Changeset 1718 for Tutorials/MCsimanneal/MCSA in GSAS.htm
- Timestamp:
- Mar 16, 2015 4:18:34 PM (8 years ago)
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Tutorials/MCsimanneal/MCSA in GSAS.htm
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QFormat="true" Name="Subtitle"/> 220 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 221 Name="Salutation"/> 222 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 223 Name="Date"/> 224 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 225 Name="Body Text First Indent"/> 226 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 227 Name="Body Text First Indent 2"/> 228 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 229 Name="Note Heading"/> 230 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 231 Name="Body Text 2"/> 232 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 233 Name="Body Text 3"/> 234 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 235 Name="Body Text Indent 2"/> 236 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 237 Name="Body Text Indent 3"/> 238 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 239 Name="Block Text"/> 240 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 241 Name="Hyperlink"/> 242 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 243 Name="FollowedHyperlink"/> 244 <w:LsdException Locked="false" Priority="22" QFormat="true" Name="Strong"/> 245 <w:LsdException Locked="false" Priority="20" QFormat="true" Name="Emphasis"/> 246 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 247 Name="Document Map"/> 248 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 249 Name="Plain Text"/> 250 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 251 Name="E-mail Signature"/> 252 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 253 Name="HTML Top of Form"/> 254 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 255 Name="HTML Bottom of Form"/> 256 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 257 Name="Normal (Web)"/> 258 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 259 Name="HTML Acronym"/> 260 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 261 Name="HTML Address"/> 262 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 263 Name="HTML Cite"/> 264 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 265 Name="HTML Code"/> 266 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 267 Name="HTML Definition"/> 268 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 269 Name="HTML Keyboard"/> 270 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 271 Name="HTML Preformatted"/> 272 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 273 Name="HTML Sample"/> 274 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 275 Name="HTML Typewriter"/> 276 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 277 Name="HTML Variable"/> 278 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 279 Name="Normal Table"/> 280 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 281 Name="annotation subject"/> 282 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 283 Name="No List"/> 284 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 285 Name="Outline List 1"/> 286 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 287 Name="Outline List 2"/> 288 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 289 Name="Outline List 3"/> 290 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 291 Name="Table Simple 1"/> 292 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 293 Name="Table Simple 2"/> 294 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 295 Name="Table Simple 3"/> 296 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 297 Name="Table Classic 1"/> 298 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 299 Name="Table Classic 2"/> 300 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 301 Name="Table Classic 3"/> 302 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 303 Name="Table Classic 4"/> 304 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 305 Name="Table Colorful 1"/> 306 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 307 Name="Table Colorful 2"/> 308 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 309 Name="Table Colorful 3"/> 310 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 311 Name="Table Columns 1"/> 312 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 313 Name="Table Columns 2"/> 314 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 315 Name="Table Columns 3"/> 316 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 317 Name="Table Columns 4"/> 318 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 319 Name="Table Columns 5"/> 320 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 321 Name="Table Grid 1"/> 322 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 323 Name="Table Grid 2"/> 324 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 325 Name="Table Grid 3"/> 326 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 327 Name="Table Grid 4"/> 328 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 329 Name="Table Grid 5"/> 330 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 331 Name="Table Grid 6"/> 332 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 333 Name="Table Grid 7"/> 334 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 335 Name="Table Grid 8"/> 336 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 337 Name="Table List 1"/> 338 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 339 Name="Table List 2"/> 340 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 341 Name="Table List 3"/> 342 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 343 Name="Table List 4"/> 344 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 345 Name="Table List 5"/> 346 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 347 Name="Table List 6"/> 348 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 349 Name="Table List 7"/> 350 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 351 Name="Table List 8"/> 352 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 353 Name="Table 3D effects 1"/> 354 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 355 Name="Table 3D effects 2"/> 356 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 357 Name="Table 3D effects 3"/> 358 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 359 Name="Table Contemporary"/> 360 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 361 Name="Table Elegant"/> 362 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 363 Name="Table Professional"/> 364 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 365 Name="Table Subtle 1"/> 366 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 367 