| 1148 | PWDR line in the GSAS-II data tree (Ive adjusted the width and height).</p> |
|---|
| 1149 | |
|---|
| 1150 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1151 | id="Picture_x0020_5" o:spid="_x0000_i1060" type="#_x0000_t75" style='width:503.25pt; |
|---|
| 1152 | height:431.25pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1153 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image005.png" o:title=""/> |
|---|
| 1154 | </v:shape><![endif]--><![if !vml]><img border=0 width=671 height=575 |
|---|
| 1155 | src="Charge%20Flipping%20-%20sucrose_files/image005.png" v:shapes="Picture_x0020_5"><![endif]></span></p> |
|---|
| 1156 | |
|---|
| 1157 | <p class=MsoNormal>It is evident from examining the plot that some improvement |
|---|
| 1158 | can be had by refining the lattice and profile parameters and perhaps the |
|---|
| 1159 | sample X position. Go to <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1160 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1161 | mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> in the GSAS-II data |
|---|
| 1162 | tree and check the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1163 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1164 | mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> box. Now select <b |
|---|
| 1165 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1166 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument |
|---|
| 1167 | parameters</span></b> for the PWDR data set in the GSAS-II data tree and check <b |
|---|
| 1168 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1169 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>, |
|---|
| 1170 | <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1171 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, |
|---|
| 1172 | <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1173 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,<b |
|---|
| 1174 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1175 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span |
|---|
| 1176 | class=GramE>X</span> </span></b>&<b style='mso-bidi-font-weight:normal'><span |
|---|
| 1177 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1178 | mso-hansi-theme-font:minor-latin'> Y</span></b>. The go to <b style='mso-bidi-font-weight: |
|---|
| 1179 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1180 | minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and |
|---|
| 1181 | check <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1182 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span |
|---|
| 1183 | class=SpellE>displ</span></span></b>.; make the <b style='mso-bidi-font-weight: |
|---|
| 1184 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1185 | minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> <b |
|---|
| 1186 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1187 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b> |
|---|
| 1188 | if you didnt do this earlier. Repeat <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1189 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1190 | mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged; |
|---|
| 1191 | I obtained an improved residual of ~9.05% with a much better fit at the high |
|---|
| 1192 | angle part of the pattern but still not fit well for the lower part.</p> |
|---|
| 1193 | |
|---|
| 1194 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1195 | id="Picture_x0020_26" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:504.75pt; |
|---|
| 1196 | height:432.75pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1197 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image006.png" o:title=""/> |
|---|
| 1198 | </v:shape><![endif]--><![if !vml]><img border=0 width=673 height=577 |
|---|
| 1199 | src="Charge%20Flipping%20-%20sucrose_files/image006.png" v:shapes="Picture_x0020_26"><![endif]></span></p> |
|---|
| 1200 | |
|---|
| 1201 | <p class=MsoNormal>What you see is that the background has a substantial |
|---|
| 1202 | diffuse scattering feature at ~5deg and there are some peak shape issues (which |
|---|
| 1203 | may be a consequence of the poor background fit). Wed like the fit to be |
|---|
| 1204 | better before trying charge flipping. First select <span class=GramE><b |
|---|
| 1205 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1206 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>,</span> |
|---|
| 1207 | set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1208 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peaks in |
|---|
| 1209 | background: No. peaks</span></b> to <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1210 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1211 | mso-hansi-theme-font:minor-latin'>1</span></b> from the pull down box; the |
|---|
| 1212 | window changes to </p> |
|---|
| 1213 | |
|---|
| 1214 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1215 | id="Picture_x0020_27" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:366pt; |
|---|
| 1216 | height:197.25pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1217 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image007.png" o:title=""/> |
|---|
| 1218 | </v:shape><![endif]--><![if !vml]><img border=0 width=488 height=263 |
|---|
| 1219 | src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span><span |
|---|
| 1220 | style='mso-spacerun:yes'> </span></p> |
|---|
| 1221 | |
|---|
| 1222 | <p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1223 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1224 | mso-hansi-theme-font:minor-latin'>5.0</span></b> for <span class=SpellE><b |
|---|
| 1225 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1226 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span>, |
|---|
| 1227 | <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1228 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b> |
|---|
| 1229 | for <span class=SpellE><b style='mso-bidi-font-weight:normal'><span |
|---|
| 1230 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1231 | mso-hansi-theme-font:minor-latin'>int</span></b></span> and <b |
|---|
| 1232 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1233 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b> |
|---|
| 1234 | for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1235 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> |
|---|
| 1236 | (as appropriate for broad diffuse peaks) and then check all three refine boxes. |
|---|
| 1237 | Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1238 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span |
|---|
| 1239 | class=SpellE>coeff</span>.</span></b> <span class=SpellE><span class=GramE>pulldown</span></span> |
|---|
| 1240 | to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1241 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b> |
|---|
| 1242 | for the <span class=SpellE>chebyschev</span> part of the background. The window |
|---|
| 1243 | should look like</p> |
|---|
| 1244 | |
|---|
| 1245 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1246 | id="Picture_x0020_28" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:402pt; |
|---|
| 1247 | height:197.25pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1248 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image008.png" o:title=""/> |
|---|
| 1249 | </v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263 |
|---|
| 1250 | src="Charge%20Flipping%20-%20sucrose_files/image008.png" v:shapes="Picture_x0020_28"><![endif]></span></p> |
|---|
| 1251 | |
|---|
| 1252 | <p class=MsoNormal>Go to the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1253 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1254 | mso-hansi-theme-font:minor-latin'>Controls</span></b> item in the GSAS-II data |
|---|
| 1255 | tree and set the <b style='mso-bidi-font-weight:normal'><span style='font-family: |
|---|
| 1256 | "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: |
|---|
| 1257 | minor-latin'>Max cycles</span></b> to <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1258 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1259 | mso-hansi-theme-font:minor-latin'>5</span></b>. Now do <b style='mso-bidi-font-weight: |
|---|
| 1260 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1261 | minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until |
|---|
| 1262 | the refinement converges. After a set of refinement cycles go to the <b |
|---|
| 1263 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1264 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> |
|---|
| 1265 | tab and check the intensities. If there are many negatives amongst the highest |
|---|
| 1266 | angle reflections do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1267 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1268 | mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this replaces all |
|---|
| 1269 | the values with those in the extracted from the profile as listed in the <b |
|---|
| 1270 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1271 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection |
|---|
| 1272 | list</span></b> for the PWDR data set. This makes all the negative intensities |
|---|
| 1273 | positive. Next in the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1274 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1275 | mso-hansi-theme-font:minor-latin'>General</span></b> tab set the <b |
|---|
| 1276 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1277 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley neg. |
|---|
| 1278 | wt.</span></b> to <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1279 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1280 | mso-hansi-theme-font:minor-latin'>0.01</span></b>; this will suppress the |
|---|
| 1281 | negative Pawley intensities. Do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1282 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1283 | mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>. After |
|---|
| 1284 | refinement, mine converged to ~5.7% and the plot looked like</p> |
|---|
| 1285 | |
|---|
| 1286 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1287 | id="Picture_x0020_29" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:507pt; |
