Changeset 1717
- Timestamp:
- Mar 16, 2015 4:10:20 PM (8 years ago)
- Location:
- Tutorials/CFsucrose
- Files:
-
- 12 edited
Legend:
- Unmodified
- Added
- Removed
-
Tutorials/CFsucrose/Charge Flipping - sucrose.htm
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<w:LsdException Locked="false" Priority="11" QFormat="true" Name="Subtitle"/> 234 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 235 Name="Salutation"/> 236 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 237 Name="Date"/> 238 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 239 Name="Body Text First Indent"/> 240 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 241 Name="Body Text First Indent 2"/> 242 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 243 Name="Note Heading"/> 244 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 245 Name="Body Text 2"/> 246 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 247 Name="Body Text 3"/> 248 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 249 Name="Body Text Indent 2"/> 250 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 251 Name="Body Text Indent 3"/> 252 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 253 Name="Block Text"/> 254 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 255 Name="Hyperlink"/> 256 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 257 Name="FollowedHyperlink"/> 258 <w:LsdException Locked="false" Priority="22" QFormat="true" Name="Strong"/> 259 <w:LsdException Locked="false" Priority="20" QFormat="true" Name="Emphasis"/> 260 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 261 Name="Document Map"/> 262 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 263 Name="Plain Text"/> 264 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 265 Name="E-mail Signature"/> 266 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 267 Name="HTML Top of Form"/> 268 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 269 Name="HTML Bottom of Form"/> 270 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 271 Name="Normal (Web)"/> 272 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 273 Name="HTML Acronym"/> 274 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 275 Name="HTML Address"/> 276 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 277 Name="HTML Cite"/> 278 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 279 Name="HTML Code"/> 280 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 281 Name="HTML Definition"/> 282 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 283 Name="HTML Keyboard"/> 284 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 285 Name="HTML Preformatted"/> 286 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 287 Name="HTML Sample"/> 288 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 289 Name="HTML Typewriter"/> 290 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 291 Name="HTML Variable"/> 292 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 293 Name="Normal Table"/> 294 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 295 Name="annotation subject"/> 296 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 297 Name="No List"/> 298 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 299 Name="Outline List 1"/> 300 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 301 Name="Outline List 2"/> 302 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 303 Name="Outline List 3"/> 304 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 305 Name="Table Simple 1"/> 306 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 307 Name="Table Simple 2"/> 308 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 309 Name="Table Simple 3"/> 310 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 311 Name="Table Classic 1"/> 312 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 313 Name="Table Classic 2"/> 314 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 315 Name="Table Classic 3"/> 316 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 317 Name="Table Classic 4"/> 318 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 319 Name="Table Colorful 1"/> 320 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 321 Name="Table Colorful 2"/> 322 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 323 Name="Table Colorful 3"/> 324 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 325 Name="Table Columns 1"/> 326 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 327 Name="Table Columns 2"/> 328 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 329 Name="Table Columns 3"/> 330 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 331 Name="Table Columns 4"/> 332 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 333 Name="Table Columns 5"/> 334 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 335 Name="Table Grid 1"/> 336 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 337 Name="Table Grid 2"/> 338 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 339 Name="Table Grid 3"/> 340 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 341 Name="Table Grid 4"/> 342 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 343 Name="Table Grid 5"/> 344 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 345 Name="Table Grid 6"/> 346 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 347 Name="Table Grid 7"/> 348 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 349 Name="Table Grid 8"/> 350 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 351 Name="Table List 1"/> 352 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 353 Name="Table List 2"/> 354 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 355 Name="Table List 3"/> 356 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 357 Name="Table List 4"/> 358 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 359 Name="Table List 5"/> 360 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 361 Name="Table List 6"/> 362 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 363 Name="Table List 7"/> 364 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 365 Name="Table List 8"/> 366 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 367 Name="Table 3D effects 1"/> 368 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 369 Name="Table 3D effects 2"/> 370 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 371 Name="Table 3D effects 3"/> 372 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 373 Name="Table Contemporary"/> 374 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 375 Name="Table Elegant"/> 376 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 377 Name="Table Professional"/> 378 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 379 Name="Table Subtle 1"/> 380 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 381 Name="Table Subtle 2"/> 382 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 383 Name="Table Web 1"/> 384 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 385 Name="Table Web 2"/> 386 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 387 Name="Table Web 3"/> 388 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 389 Name="Balloon Text"/> 390 <w:LsdException Locked="false" Priority="59" Name="Table Grid"/> 391 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 392 Name="Table Theme"/> 393 <w:LsdException Locked="false" SemiHidden="true" Name="Placeholder Text"/> 394 <w:LsdException Locked="false" Priority="1" QFormat="true" Name="No Spacing"/> 395 <w:LsdException Locked="false" Priority="60" Name="Light Shading"/> 396 <w:LsdException Locked="false" Priority="61" Name="Light List"/> 397 <w:LsdException Locked="false" Priority="62" Name="Light Grid"/> 398 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1"/> 399 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2"/> 400 <w:LsdException Locked="false" Priority="65" Name="Medium List 1"/> 401 <w:LsdException Locked="false" Priority="66" Name="Medium List 2"/> 402 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1"/> 403 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2"/> 404 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3"/> 405 <w:LsdException Locked="false" Priority="70" Name="Dark List"/> 406 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading"/> 407 <w:LsdException Locked="false" Priority="72" Name="Colorful List"/> 408 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/> 409 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/> 410 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/> 411 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/> 412 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/> 413 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/> 414 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/> 415 <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/> 416 <w:LsdException Locked="false" Priority="34" QFormat="true" 417 Name="List Paragraph"/> 418 <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/> 419 <w:LsdException Locked="false" Priority="30" QFormat="true" 420 Name="Intense Quote"/> 421 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/> 422 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/> 423 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/> 424 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/> 425 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/> 426 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/> 427 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/> 428 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/> 429 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/> 430 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/> 431 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/> 432 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/> 433 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/> 434 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/> 435 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/> 436 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/> 437 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/> 438 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/> 439 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/> 440 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/> 441 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/> 442 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/> 443 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/> 444 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/> 445 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/> 446 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/> 447 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/> 448 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/> 449 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/> 450 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/> 451 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/> 452 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/> 453 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/> 454 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/> 455 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/> 456 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/> 457 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/> 458 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/> 459 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/> 460 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/> 461 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/> 462 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/> 463 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/> 464 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/> 465 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/> 466 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/> 467 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/> 468 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/> 469 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/> 470 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/> 471 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/> 472 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/> 473 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/> 474 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/> 475 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/> 476 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/> 477 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/> 478 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/> 479 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/> 480 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/> 481 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/> 482 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/> 483 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/> 484 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/> 485 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/> 486 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/> 487 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/> 488 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/> 489 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/> 490 