Name="Table Subtle 2"/> 368 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 369 Name="Table Web 1"/> 370 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 371 Name="Table Web 2"/> 372 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 373 Name="Table Web 3"/> 374 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 375 Name="Balloon Text"/> 376 <w:LsdException Locked="false" Priority="59" Name="Table Grid"/> 377 <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true" 378 Name="Table Theme"/> 379 <w:LsdException Locked="false" SemiHidden="true" Name="Placeholder Text"/> 380 <w:LsdException Locked="false" Priority="1" QFormat="true" Name="No Spacing"/> 381 <w:LsdException Locked="false" Priority="60" Name="Light Shading"/> 382 <w:LsdException Locked="false" Priority="61" Name="Light List"/> 383 <w:LsdException Locked="false" Priority="62" Name="Light Grid"/> 384 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1"/> 385 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2"/> 386 <w:LsdException Locked="false" Priority="65" Name="Medium List 1"/> 387 <w:LsdException Locked="false" Priority="66" Name="Medium List 2"/> 388 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1"/> 389 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2"/> 390 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3"/> 391 <w:LsdException Locked="false" Priority="70" Name="Dark List"/> 392 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading"/> 393 <w:LsdException Locked="false" Priority="72" Name="Colorful List"/> 394 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/> 395 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/> 396 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/> 397 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/> 398 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/> 399 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/> 400 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/> 401 <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/> 402 <w:LsdException Locked="false" Priority="34" QFormat="true" 403 Name="List Paragraph"/> 404 <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/> 405 <w:LsdException Locked="false" Priority="30" QFormat="true" 406 Name="Intense Quote"/> 407 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/> 408 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/> 409 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/> 410 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/> 411 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/> 412 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/> 413 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/> 414 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/> 415 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/> 416 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/> 417 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/> 418 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/> 419 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/> 420 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/> 421 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/> 422 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/> 423 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/> 424 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/> 425 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/> 426 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/> 427 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/> 428 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/> 429 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/> 430 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/> 431 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/> 432 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/> 433 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/> 434 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/> 435 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/> 436 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/> 437 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/> 438 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/> 439 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/> 440 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/> 441 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/> 442 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/> 443 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/> 444 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/> 445 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/> 446 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/> 447 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/> 448 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/> 449 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/> 450 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/> 451 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/> 452 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/> 453 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/> 454 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/> 455 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/> 456 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/> 457 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/> 458 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/> 459 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/> 460 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/> 461 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/> 462 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/> 463 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/> 464 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/> 465 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/> 466 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/> 467 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/> 468 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/> 469 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/> 470 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/> 471 <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/> 472 <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/> 473 <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/> 474 <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/> 475 <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/> 476 <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/> 477 <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/> 478 <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/> 479 <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/> 480 <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/> 481 <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/> 482 <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/> 483 <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/> 484 <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/> 485 <w:LsdException Locked="false" Priority="19" QFormat="true" 486 Name="Subtle Emphasis"/> 487 <w:LsdException Locked="false" Priority="21" QFormat="true" 488 Name="Intense Emphasis"/> 489 <w:LsdException Locked="false" Priority="31" QFormat="true" 490 Name="Subtle Reference"/> 491 <w:LsdException Locked="false" Priority="32" QFormat="true" 492 Name="Intense Reference"/> 493 <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/> 494 <w:LsdException Locked="false" Priority="37" SemiHidden="true" 495 UnhideWhenUsed="true" Name="Bibliography"/> 496 <w:LsdException Locked="false" Priority="39" SemiHidden="true" 497 UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/> 498 <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/> 499 <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/> 500 <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/> 501 <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/> 502 <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/> 503 <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/> 504 <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/> 505 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/> 506 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/> 507 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/> 508 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/> 509 <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/> 510 <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/> 511 <w:LsdException Locked="false" Priority="46" 512 Name="Grid Table 1 Light Accent 1"/> 513 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/> 514 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/> 515 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/> 516 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/> 517 <w:LsdException Locked="false" Priority="51" 518 Name="Grid Table 6 Colorful Accent 1"/> 519 <w:LsdException Locked="false" Priority="52" 520 Name="Grid Table 7 Colorful Accent 1"/> 521 <w:LsdException Locked="false" Priority="46" 522 Name="Grid Table 1 Light Accent 2"/> 523 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/> 524 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/> 525 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/> 526 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/> 527 <w:LsdException Locked="false" Priority="51" 528 Name="Grid Table 6 Colorful Accent 2"/> 529 <w:LsdException Locked="false" Priority="52" 530 Name="Grid Table 7 Colorful Accent 2"/> 531 <w:LsdException Locked="false" Priority="46" 532 Name="Grid Table 1 Light Accent 3"/> 533 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/> 534 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/> 535 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/> 536 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/> 537 <w:LsdException Locked="false" Priority="51" 538 Name="Grid Table 6 Colorful Accent 3"/> 539 <w:LsdException Locked="false" Priority="52" 540 Name="Grid Table 7 Colorful Accent 3"/> 541 <w:LsdException Locked="false" Priority="46" 542 Name="Grid Table 1 Light Accent 4"/> 543 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/> 544 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/> 545 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/> 546 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/> 547 <w:LsdException Locked="false" Priority="51" 548 Name="Grid Table 6 Colorful Accent 4"/> 549 <w:LsdException Locked="false" Priority="52" 550 Name="Grid Table 7 Colorful Accent 4"/> 551 <w:LsdException Locked="false" Priority="46" 552 Name="Grid Table 1 Light Accent 5"/> 553 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/> 554 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/> 555 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/> 556 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/> 557 <w:LsdException Locked="false" Priority="51" 558 Name="Grid Table 6 Colorful Accent 5"/> 559 <w:LsdException Locked="false" Priority="52" 560 Name="Grid Table 7 Colorful Accent 5"/> 561 <w:LsdException Locked="false" Priority="46" 562 Name="Grid Table 1 Light Accent 6"/> 563 <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/> 564 <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/> 565 <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/> 566 <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/> 567 <w:LsdException Locked="false" Priority="51" 568 Name="Grid Table 6 Colorful Accent 6"/> 569 <w:LsdException Locked="false" Priority="52" 570 Name="Grid Table 7 Colorful Accent 6"/> 571 <w:LsdException Locked="false" Priority="46" 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1239 mso-pagination:widow-orphan; 936 1240 font-size:10.0pt; 937 font-family:"Calibri", "sans-serif";}1241 font-family:"Calibri",sans-serif;} 938 1242 </style> 939 1243 <![endif]--><!--[if gte mso 9]><xml> … … 955 1259 <p class=MsoNormal>In these exercises you will use GSAS-II to solve the 956 1260 structures of 3-aminoquinoline and α-d-lactose monohydrate from powder 957 diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets 958 were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>) 959 and were originally collected on NSLS beam line X3b1. The MC/SA technique is 960 needed in these cases because as you will see the data does not extend very far 961 in 2Θ so one cannot use charge flipping to solve them. The steps for each 962 begin with peak selection and fitting, then indexing to identify the lattice 963 parameters. A Pawley refinement is used to obtain a set of structure factors 964 needed for the MC/SA runs. We will use previously developed models for the two 965 molecules; I used the freeware program Avogadro (<a 966 href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>) 1261 diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets were 1262 kindly provided by Peter Stephens (SUNY StonyBrook) and were originally 1263 collected on NSLS beam line X3b1. The MC/SA technique is needed in these cases 1264 because as you will see the data does not extend very far in 2Θ so one 1265 cannot use charge flipping to solve them. The steps for each begin with peak 1266 selection and fitting, then indexing to identify the lattice parameters. A 1267 Pawley refinement is used to obtain a set of structure factors needed for the 1268 MC/SA runs. We will use previously developed models for the two molecules; I 1269 used the freeware program Avogadro (<a href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>) 967 1270 to create them.