|---|
| 1288 | height:434.25pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1289 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image009.png" o:title=""/> |
|---|
| 1290 | </v:shape><![endif]--><![if !vml]><img border=0 width=676 height=579 |
|---|
| 1291 | src="Charge%20Flipping%20-%20sucrose_files/image009.png" v:shapes="Picture_x0020_29"><![endif]></span></p> |
|---|
| 1292 | |
|---|
| 1293 | <p class=MsoNormal>Lets see if this is good enough for charge flipping.</p> |
|---|
| 1294 | |
|---|
| 1295 | <h2>Step 3: Charge flipping</h2> |
|---|
| 1296 | |
|---|
| 1297 | <p class=MsoNormal>A few steps are needed to set up for a charge flipping run. |
|---|
| 1298 | Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1299 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> |
|---|
| 1300 | and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family: |
|---|
| 1301 | "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: |
|---|
| 1302 | minor-latin'>Charge flip controls</span></b> in the middle of the <b |
|---|
| 1303 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1304 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> |
|---|
| 1305 | tab.</p> |
|---|
| 1306 | |
|---|
| 1307 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1308 | mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1309 | "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1310 | </span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1311 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1312 | mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b |
|---|
| 1313 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1314 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR |
|---|
| 1315 | 11bmb_8716.fxye Bank 1</span></b> (the only choice!). This makes the reflection |
|---|
| 1316 | set to be used those in <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1317 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1318 | mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR |
|---|
| 1319 | data set; these should match the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1320 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1321 | mso-hansi-theme-font:minor-latin'>Pawley reflection</span></b> set.</p> |
|---|
| 1322 | |
|---|
| 1323 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1324 | mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1325 | "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1326 | </span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1327 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1328 | mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b |
|---|
| 1329 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1330 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map |
|---|
| 1331 | controls</span></b>) to <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1332 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1333 | mso-hansi-theme-font:minor-latin'>20%</span></b>. This controls the map search |
|---|
| 1334 | routine.</p> |
|---|
| 1335 | |
|---|
| 1336 | <p class=MsoNormal>For powder data it is not usually advisable to select a <b |
|---|
| 1337 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1338 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing |
|---|
| 1339 | element</span></b>; if selected a periodic table appears select an element or |
|---|
| 1340 | <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1341 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None</span></b>. |
|---|
| 1342 | The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1343 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b> |
|---|
| 1344 | defines the map spacing and thus the extent of the reflection set; the observed |
|---|
| 1345 | reflection set is zero filled to this limit for charge flipping. The <b |
|---|
| 1346 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1347 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b> |
|---|
| 1348 | and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1349 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b> |
|---|
| 1350 | determine the lower threshold and upper limit for charge flipping, |
|---|
| 1351 | respectively. The latter is used to avoid Uranium solutions in the result. |
|---|
| 1352 | Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family: |
|---|
| 1353 | "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: |
|---|
| 1354 | minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom |
|---|
| 1355 | ones. For sucrose set it to <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1356 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1357 | mso-hansi-theme-font:minor-latin'>12.</span></b> When ready select <b |
|---|
| 1358 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1359 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge |
|---|
| 1360 | flipping</span></b>; a progress bar dialog will appear that tracks the residual |
|---|
| 1361 | found in each charge flipping cycle. It will quickly drop to some level |
|---|
| 1362 | (42-44%) and then for a successful charge flipping run perhaps drop again into |
|---|
| 1363 | the 20-25% range after a considerable length of time. You should save the |
|---|
| 1364 | project if you get an apparently good solution. Many times it will not drop |
|---|
| 1365 | below ~40%; just try <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1366 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1367 | mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b> again. If |
|---|
| 1368 | several tries fail to yield a solution, go back to the last step of the Pawley |
|---|
| 1369 | refinement and just repeat it (that is do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1370 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1371 | mso-hansi-theme-font:minor-latin'>Pawley update</span></b> and <b |
|---|
| 1372 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1373 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>). |
|---|
| 1374 | This will generate a different set of intensities for the highly overlapped |
|---|
| 1375 | part of the powder pattern; perhaps they will give a successful charge flip |
|---|
| 1376 | solution. Unless otherwise interrupted, GSAS-II will try 10000 times for a |
|---|
| 1377 | charge flip solution (for sucrose this takes 5-10min on my laptop). Press <b |
|---|
| 1378 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1379 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> |
|---|
| 1380 | to stop the charge flipping; a peak list and a drawing of the solution will |
|---|
| 1381 | appear. One of my runs gave</p> |
|---|
| 1382 | |
|---|
| 1383 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
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|---|
| 1385 | height:225pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1386 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image010.png" o:title=""/> |
|---|
| 1387 | </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300 |
|---|
| 1388 | src="Charge%20Flipping%20-%20sucrose_files/image010.png" v:shapes="Picture_x0020_30"><![endif]></span></p> |
|---|
| 1389 | |
|---|
| 1390 | <p class=MsoNormal><o:p> </o:p></p> |
|---|
| 1391 | |
|---|
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|---|
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|---|
| 1491 | position:absolute;z-index:251662336;margin-left:315px;margin-top:308px; |
|---|
| 1492 | width:16px;height:35px'><img width=16 height=35 |
|---|
| 1493 | src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span |
|---|
| 1494 | style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32" |
|---|
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|---|
| 1496 | visibility:visible;mso-wrap-style:square'> |
|---|
| 1497 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image012.png" o:title="" |
|---|
| 1498 | croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/> |
|---|
| 1499 | </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=575 |
|---|
| 1500 | src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p> |
|---|
| 1501 | |
|---|
| 1502 | <p class=MsoNormal>The result looks very promising! Charge flipping operates |
|---|
| 1503 | without regard to symmetry and GSAS-II attempts to locate the map with respect |
|---|
| 1504 | to the symmetry elements from the computed reflection phases. (NB: charge |
|---|
| 1505 | flipping also will give a solution without regard to handedness; this solution |
|---|
| 1506 | may be either the correct one for sucrose or its inverse.) Errors in these |
|---|
| 1507 | phases can disrupt this process so that the map and peak positions are offset |
|---|
| 1508 | from their true positions. To discover this and fix it, rotate the drawing |
|---|
| 1509 | around to check that atom positions are related via the 2<sub>1</sub> screw |
|---|
| 1510 | axis (through the multicolored cross in the center of the cell and parallel to |
|---|
| 1511 | the y-axis the green cell edge). Avoid motions with the right mouse button |
|---|
| 1512 | pressed, this moves the cross. To recover, press the <b style='mso-bidi-font-weight: |
|---|
| 1513 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1514 | minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b> key to reset the |
|---|
| 1515 | cross to the cell center. Ive placed the symbol for a 2<sub>1</sub> axis on my |
|---|
| 1516 | drawing above to show where I think it should be. If you find an offset to the |
|---|
| 1517 | map, orient it so the offset is horizontal or vertical and then press the <b |
|---|
| 1518 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1519 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>, |
|---|
| 1520 | <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1521 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>, |
|---|
| 1522 | <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1523 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> |
|---|
| 1524 | or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1525 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b> |
|---|
| 1526 | keys to shift the map and peaks as needed. The shift is in resolution units |