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/> 491 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/> 492 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/> 493 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/> 494 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/> 495 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/> 496 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/> 497 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/> 498 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/> 499 <w:LsdException Locked="false" Priority="19" QFormat="true" 500 Name="Subtle Emphasis"/> 501 <w:LsdException Locked="false" Priority="21" QFormat="true" 502 Name="Intense Emphasis"/> 503 <w:LsdException Locked="false" Priority="31" QFormat="true" 504 Name="Subtle Reference"/> 505 <w:LsdException Locked="false" Priority="32" QFormat="true" 506 Name="Intense Reference"/> 507 <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/> 508 <w:LsdException Locked="false" Priority="37" SemiHidden="true" 509 UnhideWhenUsed="true" Name="Bibliography"/> 510 <w:LsdException Locked="false" Priority="39" SemiHidden="true" 511 UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/> 512 <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/> 513 <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/> 514 <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/> 515 <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/> 516 <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/> 517 <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/> 518 <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/> 519 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/> 520 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/> 521 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/> 522 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/> 523 <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/> 524 <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/> 525 <w:LsdException Locked="false" Priority="46" 526 Name="Grid Table 1 Light Accent 1"/> 527 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/> 528 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/> 529 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/> 530 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/> 531 <w:LsdException Locked="false" Priority="51" 532 Name="Grid Table 6 Colorful Accent 1"/> 533 <w:LsdException Locked="false" Priority="52" 534 Name="Grid Table 7 Colorful Accent 1"/> 535 <w:LsdException Locked="false" Priority="46" 536 Name="Grid Table 1 Light Accent 2"/> 537 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/> 538 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/> 539 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/> 540 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/> 541 <w:LsdException Locked="false" Priority="51" 542 Name="Grid Table 6 Colorful Accent 2"/> 543 <w:LsdException Locked="false" Priority="52" 544 Name="Grid Table 7 Colorful Accent 2"/> 545 <w:LsdException Locked="false" Priority="46" 546 Name="Grid Table 1 Light Accent 3"/> 547 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/> 548 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/> 549 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/> 550 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/> 551 <w:LsdException Locked="false" Priority="51" 552 Name="Grid Table 6 Colorful Accent 3"/> 553 <w:LsdException Locked="false" Priority="52" 554 Name="Grid Table 7 Colorful Accent 3"/> 555 <w:LsdException Locked="false" Priority="46" 556 Name="Grid Table 1 Light Accent 4"/> 557 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/> 558 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/> 559 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/> 560 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/> 561 <w:LsdException Locked="false" Priority="51" 562 Name="Grid Table 6 Colorful Accent 4"/> 563 <w:LsdException Locked="false" Priority="52" 564 Name="Grid Table 7 Colorful Accent 4"/> 565 <w:LsdException Locked="false" Priority="46" 566 Name="Grid Table 1 Light Accent 5"/> 567 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/> 568 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/> 569 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/> 570 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/> 571 <w:LsdException Locked="false" Priority="51" 572 Name="Grid Table 6 Colorful Accent 5"/> 573 <w:LsdException Locked="false" Priority="52" 574 Name="Grid Table 7 Colorful Accent 5"/> 575 <w:LsdException Locked="false" Priority="46" 576 Name="Grid Table 1 Light Accent 6"/> 577 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/> 578 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/> 579 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/> 580 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/> 581 <w:LsdException Locked="false" Priority="51" 582 Name="Grid Table 6 Colorful Accent 6"/> 583 <w:LsdException Locked="false" Priority="52" 584 Name="Grid Table 7 Colorful 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mso-ascii-font-family:"Times New Roman"; 451 769 mso-fareast-font-family:"Times New Roman"; … … 464 782 mso-ansi-font-size:18.0pt; 465 783 mso-bidi-font-size:18.0pt; 466 font-family:"Times New Roman", "serif";784 font-family:"Times New Roman",serif; 467 785 mso-ascii-font-family:"Times New Roman"; 468 786 mso-fareast-font-family:"Times New Roman"; … … 480 798 mso-ansi-font-size:8.0pt; 481 799 mso-bidi-font-size:8.0pt; 482 font-family:"Tahoma", "sans-serif";800 font-family:"Tahoma",sans-serif; 483 801 mso-ascii-font-family:Tahoma; 484 802 mso-fareast-font-family:"Times New Roman"; … … 486 804 mso-hansi-font-family:Tahoma; 487 805 mso-bidi-font-family:Tahoma;} 488 span.SpellE489 {mso-style-name:"";490 mso-spl-e:yes;}491 span.GramE492 {mso-style-name:"";493 mso-gram-e:yes;}494 806 .MsoChpDefault 495 807 {mso-style-type:export-only; … … 917 1229 mso-pagination:widow-orphan; 918 1230 font-size:12.0pt; 919 font-family:"Times New Roman", "serif";1231 font-family:"Times New Roman",serif; 920 1232 mso-bidi-font-family:"Times New Roman"; 921 1233 mso-bidi-theme-font:minor-bidi;} … … 946 1258 947 1259 <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 1260 href="../../../GSASII/help/Starting%20GSAS.htm">start GSAS-II</a> and open the 1261 GSAS-II project file (I called it <b style='mso-bidi-font-weight:normal'><span 1262 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1263 mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b>) you saved from the 1264 third part of the <a 1265 href="../../../GSASII/help/Fit%20Peaks.htm#sucrose_peak_fit">peak 953 1266 fitting-indexing exercise</a>. If you didnt do that exercise, do it now.</p> 954 1267 … … 963 1276 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 964 1277 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";1278 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 966 1279 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b> 967 1280 in the GSAS-II data tree for the PWDR data set and expand the plot so that the … … 971 1284 symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area 972 1285 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> 1286 a reflection set of d<sub>min</sub> ~1Å resolution needed for charge flipping. 1287 Enter <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1288 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>23.55</span></b> 1289 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1290 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b> 979 1291 as the upper limit and make a note of the exact d-spacing (1.0125Å) using the 980 1292 mouse cursor on the plot.</p> … … 983 1295 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 984 1296 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";1297 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 986 1298 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument 987 1299 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;1300 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 989 1301 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";1302 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 991 1303 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset 992 1304 profile</span></b> to recover the default values. The peak fitting done earlier … … 1001 1313 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 1002 1314 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";1315 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1004 1316 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample 1005 1317 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:1318 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1007 1319 minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>. 1008 1320 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;1321 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1010 1322 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";1323 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1012 1324 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>.</p> 1013 1325 … … 1015 1327 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 1016 1328 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";1329 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1018 1330 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> 1019 1331 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:1332 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1021 1333 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:1334 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1023 1335 minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> 1024 1336 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;1337 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1026 1338 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 <span1029 class=SpellE>dmin</span></span></b>box.</p>1339 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1340 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b> 1341 box.</p> 1030 1342 1031 1343 <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;1344 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1033 1345 mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p> 1034 1346 … … 1060 1372 1061 1373 <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;1374 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1063 1375 mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except 1064 1376 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;1377 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1066 1378 mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a 1067 1379 dialog box will appear</p> … … 1076 1388 <p class=MsoNormal>Select either choice; the desired data set will be added to 1077 1389 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";1390 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1079 1391 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b> 1080 1392 button to see the full information</p> … … 1089 1401 <p class=MsoNormal>Ive stretched the window slightly to see the entire 1090 1402 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> 1403 histogram. Notice that it includes phase fraction, size & mustrain as well 1404 as preferred orientation, elastic strain and extinction corrections. The 1405 Babinet correction is intended for protein work where a significant region of 1406 the structure is disordered solvent. There are buttons for plotting size and 1407 mustrain surfaces</p> 1408 1409 <p class=MsoNormal>as well as preferred orientation correction curves.</p> 1100 1410 1101 1411 <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;1412 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1103 1413 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> 1414 empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span 1415 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1416 mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this 1417 makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight: 1418 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1419 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>. The table 1420 should list reflections 0-781. Select and check the refine column using the 1421 same technique you used for the peak list. </p> 1113 1422 1114 1423 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1125 1434 1126 1435 <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:1436 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1128 1437 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on 1129 1438 the main GSAS-II data tree window. Before it begins a backup of the project 1130 1439 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;1440 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1132 1441 mso-hansi-theme-font:minor-latin'>sucrose.bck0.gpx</span></b>. It can be used 1133 1442 to recover from a bad refinement. A progress dialog box will appear showing the … … 1136 1445 the refinement because it was off the end of the used part of the pattern. This 1137 1446 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";1447 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1139 1448 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley 1140 1449 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";1450 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1142 1451 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 <span1144 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 adjustedthe width and height).