</p> 968 1271 969 1272 <p class=MsoNormal>If you have not done so already, <a 970 href=" Starting%20GSAS.htm">start GSAS-II</a>.</p>971 972 <h2> <span class=GramE>Step 1.</span>Import powder data for 3-aminoquinoline</h2>1273 href="../../../GSASII/help/Starting%20GSAS.htm">start GSAS-II</a>.</p> 1274 1275 <h2>Step 1. Import powder data for 3-aminoquinoline</h2> 973 1276 974 1277 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span 975 1278 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 976 1279 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Use 977 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1280 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 978 1281 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 979 1282 Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder 980 1283 data file</span></b> menu item to read the data file into the current GSAS-II 981 1284 project. Change the file directory to <b style='mso-bidi-font-weight:normal'><span 982 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1285 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 983 1286 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 984 minor-latin'>Exercises/MCSA</span></b><span style='font-family:"Calibri", "sans-serif";1287 minor-latin'>Exercises/MCSA</span></b><span style='font-family:"Calibri",sans-serif; 985 1288 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 986 1289 Calibri;mso-bidi-theme-font:minor-latin'> to find the file; you may need to … … 991 1294 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 992 1295 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Select 993 the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span 994 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1296 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1297 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1298 Calibri;mso-bidi-theme-font:minor-latin'>Quinoli.gda</span></b><span 1299 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 995 1300 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 996 minor-latin'>Quinoli.gda</span></b></span><span style='font-family:"Calibri","sans-serif"; 997 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 998 Calibri;mso-bidi-theme-font:minor-latin'> data</span> file in the first dialog 999 and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1301 minor-latin'> data</span> file in the first dialog and press <b 1302 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1000 1303 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1001 1304 Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a 1002 Dialog box asking < span class=GramE><b style='mso-bidi-font-weight:normal'><span1003 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1305 Dialog box asking <b style='mso-bidi-font-weight:normal'><span 1306 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1004 1307 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1005 minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span 1006 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1007 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1008 minor-latin'> this the file you want?</span></b> Press <span class=GramE><b 1009 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1010 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1011 Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to 1012 proceed.</p> 1308 minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight: 1309 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1310 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1311 mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p> 1013 1312 1014 1313 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span 1015 1314 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 1016 1315 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Select 1017 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1316 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1018 1317 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1019 Calibri;mso-bidi-theme-font:minor-latin'>BNL- <span class=SpellE>I.instprm</span></span></b>1020 instrumentparameter file in the second dialog and press <b style='mso-bidi-font-weight:1021 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1318 Calibri;mso-bidi-theme-font:minor-latin'>BNL-I.instprm</span></b> instrument 1319 parameter file in the second dialog and press <b style='mso-bidi-font-weight: 1320 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1022 1321 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri; 1023 1322 mso-bidi-theme-font:minor-latin'>Open</span></b>. Youll have to change the 1024 1323 file type to <b style='mso-bidi-font-weight:normal'><span style='font-family: 1025 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1026 minor-latin'>*. <span class=SpellE>instprm</span></span></b> (GSAS-II instrument1027 p arameter file). The powder pattern will immediately appear.</p>1324 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1325 minor-latin'>*.instprm</span></b> (GSAS-II instrument parameter file). The 1326 powder pattern will immediately appear.</p> 1028 1327 1029 1328 <p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype … … 1051 1350 <v:imagedata src="MCSA%20in%20GSAS_files/image001.png" o:title=""/> 1052 1351 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1053 src="MCSA%20in%20GSAS_files/image0 31.gif" v:shapes="_x0000_i1051"><![endif]></span></p>1352 src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="_x0000_i1051"><![endif]></span></p> 1054 1353 1055 1354 <p class=MsoListParagraph><o:p> </o:p></p> … … 1059 1358 1Å or better. </p> 1060 1359 1061 <h2> <span class=GramE>Step 2.