|---|
| 1527 | (0.5Å) so the fix can only be approximate. Repeat as needed. Notice that the |
|---|
| 1528 | peak positions in the table are updated as the offset is changed. In this case, |
|---|
| 1529 | I needed just a few steps to correct the map offset. NB: you can use these keys |
|---|
| 1530 | to move the result anywhere you wish, e.g. to select a different origin for the |
|---|
| 1531 | structure but pay attention to the location of symmetry elements. After |
|---|
| 1532 | adjustment, my solution looked like</p> |
|---|
| 1533 | |
|---|
| 1534 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1535 | id="Picture_x0020_12" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:500.25pt; |
|---|
| 1536 | height:424.5pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1537 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image014.png" o:title="" |
|---|
| 1538 | croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/> |
|---|
| 1539 | </v:shape><![endif]--><![if !vml]><img border=0 width=667 height=566 |
|---|
| 1540 | src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p> |
|---|
| 1541 | |
|---|
| 1542 | <h2>Step 4: Obtain solution from charge flip result</h2> |
|---|
| 1543 | |
|---|
| 1544 | <p class=MsoNormal>The next step is to extract the unique peak positions from |
|---|
| 1545 | the map and make atoms out of them. The map peak list is initially sorted by |
|---|
| 1546 | peak magnitude; you can change the sorting to be along any of the column |
|---|
| 1547 | headings in the table by a single click on the desired heading. The <span |
|---|
| 1548 | class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: |
|---|
| 1549 | "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: |
|---|
| 1550 | minor-latin'>dzero</span></b></span> column gives the distance of each peak from |
|---|
| 1551 | the origin. The menu items under Map peaks give you several tools to aid in the |
|---|
| 1552 | peak selection process; we will just use a couple in this example. I have |
|---|
| 1553 | chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1554 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1555 | mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and then finding |
|---|
| 1556 | the unique ones. </p> |
|---|
| 1557 | |
|---|
| 1558 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1559 | mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1560 | "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1561 | </span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight: |
|---|
| 1562 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1563 | minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> column heading. This |
|---|
| 1564 | will sort the peaks in increasing z-axis coordinate.</p> |
|---|
| 1565 | |
|---|
| 1566 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1567 | mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1568 | "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1569 | </span></span></span><![endif]>Do a single click on the upper left (empty) box |
|---|
| 1570 | of the table. All entries will be colored grey indicating their selection.</p> |
|---|
| 1571 | |
|---|
| 1572 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1573 | mso-list:l1 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1574 | "Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1575 | </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1576 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1577 | mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That should |
|---|
| 1578 | select (grey) 23 out of 46 peak positions in the table and all should be near |
|---|
| 1579 | the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub> |
|---|
| 1580 | that would be all the C & O atoms! They will be colored green in the plot. If |
|---|
| 1581 | more are selected then check the map offset it may need a slight correction.</p> |
|---|
| 1582 | |
|---|
| 1583 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1584 | id="Picture_x0020_13" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:337.5pt; |
|---|
| 1585 | height:411.75pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1586 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image016.png" o:title=""/> |
|---|
| 1587 | </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=549 |
|---|
| 1588 | src="Charge%20Flipping%20-%20sucrose_files/image016.png" v:shapes="Picture_x0020_13"><![endif]></span></p> |
|---|
| 1589 | |
|---|
| 1590 | <p class=MsoNormal>The drawing shows the selected atoms in green.</p> |
|---|
| 1591 | |
|---|
| 1592 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1593 | id="Picture_x0020_14" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:7in; |
|---|
| 1594 | height:429pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1595 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image017.png" o:title="" |
|---|
| 1596 | croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/> |
|---|
| 1597 | </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=572 |
|---|
| 1598 | src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p> |
|---|
| 1599 | |
|---|
| 1600 | <p class=MsoNormal>Notice that in my case one atom is in a neighboring |
|---|
| 1601 | molecule, one can deselect it and then pick the desired equivalent. Hold the <b |
|---|
| 1602 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1603 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b> |
|---|
| 1604 | key down and use the right mouse button to pick/unpick atoms in the drawing. |
|---|
| 1605 | NB: the left mouse button will clear all the selections. The other two lone |
|---|
| 1606 | atoms belong to molecules in neighboring unit cells; well deal with them |
|---|
| 1607 | later.</p> |
|---|
| 1608 | |
|---|
| 1609 | <p class=MsoNormal>These are now ready to turn into atoms. Do <b |
|---|
| 1610 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1611 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map |
|---|
| 1612 | peaks/Move peaks</span></b>. The drawing will show white balls for each of the |
|---|
| 1613 | selected positions and the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1614 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1615 | mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 23 new H |
|---|
| 1616 | atoms. </p> |
|---|
| 1617 | |
|---|
| 1618 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1619 | id="Picture_x0020_15" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:7in; |
|---|
| 1620 | height:433.5pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1621 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image019.png" o:title="" |
|---|
| 1622 | croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/> |
|---|
| 1623 | </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=578 |
|---|
| 1624 | src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p> |
|---|
| 1625 | |
|---|
| 1626 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1627 | id="Picture_x0020_44" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt; |
|---|
| 1628 | height:414.75pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1629 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image021.png" o:title=""/> |
|---|
| 1630 | </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=553 |
|---|
| 1631 | src="Charge%20Flipping%20-%20sucrose_files/image021.png" v:shapes="Picture_x0020_44"><![endif]></span></p> |
|---|
| 1632 | |
|---|
| 1633 | <p class=MsoNormal>The atom names indicate the peak magnitude to aid |
|---|
| 1634 | identification (M100 for the largest in the <b style='mso-bidi-font-weight: |
|---|
| 1635 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1636 | minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which |
|---|
| 1637 | may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1638 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1639 | mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort |
|---|
| 1640 | them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1641 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1642 | mso-hansi-theme-font:minor-latin'>Alt</span></b> key down and then selecting a |
|---|
| 1643 | position in the table with the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1644 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1645 | mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. After sorting |
|---|
| 1646 | by magnitude, my list is now </p> |
|---|
| 1647 | |
|---|
| 1648 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1649 | id="Picture_x0020_17" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:525pt; |
|---|
| 1650 | height:417pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1651 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image022.png" o:title=""/> |
|---|
| 1652 | </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=556 |
|---|
| 1653 | src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17"><![endif]></span></p> |
|---|
| 1654 | |
|---|
| 1655 | <p class=MsoNormal>Notice that in this case the atom list is neatly sorted out |
|---|
| 1656 | into two groups with a clear gap between M79 and M64. The higher ones are likely |
|---|
| 1657 | to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of |
|---|
| 1658 | ambiguity in the middle, but just assign the top 11 as O and the rest as C and |
|---|
| 1659 | see what happens. You can do this by selecting a block of atoms, go to <b |
|---|
| 1660 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1661 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify |
|---|
| 1662 | atom parameters</span></b> and select <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1663 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1664 | mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a |
|---|
| 1665 | periodic table will appear. Select the desired element and they will be changed |
|---|
| 1666 | in the list and drawing.</p> |
|---|
| 1667 | |
|---|
| 1668 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1669 | id="Picture_x0020_18" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:7in; |
|---|
| 1670 | height:405.75pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1671 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image023.png" o:title="" |