</p>1452 to make sure it has essentially minimized. My refinement completed with Rwp 1453 ~26.3%; a dialog box appears asking if you wish to load the result. Press <b 1454 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1455 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. 1456 To see the plot select the PWDR line in the GSAS-II data tree (Ive adjusted 1457 the width and height).</p> 1149 1458 1150 1459 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1158 1467 can be had by refining the lattice and profile parameters and perhaps the 1159 1468 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;1469 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1161 1470 mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> in the GSAS-II data 1162 1471 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;1472 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1164 1473 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";1474 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1166 1475 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument 1167 1476 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";1477 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1169 1478 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";1479 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1171 1480 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";1481 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1173 1482 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'> <span1176 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 <span1183 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 wellfor the lower part.</p>1483 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1484 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> X </span></b>&<b 1485 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1486 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Y</span></b>. 1487 The go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1488 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample 1489 Parameters</span></b> and check <b style='mso-bidi-font-weight:normal'><span 1490 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1491 mso-hansi-theme-font:minor-latin'>Sample X displ</span></b>.; make the <b 1492 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1493 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer 1494 radius</span></b> <b style='mso-bidi-font-weight:normal'><span 1495 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1496 mso-hansi-theme-font:minor-latin'>1000</span></b> if you didnt do this earlier. 1497 Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1498 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine 1499 </span></b>until converged; I obtained an improved residual of ~9.05% with a 1500 much better fit at the high angle part of the pattern but still not fit well 1501 for the lower part.</p> 1193 1502 1194 1503 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1202 1511 diffuse scattering feature at ~5deg and there are some peak shape issues (which 1203 1512 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><b1205 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1206 m so-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>,</span>1207 s et <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";1513 better before trying charge flipping. First select <b style='mso-bidi-font-weight: 1514 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1515 minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>, set <b 1516 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1208 1517 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peaks in 1209 1518 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;1519 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1211 1520 mso-hansi-theme-font:minor-latin'>1</span></b> from the pull down box; the 1212 1521 window changes to </p> … … 1221 1530 1222 1531 <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><b1225 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1226 m so-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";1532 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1533 mso-hansi-theme-font:minor-latin'>5.0</span></b> for <b style='mso-bidi-font-weight: 1534 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1535 minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b>, <b 1536 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1228 1537 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"; 1538 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1539 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b> 1540 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1233 1541 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";1542 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1235 1543 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> 1236 1544 (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 1545 Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1546 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. coeff.</span></b> 1547 pulldown to <b style='mso-bidi-font-weight:normal'><span style='font-family: 1548 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1549 minor-latin'>5</span></b> for the chebyschev part of the background. The window 1243 1550 should look like</p> 1244 1551 … … 1251 1558 1252 1559 <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;1560 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1254 1561 mso-hansi-theme-font:minor-latin'>Controls</span></b> item in the GSAS-II data 1255 1562 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:1563 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1257 1564 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;1565 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1259 1566 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:1567 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1261 1568 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> until 1262 1569 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 m so-hansi-theme-font:minor-latin'>Pawley update</span></b>, this replaces all1269 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";1570 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1571 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley 1572 reflections</span></b> tab and check the intensities. If there are many 1573 negatives amongst the highest angle reflections do <b style='mso-bidi-font-weight: 1574 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1575 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley update</span></b>, this 1576 replaces all the values with those in the extracted from the profile as listed 1577 in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1271 1578 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection 1272 1579 list</span></b> for the PWDR data set each multiplied by 0.5. Additionally 1273 1580 their refinement flags are turned off. Do <b style='mso-bidi-font-weight:normal'><span 1274 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1581 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1275 1582 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b><span 1276 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1583 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1277 1584 mso-hansi-theme-font:minor-latin'>; this will adjust all the reflections in the 1278 1585 vicinity of the reset ones</span>. You may repeat this process to suppress any 1279 1586 new negatives that may appear. Then set all the Pawley refinement flags back on 1280 1587 (excluding any that lead to a singular matrix) and repeat the refinement. After 1281 refinement, mine converged to ~5.7% with very few negatives and <span1282 class=SpellE>and</span> the plotlooked like</p>1588 refinement, mine converged to ~5.7% with very few negatives and and the plot 1589 looked like</p> 1283 1590 1284 1591 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1294 1601 1295 1602 <p class=MsoNormal>A few steps are needed to set up for a charge flipping run. 1296 Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1603 Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1297 1604 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> 1298 1605 and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1299 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1606 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1300 1607 minor-latin'>Charge flip controls</span></b> in the middle of the <b 1301 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1608 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1302 1609 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> 1303 1610 tab.</p> … … 1307 1614 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 1308 1615 </span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span 1309 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1616 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1310 1617 mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b 1311 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1618 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1312 1619 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR 1313 1620 11bmb_8716.fxye Bank 1</span></b> (the only choice!). This makes the reflection 1314 1621 set to be used those in <b style='mso-bidi-font-weight:normal'><span 1315 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1622 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1316 1623 mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR 1317 1624 data set; these should match the <b style='mso-bidi-font-weight:normal'><span 1318 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1625 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1319 1626 mso-hansi-theme-font:minor-latin'>Pawley reflection</span></b> set.</p> 1320 1627 … … 1323 1630 "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 1324 1631 </span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span 1325 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1632 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1326 1633 mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b 1327 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1634 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1328 1635 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map 1329 1636 controls</span></b>) to <b style='mso-bidi-font-weight:normal'><span 1330 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1637 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1331 1638 mso-hansi-theme-font:minor-latin'>20%</span></b>. This controls the map search 1332 1639 routine.</p> 1333 1640 1334 1641 <p class=MsoNormal>For powder data it is not usually advisable to select a <b 1335 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1642 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1336 1643 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing 1337 1644 element</span></b>; if selected a periodic table appears select an element or 1338 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1645 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1339 1646 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None</span></b>. 1340 The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1647 The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1341 1648 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b> 1342 1649 defines the map spacing and thus the extent of the reflection set; the observed 1343 1650 reflection set is zero filled to this limit for charge flipping. The <b 1344 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1651 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1345 1652 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b> 1346 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1653 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1347 1654 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b> 1348 determine the lower threshold and upper limit for charge flipping, 1349 respectively. The latter is used to avoid Uranium solutions in the result. 1350 Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family: 1351 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1352 minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom 1353 ones. For sucrose set it to <b style='mso-bidi-font-weight:normal'><span 1354 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1355 mso-hansi-theme-font:minor-latin'>12.</span></b> When ready select <b 1356 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1655 determine the lower threshold and upper limit for charge flipping, respectively. 