</span>Peak picking & fitting</h2>1360 <h2>Step 2. Peak picking & fitting</h2> 1062 1361 1063 1362 <p class=MsoNormal>Next you need to select limits so that ~20 peaks are 1064 1363 selected for indexing; go to <b style='mso-bidi-font-weight:normal'><span 1065 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1364 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1066 1365 mso-hansi-theme-font:minor-latin'>Limits</span></b> and choose <b 1067 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1366 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1068 1367 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>9-25</span></b>° 1069 1368 2Θ. Next go to <b style='mso-bidi-font-weight:normal'><span 1070 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1369 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1071 1370 mso-hansi-theme-font:minor-latin'>Peak List</span></b> and pick all the peaks 1072 1371 you can see between the limits. This is most easily done by hand as the <b 1073 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1372 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1074 1373 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Auto search</span></b> 1075 1374 routine gives a lot of spurious peaks for this rather noisy and weak data; I 1076 1375 picked 21 peaks, skipping a few very weak ones. Then use <b style='mso-bidi-font-weight: 1077 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1078 minor-latin;mso-hansi-theme-font:minor-latin'>Peak fitting/LSQ <span1079 class=SpellE>PeakFit</span> </span></b>to fit them. You will need to vary at 1080 least <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";1081 mso- ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>1082 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1083 m so-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>1084 in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";1376 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1377 minor-latin;mso-hansi-theme-font:minor-latin'>Peak fitting/LSQ PeakFit </span></b>to 1378 fit them. You will need to vary at least <b style='mso-bidi-font-weight:normal'><span 1379 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1380 mso-hansi-theme-font:minor-latin'>X</span></b> & <b style='mso-bidi-font-weight: 1381 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1382 minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> in <b 1383 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1085 1384 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument 1086 Parameters</span></b> along with <span class=SpellE><b style='mso-bidi-font-weight: 1087 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1088 minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span> & <span 1089 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1090 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1091 minor-latin'>int</span></b></span> in the <b style='mso-bidi-font-weight:normal'><span 1092 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1093 mso-hansi-theme-font:minor-latin'>Peak List</span></b> to get a reasonable fit 1094 suitable for indexing.</p> 1095 1096 <h2><span class=GramE>Step 3.</span> Indexing</h2> 1385 Parameters</span></b> along with <b style='mso-bidi-font-weight:normal'><span 1386 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1387 mso-hansi-theme-font:minor-latin'>pos</span></b> & <b style='mso-bidi-font-weight: 1388 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1389 minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b> in the <b 1390 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1391 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak List</span></b> 1392 to get a reasonable fit suitable for indexing.</p> 1393 1394 <h2>Step 3. Indexing</h2> 1097 1395 1098 1396 <p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span 1099 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1397 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1100 1398 mso-hansi-theme-font:minor-latin'>Index Peak List</span></b> and do <b 1101 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1399 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1102 1400 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Load/Reload</span></b> 1103 1401 to set up the peaks for indexing. Then go to <b style='mso-bidi-font-weight: 1104 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1402 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1105 1403 minor-latin;mso-hansi-theme-font:minor-latin'>Unit Cells List</span></b> for 1106 indexing. The most likely <span class=SpellE>Bravais</span> lattice for these1107 small organic molecules is either Orthorhombic-P or Monoclinic-P; you can try 1108 both and see what comes out (Hint: its <b style='mso-bidi-font-weight:normal'><span 1109 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1110 m so-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>). The correct unit1111 cell should almost immediately appear with an M20 ~330 with a=7.748, b=7.651,1112 c=12.736, <span class=SpellE>Vol</span>=755.01. Do <b style='mso-bidi-font-weight:1113 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:1114 minor-latin ;mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Copy Cell</span></b>;1115 you can then try various space groups. Press the <b style='mso-bidi-font-weight: 1116 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1117 m inor-latin;mso-hansi-theme-font:minor-latin'>Show HKL positions</span></b> to1118 see thelines with extinctions (Hint: its <b style='mso-bidi-font-weight:normal'><span1119 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1404 indexing. The most likely Bravais lattice for these small organic molecules is 1405 either Orthorhombic-P or Monoclinic-P; you can try both and see what comes out 1406 (Hint: its <b style='mso-bidi-font-weight:normal'><span style='font-family: 1407 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1408 minor-latin'>Orthorhombic-P</span></b>). The correct unit cell should almost 1409 immediately appear with an M20 ~330 with a=7.748, b=7.651, c=12.736, 1410 Vol=755.01. Do <b style='mso-bidi-font-weight:normal'><span style='font-family: 1411 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1412 minor-latin'>Cell Index/Refine/Copy Cell</span></b>; you can then try various 1413 space groups. Press the <b style='mso-bidi-font-weight:normal'><span 1414 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1415 mso-hansi-theme-font:minor-latin'>Show HKL positions</span></b> to see the 1416 lines with extinctions (Hint: its <b style='mso-bidi-font-weight:normal'><span 1417 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1120 1418 mso-hansi-theme-font:minor-latin'>P 2<sub>1</sub> 2<sub>1</sub> 2<sub>1</sub></span></b>). 1121 1419 You can then do <b style='mso-bidi-font-weight:normal'><span style='font-family: 1122 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1420 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1123 1421 minor-latin'>Cell Index/Refine/Refine Cell</span></b> to improve the lattice 1124 1422 parameters with M20 ~380. Finally do <b style='mso-bidi-font-weight:normal'><span 1125 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1423 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1126 1424 mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Make new phase</span></b> 1127 1425 to create the phase; I named it <b style='mso-bidi-font-weight:normal'><span 1128 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1426 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1129 1427 mso-hansi-theme-font:minor-latin'>3-aminoquinoline</span></b>.