|---|
| 1672 | croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/> |
|---|
| 1673 | </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=541 |
|---|
| 1674 | src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p> |
|---|
| 1675 | |
|---|
| 1676 | <p class=MsoNormal>The original charge flipping solution is still visible and |
|---|
| 1677 | the atoms are now identified, Ive changed the drawing to show balls and sticks |
|---|
| 1678 | and labeled the atoms with their names, this is done in the <b |
|---|
| 1679 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1680 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b> |
|---|
| 1681 | tab. Double click the appropriate column heading and make the selection from |
|---|
| 1682 | the dialog box.<span style='mso-spacerun:yes'> </span></p> |
|---|
| 1683 | |
|---|
| 1684 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1685 | id="Picture_x0020_19" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:450pt; |
|---|
| 1686 | height:415.5pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1687 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image025.png" o:title=""/> |
|---|
| 1688 | </v:shape><![endif]--><![if !vml]><img border=0 width=600 height=554 |
|---|
| 1689 | src="Charge%20Flipping%20-%20sucrose_files/image025.png" v:shapes="Picture_x0020_19"><![endif]></span></p> |
|---|
| 1690 | |
|---|
| 1691 | <p class=MsoNormal>Now one can safely remove the map peaks (do <b |
|---|
| 1692 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1693 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map |
|---|
| 1694 | peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1695 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1696 | mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the |
|---|
| 1697 | charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span |
|---|
| 1698 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1699 | mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight: |
|---|
| 1700 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1701 | minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b |
|---|
| 1702 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1703 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> |
|---|
| 1704 | tab). The atom positions I obtained have two atoms (O3 & O4) not connected |
|---|
| 1705 | to the sucrose molecule because they belong to neighboring molecules. We need |
|---|
| 1706 | to discover the equivalent ones that belong to this molecule. Follow the steps:</p> |
|---|
| 1707 | |
|---|
| 1708 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1709 | mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1710 | "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1711 | </span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1712 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1713 | mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> tab and select them |
|---|
| 1714 | (hold the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1715 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ctrl</span></b> |
|---|
| 1716 | key down and select the appropriate rows). </p> |
|---|
| 1717 | |
|---|
| 1718 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1719 | mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1720 | "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1721 | </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1722 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1723 | mso-hansi-theme-font:minor-latin'>Edit/Fill unit cell</span></b>; new atoms |
|---|
| 1724 | will appear at end of list and in the drawing. </p> |
|---|
| 1725 | |
|---|
| 1726 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1727 | mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1728 | "Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1729 | </span></span></span><![endif]>Select all the atoms in the <b style='mso-bidi-font-weight: |
|---|
| 1730 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1731 | minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table by a |
|---|
| 1732 | double click on upper left corner box of the table.</p> |
|---|
| 1733 | |
|---|
| 1734 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1735 | mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1736 | "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1737 | </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1738 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1739 | mso-hansi-theme-font:minor-latin'>Edit/Fill CN-sphere</span></b>; new atoms |
|---|
| 1740 | will appear that are bonded to the molecule.</p> |
|---|
| 1741 | |
|---|
| 1742 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1743 | mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1744 | "Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1745 | </span></span></span><![endif]>Select these new atoms that are in the molecule; |
|---|
| 1746 | they will probably be outside the unit cell box. Do this on the drawing with <b |
|---|
| 1747 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1748 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift left</span></b> |
|---|
| 1749 | for the first one & <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1750 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1751 | mso-hansi-theme-font:minor-latin'>Shift right</span></b> for the rest, they |
|---|
| 1752 | will show in green. </p> |
|---|
| 1753 | |
|---|
| 1754 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1755 | mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1756 | "Times New Roman"'><span style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1757 | </span></span></span><![endif]>Look at the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1758 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1759 | mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the |
|---|
| 1760 | selections and make note of the <span class=SpellE><b style='mso-bidi-font-weight: |
|---|
| 1761 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1762 | minor-latin;mso-hansi-theme-font:minor-latin'>Sym</span></b></span><b |
|---|
| 1763 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1764 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Op</span></b> |
|---|
| 1765 | for each one. In my case they were <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1766 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1767 | mso-hansi-theme-font:minor-latin'>2+1<span class=GramE>,0,0</span></span></b> |
|---|
| 1768 | for O(4) and <b style='mso-bidi-font-weight:normal'><span style='font-family: |
|---|
| 1769 | "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: |
|---|
| 1770 | minor-latin'>2+2,-1,1</span></b> for O(3). The first number is the symmetry |
|---|
| 1771 | operator number and the 3 numbers after the <b style='mso-bidi-font-weight: |
|---|
| 1772 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1773 | minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b> are unit cell |
|---|
| 1774 | translations.</p> |
|---|
| 1775 | |
|---|
| 1776 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1777 | mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1778 | "Times New Roman"'><span style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1779 | </span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1780 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1781 | mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab.</p> |
|---|
| 1782 | |
|---|
| 1783 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1784 | mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1785 | "Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1786 | </span></span></span><![endif]>Select an atom in turn that needs to be moved, |
|---|
| 1787 | e.g. in my case <span class=GramE>O(</span>3) or O(4). </p> |
|---|
| 1788 | |
|---|
| 1789 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1790 | mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1791 | "Times New Roman"'><span style='mso-list:Ignore'>9.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1792 | </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1793 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1794 | mso-hansi-theme-font:minor-latin'>Edit/Transform <span class=GramE>atoms<span |
|---|
| 1795 | style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b> |
|---|
| 1796 | select the operator and unit cell translations, then press <b style='mso-bidi-font-weight: |
|---|
| 1797 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1798 | minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom coordinates |
|---|
| 1799 | will be transformed.</p> |
|---|
| 1800 | |
|---|
| 1801 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1802 | mso-list:l0 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1803 | "Times New Roman"'><span style='mso-list:Ignore'>10.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1804 | </span></span></span><![endif]>Repeat 8 & 9 for any other atoms to be |
|---|
| 1805 | moved.</p> |
|---|
| 1806 | |
|---|
| 1807 | <p class=MsoNormal style='margin-left:.5in'>This will complete the molecule |
|---|
| 1808 | with the extra atoms. <span class=GramE>Do</span> <b style='mso-bidi-font-weight: |
|---|
| 1809 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1810 | minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b> |
|---|
| 1811 | to see the completed molecule. Ive made it a balls & sticks with names as |
|---|
| 1812 | labels.</p> |
|---|
| 1813 | |
|---|
| 1814 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1815 | id="Picture_x0020_20" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:7in; |
|---|
| 1816 | height:6in;visibility:visible;mso-wrap-style:square'> |
|---|
| 1817 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image026.png" o:title="" |
|---|
| 1818 | cropbottom="28348f" cropleft="41090f" cropright="9483f"/> |
|---|
| 1819 | </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=576 |
|---|
| 1820 | src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p> |
|---|
| 1821 | |
|---|
| 1822 | <p class=MsoNormal>Save the project file; the next step is to complete the |