1656 The latter is used to avoid Uranium solutions in the result. Set this to <b 1657 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1658 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>10-12</span></b> 1659 for equal atom problems and larger for heavy atom ones. For sucrose set it 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'>12.</span></b> 1662 When ready 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'>Compute/Charge flipping</span></b>; a 1665 progress bar dialog will appear that tracks the residual found in each charge 1666 flipping cycle. It will quickly drop to some level (42-44%) and then for a 1667 successful charge flipping run perhaps drop again into the 20-25% range after a 1668 considerable length of time. You should save the project if you get an 1669 apparently good solution. Many times it will not drop below ~40%; just try <b 1670 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1357 1671 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge 1358 flipping</span></b>; a progress bar dialog will appear that tracks the residual 1359 found in each charge flipping cycle. It will quickly drop to some level 1360 (42-44%) and then for a successful charge flipping run perhaps drop again into 1361 the 20-25% range after a considerable length of time. You should save the 1362 project if you get an apparently good solution. Many times it will not drop 1363 below ~40%; just try <b style='mso-bidi-font-weight:normal'><span 1364 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1365 mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b> again. If 1366 several tries fail to yield a solution, go back to the last step of the Pawley 1367 refinement and just repeat it (that is do <b style='mso-bidi-font-weight:normal'><span 1368 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1369 mso-hansi-theme-font:minor-latin'>Pawley update</span></b> and <b 1370 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1371 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>). 1372 This will generate a different set of intensities for the highly overlapped 1373 part of the powder pattern; perhaps they will give a successful charge flip 1374 solution. Unless otherwise interrupted, GSAS-II will try 10000 times for a 1375 charge flip solution (for sucrose this takes 5-10min on my laptop). Press <b 1376 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1377 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> 1378 to stop the charge flipping; a peak list and a drawing of the solution will 1379 appear. One of my runs gave</p> 1672 flipping</span></b> again. If several tries fail to yield a solution, go back 1673 to the last step of the Pawley refinement and just repeat it (that is do <b 1674 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1675 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley 1676 update</span></b> and <b style='mso-bidi-font-weight:normal'><span 1677 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1678 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>). This will 1679 generate a different set of intensities for the highly overlapped part of the 1680 powder pattern; perhaps they will give a successful charge flip solution. 1681 Unless otherwise interrupted, GSAS-II will try 10000 times for a charge flip solution 1682 (for sucrose this takes 5-10min on my laptop). Press <b style='mso-bidi-font-weight: 1683 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1684 minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the 1685 charge flipping; a peak list and a drawing of the solution will appear. One of 1686 my runs gave</p> 1380 1687 1381 1688 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1489 1796 position:absolute;z-index:251662336;margin-left:315px;margin-top:308px; 1490 1797 width:16px;height:35px'><img width=16 height=35 1491 src="Charge%20Flipping%20-%20sucrose_files/image0 52.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span1798 src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span 1492 1799 style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32" 1493 1800 o:spid="_x0000_i1054" type="#_x0000_t75" style='width:502.5pt;height:431.25pt; … … 1496 1803 croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/> 1497 1804 </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=575 1498 src="Charge%20Flipping%20-%20sucrose_files/image0 53.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>1805 src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p> 1499 1806 1500 1807 <p class=MsoNormal>The result looks very promising! Charge flipping operates … … 1503 1810 flipping also will give a solution without regard to handedness; this solution 1504 1811 may be either the correct one for sucrose or its inverse.) Errors in these 1505 phases can disrupt this process so that the map and peak positions are offset 1506 from their true positions. To discover this and fix it, rotate the drawing 1507 around to check that atom positions are related via the 2<sub>1</sub> screw 1508 axis (through the multicolored cross in the center of the cell and parallel to 1509 the y-axis the green cell edge). Avoid motions with the right mouse button1510 pressed, this moves the cross. To recover, press the <b style='mso-bidi-font-weight: 1511 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1512 m inor-latin;mso-hansi-theme-font:minor-latin'>C</span></b> key to resetthe1513 c ross to the cell center. Ive placed the symbol for a 2<sub>1</sub> axis on my1514 drawing above to show where I think it should be. If you find an offset to the 1515 map,orient it so the offset is horizontal or vertical and then press the <b1516 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1812 phases can disrupt this process so that the map and peak positions are offset from 1813 their true positions. To discover this and fix it, rotate the drawing around to 1814 check that atom positions are related via the 2<sub>1</sub> screw axis (through 1815 the multicolored cross in the center of the cell and parallel to the y-axis 1816 the green cell edge). Avoid motions with the right mouse button pressed, this 1817 moves the cross. To recover, press the <b style='mso-bidi-font-weight:normal'><span 1818 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1819 mso-hansi-theme-font:minor-latin'>C</span></b> key to reset the cross to the 1820 cell center. Ive placed the symbol for a 2<sub>1</sub> axis on my drawing 1821 above to show where I think it should be. If you find an offset to the map, 1822 orient it so the offset is horizontal or vertical and then press the <b 1823 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1517 1824 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>, 1518 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1825 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1519 1826 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>, 1520 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1827 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1521 1828 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> 1522 or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1829 or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1523 1830 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b> 1524 1831 keys to shift the map and peaks as needed. The shift is in resolution units … … 1536 1843 croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/> 1537 1844 </v:shape><![endif]--><![if !vml]><img border=0 width=667 height=566 1538 src="Charge%20Flipping%20-%20sucrose_files/image0 54.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>1845 src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p> 1539 1846 1540 1847 <h2>Step 4: Obtain solution from charge flip result</h2> … … 1543 1850 the map and make atoms out of them. The map peak list is initially sorted by 1544 1851 peak magnitude; you can change the sorting to be along any of the column 1545 headings in the table by a single click on the desired heading. The <span 1546 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1547 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1548 minor-latin'>dzero</span></b></span> column gives the distance of each peak from 1549 the origin. The menu items under Map peaks give you several tools to aid in the 1550 peak selection process; we will just use a couple in this example. I have 1551 chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:normal'><span 1552 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1553 mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and then finding 1554 the unique ones. </p> 1852 headings in the table by a single click on the desired heading. The <b 1853 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1854 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b> 1855 column gives the distance of each peak from the origin. The menu items under 1856 Map peaks give you several tools to aid in the peak selection process; we will 1857 just use a couple in this example. I have chosen to proceed by sorting the 1858 atoms by <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1859 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>, 1860 selecting all and then finding the unique ones. </p> 1555 1861 1556 1862 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 1558 1864 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 1559 1865 </span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight: 1560 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1866 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1561 1867 minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> column heading. This 1562 1868 will sort the peaks in increasing z-axis coordinate.</p> … … 1572 1878 "Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 1573 1879 </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span 1574 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1575 mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That should 1576 select (grey) 23 out of 46 peak positions in the table and all should be near 1577 the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub> 1578 that would be all the C & O atoms! They will be colored green in the plot. 1579 If more are selected then check the map offset it may need a slight 1580 correction.</p> 1880 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1881 mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That 1882 should select (grey) 23 out of 46 peak positions in the table and all should be 1883 near the top of the list. Given the formula for sucrose is C<sub>12</sub>H<sub>22</sub>O<sub>11</sub> 1884 that would be all the C & O atoms! They will be colored green in the plot. If 1885 more are selected then check the map offset it may need a slight correction.</p> 1581 1886 1582 1887 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1595 1900 croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/> 1596 1901 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=572 1597 src="Charge%20Flipping%20-%20sucrose_files/image0 55.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>1902 src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p> 1598 1903 1599 1904 <p class=MsoNormal>Notice that in my case one atom is in a neighboring 1600 1905 molecule, one can deselect it and then pick the desired equivalent. Hold the <b 1601 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1906 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1602 1907 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift</span></b> 1603 1908 key down and use the right mouse button to pick/unpick atoms in the drawing. … … 1607 1912 1608 1913 <p class=MsoNormal>These are now ready to turn into atoms. Do <b 1609 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1914 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1610 1915 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map 1611 1916 peaks/Move peaks</span></b>. The drawing will show white balls for each of the 1612 1917 selected positions and the <b style='mso-bidi-font-weight:normal'><span 1613 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1918 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1614 1919 mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 23 new H 1615 1920 atoms. </p> … … 1621 1926 croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/> 1622 1927 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=578 1623 src="Charge%20Flipping%20-%20sucrose_files/image0 56.