</p> 1130 1428 1131 <h2> <span class=GramE>Step 4.</span>Setup for Pawley refinement</h2>1429 <h2>Step 4. Setup for Pawley refinement</h2> 1132 1430 1133 1431 <p class=MsoNormal>There are a number of steps that must be done in preparation … … 1139 1437 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 1140 1438 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Select 1141 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1439 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1142 1440 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b> 1143 1441 in the GSAS-II data tree for the PWDR data set and expand the plot so that the … … 1153 1451 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 1154 1452 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Select 1155 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1453 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1156 1454 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument 1157 1455 Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span 1158 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1456 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1159 1457 mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b 1160 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1458 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1161 1459 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset 1162 1460 profile</span></b> to recover the default values. The peak fitting done earlier … … 1171 1469 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 1172 1470 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Select 1173 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1174 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b>1175 and uncheck refinement of <b style='mso-bidi-font-weight:normal'><span 1176 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1177 m so-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>1471 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1472 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample 1473 Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight: 1474 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1475 minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p> 1178 1476 1179 1477 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span 1180 1478 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 1181 1479 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Go 1182 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1480 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1183 1481 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b> 1184 1482 to find the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1185 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1483 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1186 1484 minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight: 1187 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1485 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1188 1486 minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> 1189 1487 box and enter the d-spacing (1.8133) into the <b style='mso-bidi-font-weight: 1190 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1191 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b> 1192 box.</p> 1488 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1489 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b> box.</p> 1193 1490 1194 1491 <p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span 1195 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1492 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1196 1493 mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p> 1197 1494 … … 1201 1498 <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/> 1202 1499 </v:shape><![endif]--><![if !vml]><img border=0 width=621 height=500 1203 src="MCSA%20in%20GSAS_files/image0 32.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>1500 src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_2"><![endif]></span></p> 1204 1501 1205 1502 <p class=MsoNormal><o:p> </o:p></p> 1206 1503 1207 1504 <p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span 1208 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1505 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1209 1506 mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except 1210 1507 for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span 1211 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1508 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1212 1509 mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a 1213 1510 dialog box will appear</p> … … 1218 1515 <v:imagedata src="MCSA%20in%20GSAS_files/image005.png" o:title=""/> 1219 1516 </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336 1220 src="MCSA%20in%20GSAS_files/image0 33.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>1517 src="MCSA%20in%20GSAS_files/image006.gif" v:shapes="Picture_x0020_3"><![endif]></span></p> 1221 1518 1222 1519 <p class=MsoNormal><o:p> </o:p></p> … … 1224 1521 <p class=MsoNormal>Select either choice; the desired data set will be added to 1225 1522 this phase for analysis. The data tab now shows the new data set; check the <b 1226 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1523 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1227 1524 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b> 1228 1525 button to see the full information</p> … … 1233 1530 <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/> 1234 1531 </v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500 1235 src="MCSA%20in%20GSAS_files/image0 34.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>1532 src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_28"><![endif]></span></p> 1236 1533 1237 1534 <p class=MsoNormal><o:p> </o:p></p> 1238 1535 1239 1536 <p class=MsoNormal>This is the location for all the phase dependent parameters 1240 for this histogram. Notice that it includes phase fraction, size & <span 1241 class=SpellE>mustrain</span> as well as preferred orientation, elastic strain 1242 and extinction corrections. The <span class=SpellE>Babinet</span> correction is 1243 intended for protein work where a significant region of the structure is 1244 disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span> 1245 surfaces and preferred orientation correction curves.</p> 1537 for this histogram. Notice that it includes phase fraction, size & mustrain 1538 as well as preferred orientation, elastic strain and extinction corrections. 