|---|
| 1823 | structure by finding H-atoms and then do the final Rietveld refinements.</p> |
|---|
| 1824 | |
|---|
| 1825 | <h2>Step 5: Complete the structure</h2> |
|---|
| 1826 | |
|---|
| 1827 | <p class=MsoNormal>To complete the structure you will need to perform a |
|---|
| 1828 | preliminary Rietveld refinement. This will make the atom positions more |
|---|
| 1829 | accurate and prepare a set of calculated structure factors needed to generate a |
|---|
| 1830 | difference Fourier map good enough to maybe reveal the H atoms. There are a |
|---|
| 1831 | number of steps needed to set all the controls from the previous Pawley |
|---|
| 1832 | refinement to get a successful start for the Rietveld refinement.</p> |
|---|
| 1833 | |
|---|
| 1834 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1835 | mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1836 | "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1837 | </span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1838 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1839 | mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the |
|---|
| 1840 | GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1841 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1842 | mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You dont want to |
|---|
| 1843 | start with these when the scale factor is unknown.</p> |
|---|
| 1844 | |
|---|
| 1845 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1846 | mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1847 | "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1848 | </span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1849 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1850 | mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b |
|---|
| 1851 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1852 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram |
|---|
| 1853 | scale factor</span></b> box. This is the scale factor for the data set. Uncheck |
|---|
| 1854 | the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1855 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span |
|---|
| 1856 | class=SpellE>displ</span></span></b>.</p> |
|---|
| 1857 | |
|---|
| 1858 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1859 | mso-list:l5 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1860 | "Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1861 | </span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1862 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1863 | mso-hansi-theme-font:minor-latin'>Phases/sucrose General</span></b> tab and |
|---|
| 1864 | uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1865 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit |
|---|
| 1866 | cell</span></b> and <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1867 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1868 | mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The |
|---|
| 1869 | latter is most important; if you forget you will just get another Pawley |
|---|
| 1870 | refinement!</p> |
|---|
| 1871 | |
|---|
| 1872 | <p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1873 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1874 | mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main |
|---|
| 1875 | GSAS-II data tree menu; only scale and background are refined. I got <span |
|---|
| 1876 | class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear |
|---|
| 1877 | intensity differences; the atom positions obviously need refinement.</p> |
|---|
| 1878 | |
|---|
| 1879 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1880 | id="Picture_x0020_21" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:502.5pt; |
|---|
| 1881 | height:430.5pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1882 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image028.png" o:title=""/> |
|---|
| 1883 | </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=574 |
|---|
| 1884 | src="Charge%20Flipping%20-%20sucrose_files/image028.png" v:shapes="Picture_x0020_21"><![endif]></span></p> |
|---|
| 1885 | |
|---|
| 1886 | <p class=MsoNormal>Ive shifted & zoomed in to make the differences more |
|---|
| 1887 | obvious.</p> |
|---|
| 1888 | |
|---|
| 1889 | <p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1890 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1891 | mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and select the <b |
|---|
| 1892 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1893 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> |
|---|
| 1894 | tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub> |
|---|
| 1895 | has an arbitrary location along the y-axis. Then double click the <b |
|---|
| 1896 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1897 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> |
|---|
| 1898 | column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight: |
|---|
| 1899 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1900 | minor-latin;mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and |
|---|
| 1901 | press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1902 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. |
|---|
| 1903 | The atoms table will show the refinement controls</p> |
|---|
| 1904 | |
|---|
| 1905 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1906 | id="Picture_x0020_22" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt; |
|---|
| 1907 | height:225pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1908 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image029.png" o:title=""/> |
|---|
| 1909 | </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300 |
|---|
| 1910 | src="Charge%20Flipping%20-%20sucrose_files/image029.png" v:shapes="Picture_x0020_22"><![endif]></span></p> |
|---|
| 1911 | |
|---|
| 1912 | <p class=MsoNormal>To deal with the warning we need to set a Hold on one atom |
|---|
| 1913 | y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1914 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1915 | mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II |
|---|
| 1916 | data tree.</p> |
|---|
| 1917 | |
|---|
| 1918 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1919 | id="Picture_x0020_23" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:225pt; |
|---|
| 1920 | height:187.5pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1921 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image030.png" o:title=""/> |
|---|
| 1922 | </v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250 |
|---|
| 1923 | src="Charge%20Flipping%20-%20sucrose_files/image030.png" v:shapes="Picture_x0020_23"><![endif]></span></p> |
|---|
| 1924 | |
|---|
| 1925 | <p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1926 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1927 | mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select <b |
|---|
| 1928 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1929 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span |
|---|
| 1930 | class=GramE>:dAy:0</span> for O(1)</span></b> from the dialog box. This will |
|---|
| 1931 | fix the shift along y for the <span class=GramE>O(</span>1) atom.</p> |
|---|
| 1932 | |
|---|
| 1933 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1934 | id="Picture_x0020_53" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:259.5pt; |
|---|
| 1935 | height:271.5pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1936 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image031.png" o:title=""/> |
|---|
| 1937 | </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=362 |
|---|
| 1938 | src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_53"><![endif]></span></p> |
|---|
| 1939 | |
|---|
| 1940 | <p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1941 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1942 | mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will |
|---|
| 1943 | show the hold</p> |
|---|
| 1944 | |
|---|
| 1945 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 1946 | id="Picture_x0020_54" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:225pt; |
|---|
| 1947 | height:187.5pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 1948 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image032.png" o:title=""/> |
|---|
| 1949 | </v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250 |
|---|
| 1950 | src="Charge%20Flipping%20-%20sucrose_files/image032.png" v:shapes="Picture_x0020_54"><![endif]></span></p> |
|---|
| 1951 | |
|---|
| 1952 | <p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1953 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1954 | mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span |
|---|
| 1955 | class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice |
|---|
| 1956 | parameters (in the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1957 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1958 | mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b |
|---|
| 1959 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1960 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>), |
|---|
| 1961 | the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1962 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument |
|---|
| 1963 | parameters</span></b> <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1964 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1965 | mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight: |
|---|
| 1966 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1967 | minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b |
|---|
| 1968 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1969 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>, |
|---|
| 1970 | <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1971 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b> |
|---|
| 1972 | & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1973 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> |
|---|
| 1974 | and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1975 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span |