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>1928 src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p> 1624 1929 1625 1930 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1632 1937 <p class=MsoNormal>The atom names indicate the peak magnitude to aid 1633 1938 identification (M100 for the largest in the <b style='mso-bidi-font-weight: 1634 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1939 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1635 1940 minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which 1636 1941 may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span 1637 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1942 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1638 1943 mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort 1639 1944 them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span 1640 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1945 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1641 1946 mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight: 1642 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1947 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1643 1948 minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down 1644 1949 and then selecting a position in the table with the <b style='mso-bidi-font-weight: 1645 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1950 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1646 1951 minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On 1647 1952 Linux machines the <b style='mso-bidi-font-weight:normal'><span 1648 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1953 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1649 1954 mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by 1650 1955 the operating system; use <b style='mso-bidi-font-weight:normal'><span 1651 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1652 mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms. After1653 sorting by magnitude, my list is now </p>1956 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1957 mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms. 1958 After sorting by magnitude, my list is now </p> 1654 1959 1655 1960 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1665 1970 of ambiguity in the middle, but just assign the top 11 as O and the rest as C 1666 1971 and see what happens. You can do this by selecting a block of atoms, go to <b 1667 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1972 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1668 1973 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify 1669 1974 atom parameters</span></b> and select <b style='mso-bidi-font-weight:normal'><span 1670 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1671 mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a 1672 periodic table will appear. Select the desired element and they will be changed 1673 in thelist and drawing.</p>1975 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1976 mso-hansi-theme-font:minor-latin'>Type</span></b> from the dialog box; a periodic 1977 table will appear. Select the desired element and they will be changed in the 1978 list and drawing.</p> 1674 1979 1675 1980 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1679 1984 croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/> 1680 1985 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=541 1681 src="Charge%20Flipping%20-%20sucrose_files/image0 57.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>1682 1683 <p class=MsoNormal>The original charge flipping solution is still visible and 1684 the atoms are now identified, Ive changed the drawing to show balls and sticks 1685 and labeled the atoms with their names, this is done in the <b 1686 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1687 m so-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw atoms</span></b>1688 tab. Double click the appropriate column heading and make the selection from 1689 the dialogbox.<span style='mso-spacerun:yes'> </span></p>1986 src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p> 1987 1988 <p class=MsoNormal>The original charge flipping solution is still visible and the 1989 atoms are now identified, Ive changed the drawing to show balls and sticks and 1990 labeled the atoms with their names, this is done in the <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'>Draw atoms</span></b> tab. Double 1993 click the appropriate column heading and make the selection from the dialog 1994 box.<span style='mso-spacerun:yes'> </span></p> 1690 1995 1691 1996 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1697 2002 1698 2003 <p class=MsoNormal>Now one can safely remove the map peaks (do <b 1699 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2004 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1700 2005 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map 1701 2006 peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span 1702 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2007 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1703 2008 mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the 1704 charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span 1705 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1706 mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight: 1707 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1708 minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b 1709 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2009 charge flip map (do <b style='mso-bidi-font-weight:normal'><span 2010 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2011 mso-hansi-theme-font:minor-latin'>Clear map</span></b> in the <b 2012 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1710 2013 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> 1711 2014 tab). The atom positions I obtained have two atoms (O3 & O4) not connected … … 1717 2020 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 1718 2021 </span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span 1719 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2022 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1720 2023 mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> tab and select them 1721 (hold the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2024 (hold the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1722 2025 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ctrl</span></b> 1723 2026 key down and select the appropriate rows). </p> … … 1727 2030 "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 1728 2031 </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span 1729 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2032 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1730 2033 mso-hansi-theme-font:minor-latin'>Edit/Fill unit cell</span></b>; new atoms 1731 2034 will appear at end of list and in the drawing. </p> … … 1735 2038 "Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 1736 2039 </span></span></span><![endif]>Select all the atoms in the <b style='mso-bidi-font-weight: 1737 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2040 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1738 2041 minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table by a 1739 2042 double click on upper left corner box of the table.</p> … … 1743 2046 "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 1744 2047 </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span 1745 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2048 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1746 2049 mso-hansi-theme-font:minor-latin'>Edit/Fill CN-sphere</span></b>; new atoms 1747 2050 will appear that are bonded to the molecule.</p> … … 1752 2055 </span></span></span><![endif]>Select these new atoms that are in the molecule; 1753 2056 they will probably be outside the unit cell box. Do this on the drawing with <b 1754 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2057 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1755 2058 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Shift left</span></b> 1756 2059 for the first one & <b style='mso-bidi-font-weight:normal'><span 1757 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2060 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1758 2061 mso-hansi-theme-font:minor-latin'>Shift right</span></b> for the rest, they 1759 2062 will show in green. </p> … … 1763 2066 "Times New Roman"'><span style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'> 1764 2067 </span></span></span><![endif]>Look at the <b style='mso-bidi-font-weight:normal'><span 1765 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2068 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1766 2069 mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the 1767 selections and make note of the <span class=SpellE><b style='mso-bidi-font-weight: 1768 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1769 minor-latin;mso-hansi-theme-font:minor-latin'>Sym</span></b></span><b 1770 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1771 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Op</span></b> 1772 for each one. In my case they were <b style='mso-bidi-font-weight:normal'><span 1773 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1774 mso-hansi-theme-font:minor-latin'>2+1<span class=GramE>,0,0</span></span></b> 1775 for O(4) and <b style='mso-bidi-font-weight:normal'><span style='font-family: 1776 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1777 minor-latin'>2+2,-1,1</span></b> for O(3). The first number is the symmetry 1778 operator number and the 3 numbers after the <b style='mso-bidi-font-weight: 1779 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1780 minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b> are unit cell 1781 translations.</p> 2070 selections and make note of the <b style='mso-bidi-font-weight:normal'><span 2071 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2072 mso-hansi-theme-font:minor-latin'>Sym Op</span></b> for each one. In my case 2073 they were <b style='mso-bidi-font-weight:normal'><span style='font-family: 2074 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2075 minor-latin'>2+1,0,0</span></b> for O(4) and <b style='mso-bidi-font-weight: 2076 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2077 minor-latin;mso-hansi-theme-font:minor-latin'>2+2,-1,1</span></b> for O(3). 2078 The first number is the symmetry operator number and the 3 numbers after the <b 2079 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2080 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b> 2081 are unit cell translations.</p> 1782 2082 1783 2083 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 1785 2085 "Times New Roman"'><span style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'> 1786 2086 </span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span 1787 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2087 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1788 2088 mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab.</p> 1789 2089 … … 1792 2092 "Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'> 1793 2093 </span></span></span><![endif]>Select an atom in turn that needs to be moved, 1794 e.g. in my case <span class=GramE>O(</span>3) or O(4). </p>2094 e.g. in my case O(3) or O(4). </p> 1795 2095 1796 2096 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 1798 2098 "Times New Roman"'><span style='mso-list:Ignore'>9.<span style='font:7.0pt "Times New Roman"'> 1799 2099 </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span 1800 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1801 mso-hansi-theme-font:minor-latin'>Edit/Transform <span class=GramE>atoms<span 1802 style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b> 1803 select the operator and unit cell translations, then press <b style='mso-bidi-font-weight: 1804 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 2100 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2101 mso-hansi-theme-font:minor-latin'>Edit/Transform atoms</span></b>, select the 2102 operator and unit cell translations, then press <b style='mso-bidi-font-weight: 2103 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1805 2104 minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom 1806 2105 coordinates will be transformed.</p> … … 1813 2112 1814 2113 <p class=MsoNormal style='margin-left:.5in'>This will complete the molecule 1815 with the extra atoms. <span class=GramE>Do</span> <b style='mso-bidi-font-weight: 1816 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1817 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b> 1818 to see the completed molecule. Ive made it a balls & sticks with names as 1819 labels.</p> 2114 with the extra atoms. Do <b style='mso-bidi-font-weight:normal'><span 2115 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2116 mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b> to see the 2117 completed molecule. Ive made it a balls & sticks with names as labels.</p> 1820 2118 1821 2119 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1825 2123 cropbottom="28348f" cropleft="41090f" cropright="9483f"/> 1826 2124 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=576 1827 src="Charge%20Flipping%20-%20sucrose_files/image0 58.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>2125 src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p> 1828 2126 1829 2127 <p class=MsoNormal>Save the project file; the next step is to complete the 1830 structure by finding H-atoms and then do the final <span class=SpellE>Rietveld</span> 1831 refinements.