|---|
| 1976 | class=SpellE>displ</span></span></b>. You can also include refinement of atom |
|---|
| 1977 | thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My |
|---|
| 1978 | refinement improved slightly to Rwp~10.0%. Lets see if a difference Fourier |
|---|
| 1979 | map will show anything.<br> |
|---|
| 1980 | Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1981 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose |
|---|
| 1982 | General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 1983 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 1984 | mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway |
|---|
| 1985 | down the window.</p> |
|---|
| 1986 | |
|---|
| 1987 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1988 | mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 1989 | "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 1990 | </span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight: |
|---|
| 1991 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 1992 | minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b |
|---|
| 1993 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1994 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b> |
|---|
| 1995 | for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 1996 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p> |
|---|
| 1997 | |
|---|
| 1998 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 1999 | mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 2000 | "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 2001 | </span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2002 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2003 | mso-hansi-theme-font:minor-latin'>PWDR 11bmb_8716.fxye Bank 1</span></b> for |
|---|
| 2004 | the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2005 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection |
|---|
| 2006 | set from</span></b> item (the only choice). The Fourier calculation will use |
|---|
| 2007 | the structure factors shown in the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2008 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2009 | mso-hansi-theme-font:minor-latin'>Reflection list</span></b> item for this PWDR |
|---|
| 2010 | data set.</p> |
|---|
| 2011 | |
|---|
| 2012 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 2013 | mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 2014 | "Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 2015 | </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2016 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2017 | mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b |
|---|
| 2018 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2019 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> |
|---|
| 2020 | tab window. The map will be computed via fast Fourier techniques and is very |
|---|
| 2021 | fast. A few lines summarizing the map is printed on the console, the structure |
|---|
| 2022 | plot may show a single green dot somewhere (it could be hidden beneath an |
|---|
| 2023 | atom!), this is the highest point in the map.</p> |
|---|
| 2024 | |
|---|
| 2025 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 2026 | mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 2027 | "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 2028 | </span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2029 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2030 | mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b |
|---|
| 2031 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2032 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour |
|---|
| 2033 | level</span></b> slider until something appears on the map. You can also reduce |
|---|
| 2034 | the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2035 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b> |
|---|
| 2036 | to help clarify the view.</p> |
|---|
| 2037 | |
|---|
| 2038 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2039 | id="Picture_x0020_35" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:502.5pt; |
|---|
| 2040 | height:435.75pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2041 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image033.png" o:title="" |
|---|
| 2042 | croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/> |
|---|
| 2043 | </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=581 |
|---|
| 2044 | src="Charge%20Flipping%20-%20sucrose_files/image034.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p> |
|---|
| 2045 | |
|---|
| 2046 | <p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots |
|---|
| 2047 | whose size are proportional to the electron density. There are peaks that might |
|---|
| 2048 | be H-atom positions as well as features that suggest C & O-atoms out of |
|---|
| 2049 | position. Recall that the refinement was just done without any H-atoms; it will |
|---|
| 2050 | make the best fit compensating for the missing H-atoms by displacing the C |
|---|
| 2051 | & O atoms in the direction of the missing H-atoms. </p> |
|---|
| 2052 | |
|---|
| 2053 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 2054 | mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 2055 | "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 2056 | </span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2057 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2058 | mso-hansi-theme-font:minor-latin'>Phases/<span class=GramE>sucrose<span |
|---|
| 2059 | style='mso-spacerun:yes'> </span>Draw</span> Atoms</span></b> tab.</p> |
|---|
| 2060 | |
|---|
| 2061 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 2062 | mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 2063 | "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 2064 | </span></span></span><![endif]>Select a C or O atom with possible H-atom |
|---|
| 2065 | density nearby. It will appear green. Do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2066 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2067 | mso-hansi-theme-font:minor-latin'>Edit/View point</span></b>; this will |
|---|
| 2068 | position the cross on the selected atom.</p> |
|---|
| 2069 | |
|---|
| 2070 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 2071 | mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 2072 | "Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 2073 | </span></span></span><![endif]>Using the mouse, position the multicolored cross |
|---|
| 2074 | directly in the center of the nearby H atom peak. Rotate the drawing around |
|---|
| 2075 | with the left mouse button and shift the cross with the right mouse button. You |
|---|
| 2076 | can zoom in using the roll wheel on the mouse (or else use the <b |
|---|
| 2077 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2078 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Camera |
|---|
| 2079 | distance</span></b> slider in the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2080 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2081 | mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab if your mouse |
|---|
| 2082 | lacks a wheel).</p> |
|---|
| 2083 | |
|---|
| 2084 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2085 | id="Picture_x0020_36" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:7in; |
|---|
| 2086 | height:435.75pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2087 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image035.png" o:title="" |
|---|
| 2088 | croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/> |
|---|
| 2089 | </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=581 |
|---|
| 2090 | src="Charge%20Flipping%20-%20sucrose_files/image036.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p> |
|---|
| 2091 | |
|---|
| 2092 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 2093 | mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 2094 | "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 2095 | </span></span></span><![endif]>Go to the Atoms tab and do <b style='mso-bidi-font-weight: |
|---|
| 2096 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 2097 | minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>, |
|---|
| 2098 | a white ball will appear at the selected position and an H-atom (name = <b |
|---|
| 2099 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2100 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>) |
|---|
| 2101 | will be appended to the end of the atom list. Repeat steps 1-4 for as many |
|---|
| 2102 | recognizable H-atom positions you can find; the goal is to find all 22 of them |
|---|
| 2103 | (you probably will find less than that, but you could guess many of the rest). |
|---|
| 2104 | I easily found all but 5 of them.</p> |
|---|
| 2105 | |
|---|
| 2106 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2107 | id="Picture_x0020_38" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:7in; |
|---|
| 2108 | height:427.5pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2109 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image037.png" o:title="" |
|---|
| 2110 | croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/> |
|---|
| 2111 | </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=570 |
|---|
| 2112 | src="Charge%20Flipping%20-%20sucrose_files/image038.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p> |
|---|
| 2113 | |
|---|
| 2114 | <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; |
|---|
| 2115 | mso-list:l4 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family: |
|---|
| 2116 | "Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> |
|---|
| 2117 | </span></span></span><![endif]>Change their <b style='mso-bidi-font-weight: |
|---|
| 2118 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 2119 | minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> to <b |
|---|
| 2120 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2121 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>, |
|---|
| 2122 | they will be renamed and make then all ball & stick. Do a <b |
|---|
| 2123 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2124 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; |
|---|
| 2125 | there should be a drop in <span class=SpellE>Rwp</span>. Then repeat the <b |
|---|
| 2126 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2127 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier |
|---|
| 2128 | map</span></b> in the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2129 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2130 | mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust the <b |
|---|
| 2131 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2132 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour |
|---|
| 2133 | level</span></b> and <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2134 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2135 | mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for the |
|---|
| 2136 | remaining H-atoms; you may have to guess positions for some of them using known |
|---|
| 2137 | stereochemistry rules. My model looked like</p> |
|---|
| 2138 | |
|---|
| 2139 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2140 | id="Picture_x0020_39" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:502.5pt; |
|---|
| 2141 | height:421.5pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2142 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image039.png" o:title="" |
|---|
| 2143 | croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/> |
|---|
| 2144 | </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=562 |
|---|
| 2145 | src="Charge%20Flipping%20-%20sucrose_files/image040.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p> |
|---|
| 2146 | |
|---|
| 2147 | <p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2148 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2149 | mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> to finish this |
|---|
| 2150 | stage in the structure analysis. My <span class=SpellE>Rwp</span> was ~8.02% |
|---|
| 2151 | with all the H-atoms included (but not refined). The fit looks pretty good</p> |
|---|
| 2152 | |
|---|
| 2153 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2154 | id="Picture_x0020_40" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt; |
|---|
| 2155 | height:450pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2156 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image041.png" o:title=""/> |
|---|
| 2157 | </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 |
|---|
| 2158 | src="Charge%20Flipping%20-%20sucrose_files/image041.png" v:shapes="Picture_x0020_40"><![endif]></span></p> |
|---|
| 2159 | |
|---|
| 2160 | <h2>Step 6: Final refinement</h2> |
|---|
| 2161 | |
|---|
| 2162 | <p class=MsoNormal>Looking at the fit, there may be room for improvement and |
|---|
| 2163 | wed like to refine the H-atom positions. First we need to change the profile |
|---|
| 2164 | model to include crystallite size and <span class=SpellE>mustrain</span> |
|---|
| 2165 | broadening. Go to <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2166 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2167 | mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>, set <b |
|---|
| 2168 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2169 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b> |
|---|
| 2170 | and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2171 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> |
|---|
| 2172 | to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2173 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>zero</span></b> |
|---|
| 2174 | and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family: |
|---|
| 2175 | "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: |
|---|
| 2176 | minor-latin'>Refine</span></b> flags for them.</p> |
|---|
| 2177 | |
|---|
| 2178 | <p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2179 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2180 | mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and look at the <b |
|---|
| 2181 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2182 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b> |
|---|
| 2183 | tab; make sure the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2184 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2185 | mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the |
|---|
| 2186 | boxes for both <span class=SpellE><b style='mso-bidi-font-weight:normal'><span |
|---|
| 2187 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2188 | mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b style='mso-bidi-font-weight: |
|---|
| 2189 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 2190 | minor-latin;mso-hansi-theme-font:minor-latin'>. <span class=GramE>size</span></span></b> |
|---|
| 2191 | and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span |
|---|
| 2192 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2193 | mso-hansi-theme-font:minor-latin'>microstrain</span></b></span>.</p> |
|---|
| 2194 | |
|---|
| 2195 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2196 | id="Picture_x0020_41" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:480pt; |
|---|
| 2197 | height:339pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2198 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image042.png" o:title=""/> |
|---|
| 2199 | </v:shape><![endif]--><![if !vml]><img border=0 width=640 height=452 |
|---|
| 2200 | src="Charge%20Flipping%20-%20sucrose_files/image042.png" v:shapes="Picture_x0020_41"><![endif]></span></p> |
|---|
| 2201 | |
|---|
| 2202 | <p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2203 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2204 | mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span |
|---|
| 2205 | class=SpellE>Rwp</span> will start out high but should converge to where it was |
|---|
| 2206 | before this change. I got 8.08% and the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2207 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2208 | mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p> |
|---|
| 2209 | |
|---|
| 2210 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2211 | id="Picture_x0020_42" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:480pt; |
|---|
| 2212 | height:334.5pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2213 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image043.png" o:title=""/> |
|---|
| 2214 | </v:shape><![endif]--><![if !vml]><img border=0 width=640 height=446 |
|---|
| 2215 | src="Charge%20Flipping%20-%20sucrose_files/image043.png" v:shapes="Picture_x0020_42"><![endif]></span></p> |
|---|
| 2216 | |
|---|
| 2217 | <p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2218 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2219 | mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span |
|---|
| 2220 | class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: |
|---|
| 2221 | "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: |
|---|
| 2222 | minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span |
|---|
| 2223 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2224 | mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens |
|---|
| 2225 | phenomenological model for <span class=SpellE>microstrain</span> which has 9 |
|---|
| 2226 | terms for monoclinic structures. Check all the boxes for it.</p> |
|---|
| 2227 | |
|---|
| 2228 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2229 | id="Picture_x0020_43" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:480pt; |
|---|
| 2230 | height:303.75pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2231 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image044.png" o:title=""/> |
|---|
| 2232 | </v:shape><![endif]--><![if !vml]><img border=0 width=640 height=405 |
|---|
| 2233 | src="Charge%20Flipping%20-%20sucrose_files/image044.png" v:shapes="Picture_x0020_43"><![endif]></span></p> |
|---|
| 2234 | |
|---|
| 2235 | <p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2236 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2237 | mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span |
|---|
| 2238 | class=SpellE>Rwp</span> will start out high but should converge lower than |
|---|
| 2239 | where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight: |
|---|
| 2240 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 2241 | minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like. |
|---|
| 2242 | If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span |
|---|
| 2243 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2244 | mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b |
|---|
| 2245 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2246 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot |
|---|
| 2247 | type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span> |
|---|
| 2248 | surface plot for ground sucrose.</p> |
|---|
| 2249 | |
|---|
| 2250 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2251 | id="Picture_x0020_45" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:480pt; |
|---|
| 2252 | height:305.25pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2253 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image045.png" o:title=""/> |
|---|
| 2254 | </v:shape><![endif]--><![if !vml]><img border=0 width=640 height=407 |
|---|
| 2255 | src="Charge%20Flipping%20-%20sucrose_files/image045.png" v:shapes="Picture_x0020_45"><![endif]></span></p> |
|---|
| 2256 | |
|---|
| 2257 | <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span |
|---|
| 2258 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2259 | mso-hansi-theme-font:minor-latin;mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2260 | id="Picture_x0020_47" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt; |
|---|
| 2261 | height:450pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2262 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image046.png" o:title=""/> |
|---|
| 2263 | </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 |
|---|
| 2264 | src="Charge%20Flipping%20-%20sucrose_files/image046.png" v:shapes="Picture_x0020_47"><![endif]></span></b></p> |
|---|
| 2265 | |
|---|
| 2266 | <p class=MsoNormal>Before refining H-atom positions it would be wise to create |
|---|
| 2267 | restraints on their bond distances and angles. Locate <b style='mso-bidi-font-weight: |