</p> 2128 structure by finding H-atoms and then do the final Rietveld refinements.</p> 1832 2129 1833 2130 <h2>Step 5: Complete the structure</h2> 1834 2131 1835 2132 <p class=MsoNormal>To complete the structure you will need to perform a 1836 preliminary <span class=SpellE>Rietveld</span> refinement. This will make the 1837 atom positions more accurate and prepare a set of calculated structure factors 1838 needed to generate a difference Fourier map good enough to maybe reveal the H 1839 atoms. There are a number of steps needed to set all the controls from the 1840 previous Pawley refinement to get a successful start for the <span 1841 class=SpellE>Rietveld</span> refinement.</p> 2133 preliminary Rietveld refinement. This will make the atom positions more 2134 accurate and prepare a set of calculated structure factors needed to generate a 2135 difference Fourier map good enough to maybe reveal the H atoms. There are a 2136 number of steps needed to set all the controls from the previous Pawley 2137 refinement to get a successful start for the Rietveld refinement.</p> 1842 2138 1843 2139 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 1845 2141 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 1846 2142 </span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span 1847 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2143 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1848 2144 mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the 1849 2145 GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span 1850 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2146 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1851 2147 mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You dont want to 1852 2148 start with these when the scale factor is unknown.</p> … … 1856 2152 "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 1857 2153 </span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span 1858 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2154 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1859 2155 mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b 1860 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2156 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1861 2157 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram 1862 2158 scale factor</span></b> box. This is the scale factor for the data set. Uncheck 1863 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1864 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span1865 class=SpellE>displ</span></span></b>.</p>2159 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2160 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X 2161 displ</span></b>.</p> 1866 2162 1867 2163 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 1869 2165 "Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 1870 2166 </span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span 1871 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2167 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1872 2168 mso-hansi-theme-font:minor-latin'>Phases/sucrose General</span></b> tab and 1873 uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2169 uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1874 2170 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit 1875 2171 cell</span></b> and <b style='mso-bidi-font-weight:normal'><span 1876 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2172 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1877 2173 mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The 1878 2174 latter is most important; if you forget you will just get another Pawley … … 1880 2176 1881 2177 <p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span 1882 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2178 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1883 2179 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main 1884 GSAS-II data tree menu; only scale and background are refined. I got <span1885 class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear 1886 intensity differences; the atom positions obviouslyneed refinement.</p>2180 GSAS-II data tree menu; only scale and background are refined. I got a Rwp 2181 ~20%. The plot shows clear intensity differences; the atom positions obviously 2182 need refinement.</p> 1887 2183 1888 2184 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1897 2193 1898 2194 <p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span 1899 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2195 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1900 2196 mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and select the <b 1901 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2197 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1902 2198 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> 1903 2199 tab. Note the warning at the bottom of the window; the origin in space group P2<sub>1</sub> 1904 2200 has an arbitrary location along the y-axis. Then double click the <b 1905 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2201 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1906 2202 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> 1907 2203 column heading, a dialog box will appear, select the <b style='mso-bidi-font-weight: 1908 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2204 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1909 2205 minor-latin;mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and 1910 press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2206 press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1911 2207 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. 1912 2208 The atoms table will show the refinement controls</p> … … 1921 2217 <p class=MsoNormal>To deal with the warning we need to set a Hold on one atom 1922 2218 y-coordinate. Select <b style='mso-bidi-font-weight:normal'><span 1923 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2219 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1924 2220 mso-hansi-theme-font:minor-latin'>Constraints</span></b> in the main GSAS-II 1925 2221 data tree.</p> … … 1933 2229 1934 2230 <p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span 1935 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2231 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1936 2232 mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select <b 1937 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1938 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0: <span1939 class=GramE>:dAy:0</span> for O(1)</span></b> from the dialog box. This will 1940 fix the shift along y for the <span class=GramE>O(</span>1) atom.</p>2233 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2234 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0::dAy:0 for 2235 O(1)</span></b> from the dialog box. This will fix the shift along y for the 2236 O(1) atom.</p> 1941 2237 1942 2238 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1948 2244 1949 2245 <p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span 1950 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2246 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1951 2247 mso-hansi-theme-font:minor-latin'>OK</span></b>; the Constraints window will 1952 2248 show the hold</p> … … 1960 2256 1961 2257 <p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span 1962 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1963 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span 1964 class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice 1965 parameters (in the <b style='mso-bidi-font-weight:normal'><span 1966 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1967 mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b 1968 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2258 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2259 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my Rwp is 2260 now ~10.3%. You can now safely refine lattice parameters (in the <b 2261 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2262 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> 2263 tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1969 2264 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>), 1970 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2265 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1971 2266 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument 1972 2267 parameters</span></b> <b style='mso-bidi-font-weight:normal'><span 1973 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2268 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1974 2269 mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight: 1975 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2270 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1976 2271 minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b 1977 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2272 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1978 2273 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>, 1979 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2274 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1980 2275 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b> 1981 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2276 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1982 2277 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> 1983 and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1984 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span 1985 class=SpellE>displ</span></span></b>. You can also include refinement of atom 1986 thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My 1987 refinement improved slightly to Rwp~10.0%. Lets see if a difference Fourier 1988 map will show anything.<br> 1989 Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2278 and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2279 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X 2280 displ</span></b>. You can also include refinement of atom thermal motion (U<sub>iso</sub>) 2281 parameters. My refinement improved slightly to Rwp~10.0%. Lets see if a 2282 difference Fourier map will show anything.<br> 2283 Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1990 2284 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose 1991 2285 General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span 1992 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1993 mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway 1994 downthe window.</p>2286 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2287 mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway down 2288 the window.</p> 1995 2289 1996 2290 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; 1997 2291 mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family: 1998 2292 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 1999 </span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight: 2000 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 2001 minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b 2002 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2003 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b> 2004 for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2293 </span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span 2294 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2295 mso-hansi-theme-font:minor-latin'>delt-F</span></b> for the <b 2296 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2005 2297 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p> 2006 2298 … … 2009 2301 "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 2010 2302 </span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span 2011 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2303 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2012 2304 mso-hansi-theme-font:minor-latin'>PWDR 11bmb_8716.fxye Bank 1</span></b> for 2013 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2305 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2014 2306 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection 2015 2307 set from</span></b> item (the only choice). The Fourier calculation will use 2016 2308 the structure factors shown in the <b style='mso-bidi-font-weight:normal'><span 2017 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2309 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2018 2310 mso-hansi-theme-font:minor-latin'>Reflection list</span></b> item for this PWDR 2019 2311 data set.