|---|
| 2268 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 2269 | minor-latin;mso-hansi-theme-font:minor-latin'>Restraints</span></b> in the main |
|---|
| 2270 | GSAS-II data tree; there will be an almost blank window telling you there are |
|---|
| 2271 | no bond restraints for sucrose. Do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2272 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2273 | mso-hansi-theme-font:minor-latin'>Edit/Add <span class=GramE>restraints<span |
|---|
| 2274 | style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b> |
|---|
| 2275 | a dialog box will appear asking for the origin atom for the bond. </p> |
|---|
| 2276 | |
|---|
| 2277 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2278 | id="Picture_x0020_48" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:259.5pt; |
|---|
| 2279 | height:252pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2280 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image047.png" o:title=""/> |
|---|
| 2281 | </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336 |
|---|
| 2282 | src="Charge%20Flipping%20-%20sucrose_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span></p> |
|---|
| 2283 | |
|---|
| 2284 | <p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2285 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2286 | mso-hansi-theme-font:minor-latin'>all H</span></b> and press <b |
|---|
| 2287 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2288 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. |
|---|
| 2289 | A new dialog box will appear asking for the target atoms for the bonds.</p> |
|---|
| 2290 | |
|---|
| 2291 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2292 | id="Picture_x0020_49" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:259.5pt; |
|---|
| 2293 | height:252pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2294 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image048.png" o:title=""/> |
|---|
| 2295 | </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336 |
|---|
| 2296 | src="Charge%20Flipping%20-%20sucrose_files/image048.png" v:shapes="Picture_x0020_49"><![endif]></span></p> |
|---|
| 2297 | |
|---|
| 2298 | <p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2299 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2300 | mso-hansi-theme-font:minor-latin'>all C</span></b> and <b style='mso-bidi-font-weight: |
|---|
| 2301 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 2302 | minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b> and a third |
|---|
| 2303 | dialog box appears asking for the bond length</p> |
|---|
| 2304 | |
|---|
| 2305 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2306 | id="Picture_x0020_50" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:147pt; |
|---|
| 2307 | height:78.75pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2308 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image049.png" o:title=""/> |
|---|
| 2309 | </v:shape><![endif]--><![if !vml]><img border=0 width=196 height=105 |
|---|
| 2310 | src="Charge%20Flipping%20-%20sucrose_files/image049.png" v:shapes="Picture_x0020_50"><![endif]></span><span |
|---|
| 2311 | style='mso-spacerun:yes'> </span></p> |
|---|
| 2312 | |
|---|
| 2313 | <p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2314 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2315 | mso-hansi-theme-font:minor-latin'>1.09</span></b> and press <b |
|---|
| 2316 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2317 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. |
|---|
| 2318 | I got a short list of 8 H-C and H-O restraints, but I expect 22 of them. Change |
|---|
| 2319 | the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2320 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Search range</span></b> |
|---|
| 2321 | to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2322 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.5</span></b> |
|---|
| 2323 | and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family: |
|---|
| 2324 | "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: |
|---|
| 2325 | minor-latin'>Edit/Add restraints</span></b>. There are now 22 restraints on H-C |
|---|
| 2326 | and H-O bond lengths.</p> |
|---|
| 2327 | |
|---|
| 2328 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2329 | id="Picture_x0020_51" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:450pt; |
|---|
| 2330 | height:423pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2331 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image050.png" o:title=""/> |
|---|
| 2332 | </v:shape><![endif]--><![if !vml]><img border=0 width=600 height=564 |
|---|
| 2333 | src="Charge%20Flipping%20-%20sucrose_files/image050.png" v:shapes="Picture_x0020_51"><![endif]></span></p> |
|---|
| 2334 | |
|---|
| 2335 | <p class=MsoNormal>Next select the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2336 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2337 | mso-hansi-theme-font:minor-latin'>Angle restraints</span></b> tab and again |
|---|
| 2338 | there arent any. Do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2339 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2340 | mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box |
|---|
| 2341 | will appear asking for the A atom in the angle A-B-C. Select <b |
|---|
| 2342 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2343 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all H</span></b>. |
|---|
| 2344 | The next dialog asks for the B atom in the A-B-C angle, select <b |
|---|
| 2345 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2346 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all C</span></b> |
|---|
| 2347 | and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2348 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b>. |
|---|
| 2349 | The third dialog asks for the angle and has a default of <b style='mso-bidi-font-weight: |
|---|
| 2350 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 2351 | minor-latin;mso-hansi-theme-font:minor-latin'>109.54</span></b>. This is the |
|---|
| 2352 | tetrahedral angle so just press <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2353 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2354 | mso-hansi-theme-font:minor-latin'>OK</span></b>. 36 restraints will be listed; |
|---|
| 2355 | they are listed in order of the B atom. O-atoms should have one angle apiece; |
|---|
| 2356 | C-atoms will have more. </p> |
|---|
| 2357 | |
|---|
| 2358 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 2359 | id="Picture_x0020_52" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:450pt; |
|---|
| 2360 | height:365.25pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 2361 | <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image051.png" o:title=""/> |
|---|
| 2362 | </v:shape><![endif]--><![if !vml]><img border=0 width=600 height=487 |
|---|
| 2363 | src="Charge%20Flipping%20-%20sucrose_files/image051.png" v:shapes="Picture_x0020_52"><![endif]></span></p> |
|---|
| 2364 | |
|---|
| 2365 | <p class=MsoNormal>Now go back the <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2366 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2367 | mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab in <b style='mso-bidi-font-weight: |
|---|
| 2368 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 2369 | minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>, select |
|---|
| 2370 | <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2371 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b> |
|---|
| 2372 | from the dialog box by double clicking on the <b style='mso-bidi-font-weight: |
|---|
| 2373 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 2374 | minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column. Then do <b |
|---|
| 2375 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2376 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Set |
|---|
| 2377 | atom refinement flags</span></b>. Select <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2378 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2379 | mso-hansi-theme-font:minor-latin'>X-coordinates</span></b>; this will set those |
|---|
| 2380 | for all H-atoms. Now do <b style='mso-bidi-font-weight:normal'><span |
|---|
| 2381 | style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; |
|---|
| 2382 | mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>, the console will |
|---|
| 2383 | list progress on the Penalty function (i.e. the restraints) and the <span |
|---|
| 2384 | class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase the <b |
|---|
| 2385 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2386 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Restraint |
|---|
| 2387 | weight factors</span></b> to tighten them up at some expense in <span |
|---|
| 2388 | class=SpellE>Rwp</span>. In the end I chose <b style='mso-bidi-font-weight: |
|---|
| 2389 | normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: |
|---|
| 2390 | minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b> for both <b |
|---|
| 2391 | style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2392 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond</span></b> |
|---|
| 2393 | and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; |
|---|
| 2394 | mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b> |
|---|
| 2395 | restraints to give a final <span class=SpellE>Rwp</span> ~7.1%. NB: the H-atom |
|---|
| 2396 | positions may not be correct even though the refinement apparently succeeded. |
|---|
| 2397 | You should check that the OH ones all give reasonable H-bonds to neighboring |
|---|
| 2398 | O-atoms. As this is powder data such changes will hardly affect the fit but |
|---|
| 2399 | will be more satisfying. At present such checking is outside the scope of |
|---|
| 2400 | GSAS-II.</p> |
|---|
| 2401 | |
|---|
| 2402 | <p class=MsoNormal><o:p> </o:p></p> |
|---|
| 2403 | |
|---|
| 2404 | <p class=MsoNormal><o:p> </o:p></p> |
|---|
| 2405 | |
|---|
| 2406 | </div> |
|---|
| 2407 | |
|---|
| 2408 | </body> |
|---|
| 2409 | |
|---|
| 2410 | </html> |
|---|