</p> … … 2023 2315 "Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 2024 2316 </span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span 2025 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2317 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2026 2318 mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b 2027 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2319 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2028 2320 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> 2029 2321 tab window. The map will be computed via fast Fourier techniques and is very … … 2036 2328 "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 2037 2329 </span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span 2038 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2330 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2039 2331 mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b 2040 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2332 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2041 2333 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour 2042 2334 level</span></b> slider until something appears on the map. You can also reduce 2043 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2335 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2044 2336 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map radius</span></b> 2045 2337 to help clarify the view.</p> … … 2051 2343 croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/> 2052 2344 </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=581 2053 src="Charge%20Flipping%20-%20sucrose_files/image0 59.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>2054 2055 <p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots2056 whose size are proportional to the electron density. There are peaks that might 2057 be H-atom positions as well as features that suggest C & O-atoms out of 2058 position. Recall that the refinement was just done without any H-atoms; it will 2059 make the best fit compensating for the missing H-atoms by displacing the C 2060 & O atomsin the direction of the missing H-atoms. </p>2345 src="Charge%20Flipping%20-%20sucrose_files/image034.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p> 2346 2347 <p class=MsoNormal>What is drawn here are green dots whose size are 2348 proportional to the electron density. There are peaks that might be H-atom 2349 positions as well as features that suggest C & O-atoms out of position. 2350 Recall that the refinement was just done without any H-atoms; it will make the 2351 best fit compensating for the missing H-atoms by displacing the C & O atoms 2352 in the direction of the missing H-atoms. </p> 2061 2353 2062 2354 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 2064 2356 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 2065 2357 </span></span></span><![endif]>Go to the <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'>Phases/ <span class=GramE>sucrose<span2068 style='mso-spacerun:yes'> </span>Draw </span>Atoms</span></b> tab.</p>2358 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2359 mso-hansi-theme-font:minor-latin'>Phases/sucrose<span 2360 style='mso-spacerun:yes'> </span>Draw Atoms</span></b> tab.</p> 2069 2361 2070 2362 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 2073 2365 </span></span></span><![endif]>Select a C or O atom with possible H-atom 2074 2366 density nearby. It will appear green. Do <b style='mso-bidi-font-weight:normal'><span 2075 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2367 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2076 2368 mso-hansi-theme-font:minor-latin'>Edit/View point</span></b>; this will 2077 2369 position the cross on the selected atom.</p> … … 2084 2376 with the left mouse button and shift the cross with the right mouse button. You 2085 2377 can zoom in using the roll wheel on the mouse (or else use the <b 2086 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2378 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2087 2379 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Camera 2088 2380 distance</span></b> slider in the <b style='mso-bidi-font-weight:normal'><span 2089 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2381 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2090 2382 mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab if your mouse 2091 2383 lacks a wheel).</p> … … 2097 2389 croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/> 2098 2390 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=581 2099 src="Charge%20Flipping%20-%20sucrose_files/image0 60.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>2391 src="Charge%20Flipping%20-%20sucrose_files/image036.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p> 2100 2392 2101 2393 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 2103 2395 "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 2104 2396 </span></span></span><![endif]>Go to the Atoms tab and do <b style='mso-bidi-font-weight: 2105 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2397 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2106 2398 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>, 2107 2399 a white ball will appear at the selected position and an H-atom (name = <b 2108 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2400 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2109 2401 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>) 2110 2402 will be appended to the end of the atom list. Repeat steps 1-4 for as many … … 2119 2411 croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/> 2120 2412 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=570 2121 src="Charge%20Flipping%20-%20sucrose_files/image0 61.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>2413 src="Charge%20Flipping%20-%20sucrose_files/image038.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p> 2122 2414 2123 2415 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 2125 2417 "Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> 2126 2418 </span></span></span><![endif]>Change their <b style='mso-bidi-font-weight: 2127 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2419 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2128 2420 minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> to <b 2129 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2421 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2130 2422 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b>, 2131 2423 they will be renamed and make then all ball & stick. Do a <b 2132 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2424 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2133 2425 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; 2134 there should be a drop in <span class=SpellE>Rwp</span>. Then repeat the <b 2135 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2136 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier 2137 map</span></b> in the <b style='mso-bidi-font-weight:normal'><span 2138 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2139 mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust the <b 2140 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2141 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour 2142 level</span></b> and <b style='mso-bidi-font-weight:normal'><span 2143 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2144 mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for 2145 the remaining H-atoms; you may have to guess positions for some of them using 2146 known stereochemistry rules. My model looked like</p> 2426 there should be a drop in Rwp. Then repeat the <b style='mso-bidi-font-weight: 2427 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2428 minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> in 2429 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2430 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> 2431 tab, adjust the <b style='mso-bidi-font-weight:normal'><span style='font-family: 2432 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2433 minor-latin'>Contour level</span></b> and <b style='mso-bidi-font-weight:normal'><span 2434 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2435 mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for the 2436 remaining H-atoms; you may have to guess positions for some of them using known 2437 stereochemistry rules. My model looked like</p> 2147 2438 2148 2439 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 2152 2443 croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/> 2153 2444 </v:shape><![endif]--><![if !vml]><img border=0 width=670 height=562 2154 src="Charge%20Flipping%20-%20sucrose_files/image0 62.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>2445 src="Charge%20Flipping%20-%20sucrose_files/image040.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p> 2155 2446 2156 2447 <p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span 2157 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2448 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2158 2449 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> to finish this 2159 stage in the structure analysis. My <span class=SpellE>Rwp</span> was ~8.02%2160 with all the H-atomsincluded (but not refined). The fit looks pretty good</p>2450 stage in the structure analysis. My Rwp was ~8.02% with all the H-atoms 2451 included (but not refined). The fit looks pretty good</p> 2161 2452 2162 2453 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 2171 2462 <p class=MsoNormal>Looking at the fit, there may be room for improvement and 2172 2463 wed like to refine the H-atom positions. First we need to change the profile 2173 model to include crystallite size and <span class=SpellE>mustrain</span>2174 broadening. Go to <b style='mso-bidi-font-weight:normal'><span 2175 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2176 mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>, set <b 2177 style=' mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";2178 mso- ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>2179 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2180 m so-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>2181 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";2464 model to include crystallite size and mustrain broadening. Go to <b 2465 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2466 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument 2467 Parameters</span></b>, set <b style='mso-bidi-font-weight:normal'><span 2468 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2469 mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight: 2470 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2471 minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> to <b 2472 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2182 2473 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>zero</span></b> 2183 2474 and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family: 2184 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:2475 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2185 2476 minor-latin'>Refine</span></b> flags for them.</p> 2186 2477 2187 2478 <p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span 2188 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2479 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2189 2480 mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> and look at the <b 2190 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2481 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2191 2482 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b> 2192 2483 tab; make sure the <b style='mso-bidi-font-weight:normal'><span 2193 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2484 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2194 2485 mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the 2195 boxes for both <span class=SpellE><b style='mso-bidi-font-weight:normal'><span 2196 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2197 mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b style='mso-bidi-font-weight: 2198 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 2199 minor-latin;mso-hansi-theme-font:minor-latin'>. <span class=GramE>size</span></span></b> 2200 and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span 2201 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2202 mso-hansi-theme-font:minor-latin'>microstrain</span></b></span>.</p> 2486 boxes for both <b style='mso-bidi-font-weight:normal'><span style='font-family: 2487 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2488 minor-latin'>Cryst. size</span></b> and <b style='mso-bidi-font-weight:normal'><span 2489 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2490 mso-hansi-theme-font:minor-latin'>microstrain</span></b>.</p> 2203 2491 2204 2492 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 2210 2498 2211 2499 <p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span 2212 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2213 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span2214 class=SpellE>Rwp</span> will start out high but should converge to where it was 2215 before this change. I got 8.08% and the <b style='mso-bidi-font-weight:normal'><span 2216 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2217 m so-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>2500 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2501 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the Rwp will 2502 start out high but should converge to where it was before this change. I got 2503 8.08% and the <b style='mso-bidi-font-weight:normal'><span style='font-family: 2504 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2505 minor-latin'>Data tab</span></b> looked like</p> 2218 2506 2219 2507 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 2225 2513 2226 2514 <p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span 2227 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2228 mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span 2229 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 2230 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2231 minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span 2232 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2233 mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens 2234 phenomenological model for <span class=SpellE>microstrain</span> which has 9 2235 terms for monoclinic structures. Check all the boxes for it.</p> 2515 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2516 mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <b 2517 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2518 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Mustrain 2519 model</span></b>; this is the Stephens phenomenological model for microstrain 2520 which has 9 terms for monoclinic structures. Check all the boxes for it.</p> 2236 2521 2237 2522 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 2243 2528 2244 2529 <p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span 2245 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2246 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span 2247 class=SpellE>Rwp</span> will start out high but should converge lower than 2248 where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight: 2249 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 2250 minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like. 2251 If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span 2252 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2253 mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b 2254 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2255 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot 2256 type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span> 2257 surface plot for ground sucrose.</p> 2530 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2531 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the Rwp will 2532 start out high but should converge lower than where it was before this change. 2533 I got 7.65% and the <b style='mso-bidi-font-weight:normal'><span 2534 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2535 mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like. If you check 2536 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2537 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Mustrain</span></b> 2538 button in the <b style='mso-bidi-font-weight:normal'><span style='font-family: 2539 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2540 minor-latin'>Select plot type</span></b> box, you will see the interesting 2541 mustrain surface plot for ground sucrose.</p> 2258 2542 2259 2543 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 2265 2549 2266 2550 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span 2267 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2551 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2268 2552 mso-hansi-theme-font:minor-latin;mso-no-proof:yes'><!--[if gte vml 1]><v:shape 2269 2553 id="Picture_x0020_47" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt; … … 2275 2559 <p class=MsoNormal>Before refining H-atom positions it would be wise to create 2276 2560 restraints on their bond distances and angles. Locate <b style='mso-bidi-font-weight: 2277 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2561 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2278 2562 minor-latin;mso-hansi-theme-font:minor-latin'>Restraints</span></b> in the main 2279 2563 GSAS-II data tree; there will be an almost blank window telling you there are 2280 2564 no bond restraints for sucrose. Do <b style='mso-bidi-font-weight:normal'><span 2281 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2282 mso-hansi-theme-font:minor-latin'>Edit/Add <span class=GramE>restraints<span 2283 style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b> 2284 a dialog box will appear asking for the origin atom for the bond. </p> 2565 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2566 mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box 2567 will appear asking for the origin atom for the bond. </p> 2285 2568 2286 2569 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 2292 2575 2293 2576 <p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span 2294 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2577 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2295 2578 mso-hansi-theme-font:minor-latin'>all H</span></b> and press <b 2296 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2579 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2297 2580 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. 2298 2581 A new dialog box will appear asking for the target atoms for the bonds.</p> … … 2306 2589 2307 2590 <p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span 2308 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2591 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2309 2592 mso-hansi-theme-font:minor-latin'>all C</span></b> and <b style='mso-bidi-font-weight: 2310 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2593 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2311 2594 minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b> and a third 2312 2595 dialog box appears asking for the bond length</p> … … 2321 2604 2322 2605 <p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span 2323 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2606 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2324 2607 mso-hansi-theme-font:minor-latin'>1.09</span></b> and press <b 2325 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2608 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2326 2609 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. 2327 2610 I got a short list of 8 H-C and H-O restraints, but I expect 22 of them. Change 2328 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2611 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2329 2612 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Search range</span></b> 2330 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2613 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2331 2614 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.5</span></b> 2332 2615 and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family: 2333 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:2616 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2334 2617 minor-latin'>Edit/Add restraints</span></b>. There are now 22 restraints on H-C 2335 2618 and H-O bond lengths.</p> … … 2343 2626 2344 2627 <p class=MsoNormal>Next select the <b style='mso-bidi-font-weight:normal'><span 2345 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2628 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2346 2629 mso-hansi-theme-font:minor-latin'>Angle restraints</span></b> tab and again 2347 2630 there arent any. Do <b style='mso-bidi-font-weight:normal'><span 2348 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2631 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2349 2632 mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box 2350 2633 will appear asking for the A atom in the angle A-B-C. Select <b 2351 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2634 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2352 2635 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all H</span></b>. 2353 2636 The next dialog asks for the B atom in the A-B-C angle, select <b 2354 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2637 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2355 2638 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all C</span></b> 2356 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2639 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2357 2640 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>all O</span></b>. 2358 2641 The third dialog asks for the angle and has a default of <b style='mso-bidi-font-weight: 2359 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2642 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2360 2643 minor-latin;mso-hansi-theme-font:minor-latin'>109.54</span></b>. This is the 2361 2644 tetrahedral angle so just press <b style='mso-bidi-font-weight:normal'><span 2362 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2645 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2363 2646 mso-hansi-theme-font:minor-latin'>OK</span></b>. 36 restraints will be listed; 2364 2647 they are listed in order of the B atom. O-atoms should have one angle apiece; … … 2373 2656 2374 2657 <p class=MsoNormal>Now go back the <b style='mso-bidi-font-weight:normal'><span 2375 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2658 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2376 2659 mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab in <b style='mso-bidi-font-weight: 2377 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2660 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2378 2661 minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>, select 2379 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2662 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2380 2663 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b> 2381 2664 from the dialog box by double clicking on the <b style='mso-bidi-font-weight: 2382 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2665 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2383 2666 minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column. Then do <b 2384 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2667 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2385 2668 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Set 2386 2669 atom refinement flags</span></b>. Select <b style='mso-bidi-font-weight:normal'><span 2387 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2670 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2388 2671 mso-hansi-theme-font:minor-latin'>X-coordinates</span></b>; this will set those 2389 2672 for all H-atoms. Now do <b style='mso-bidi-font-weight:normal'><span 2390 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2673 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2391 2674 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>, the console will 2392 list progress on the Penalty function (i.e. the restraints) and the <span 2393 class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase the <b 2394 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2395 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Restraint 2396 weight factors</span></b> to tighten them up at some expense in <span 2397 class=SpellE>Rwp</span>. In the end I chose <b style='mso-bidi-font-weight: 2398 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 2675 list progress on the Penalty function (i.e. the restraints) and the Rwp drops 2676 in my case to ~7.05%. One can increase the <b style='mso-bidi-font-weight:normal'><span 2677 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2678 mso-hansi-theme-font:minor-latin'>Restraint weight factors</span></b> to 2679 tighten them up at some expense in Rwp. In the end I chose <b style='mso-bidi-font-weight: 2680 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2399 2681 minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b> for both <b 2400 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2682 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2401 2683 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond</span></b> 2402 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2684 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2403 2685 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b> 2404 restraints to give a final <span class=SpellE>Rwp</span> ~7.1%. NB: the H-atom 2405 positions may not be correct even though the refinement apparently succeeded. 2406 You should check that the OH ones all give reasonable H-bonds to neighboring 2407 O-atoms. As this is powder data such changes will hardly affect the fit but 2408 will be more satisfying. At present such checking is outside the scope of 2409 GSAS-II.</p> 2686 restraints to give a final Rwp ~7.1%. NB: the H-atom positions may not be 2687 correct even though the refinement apparently succeeded. You should check that 2688 the OH ones all give reasonable H-bonds to neighboring O-atoms. As this is 2689 powder data such changes will hardly affect the fit but will be more 2690 satisfying. At present such checking is outside the scope of GSAS-II.</p> 2410 2691 2411 2692 <p class=MsoNormal><o:p> </o:p></p> -
Tutorials/CFsucrose/Charge Flipping - sucrose_files/filelist.xml
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