1539 The Babinet correction is intended for protein work where a significant region 1540 of the structure is disordered solvent. There are buttons for plotting size and 1541 mustrain surfaces and preferred orientation correction curves.</p> 1246 1542 1247 1543 <p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span 1248 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1544 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1249 1545 mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be 1250 empty except for column headings. <span class=GramE>Do</span> <b 1251 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1252 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley 1253 create</span></b>; this makes the reflection set over the range covered by 1254 setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1255 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span 1256 class=SpellE>dmin</span></span></b>. The table should list reflections 0-91. 1257 Select and check the <b style='mso-bidi-font-weight:normal'><span 1258 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1259 mso-hansi-theme-font:minor-latin'>refine</span></b> column using the same 1260 technique you used for the peak list. </p> 1546 empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span 1547 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1548 mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this 1549 makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight: 1550 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1551 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>. The table 1552 should list reflections 0-91. Select and check the <b style='mso-bidi-font-weight: 1553 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1554 minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column using 1555 the same technique you used for the peak list. </p> 1261 1556 1262 1557 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1265 1560 <v:imagedata src="MCSA%20in%20GSAS_files/image009.png" o:title=""/> 1266 1561 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300 1267 src="MCSA%20in%20GSAS_files/image0 35.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>1562 src="MCSA%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_5"><![endif]></span></p> 1268 1563 1269 1564 <p class=MsoNormal><o:p> </o:p></p> … … 1272 1567 you didnt skip a step as it might not work correctly if you did.</p> 1273 1568 1274 <h2> <span class=GramE>Step 5.</span>Pawley refinement</h2>1569 <h2>Step 5. Pawley refinement</h2> 1275 1570 1276 1571 <p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight: 1277 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1572 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1278 1573 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on 1279 1574 the main GSAS-II data tree window. Before it begins a backup of the project 1280 1575 file is made; the name will be <b style='mso-bidi-font-weight:normal'><span 1281 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1576 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1282 1577 mso-hansi-theme-font:minor-latin'>aminoquinoline.bck0.gpx</span></b>. It can be 1283 1578 used to recover from a bad refinement. A progress dialog box will appear 1284 showing the residual as the refinement proceeds. My refinement completed with <span1285 class=SpellE>Rwp</span> ~12.9%; a dialog box appears asking if you wish to load 1286 the result. Press <b style='mso-bidi-font-weight:normal'><span 1287 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1288 mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the 1289 PWDR line in the GSAS-II data tree (Ive adjustedthe width and height).</p>1579 showing the residual as the refinement proceeds. My refinement completed with 1580 Rwp ~12.9%; a dialog box appears asking if you wish to load the result. Press <b 1581 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1582 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. 1583 To see the plot select the PWDR line in the GSAS-II data tree (Ive adjusted 1584 the width and height).</p> 1290 1585 1291 1586 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1294 1589 <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/> 1295 1590 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1296 src="MCSA%20in%20GSAS_files/image0 36.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>1591 src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_6"><![endif]></span></p> 1297 1592 1298 1593 <p class=MsoNormal><o:p> </o:p></p> … … 1302 1597 background model. One easy way to fit that broad hump is to add a peak to the 1303 1598 background. Go to <b style='mso-bidi-font-weight:normal'><span 1304 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1599 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1305 1600 mso-hansi-theme-font:minor-latin'>Background</span></b> and set <b 1306 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1601 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1307 1602 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. peaks</span></b> 1308 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1603 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1309 1604 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>, 1310 then change <span class=SpellE><b style='mso-bidi-font-weight:normal'><span 1311 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1312 mso-hansi-theme-font:minor-latin'>pos</span></b></span> to <b style='mso-bidi-font-weight: 1313 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1314 minor-latin;mso-hansi-theme-font:minor-latin'>19</span></b>, <span 1315 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1316 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1317 minor-latin'>int</span></b></span> to <b style='mso-bidi-font-weight:normal'><span 1318 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1319 mso-hansi-theme-font:minor-latin'>100000</span></b> and <b style='mso-bidi-font-weight: 1320 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1321 minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> to <b 1322 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1605 then change <b style='mso-bidi-font-weight:normal'><span style='font-family: 1606 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1607 minor-latin'>pos</span></b> to <b style='mso-bidi-font-weight:normal'><span 1608 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1609 mso-hansi-theme-font:minor-latin'>19</span></b>, <b style='mso-bidi-font-weight: 1610 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1611 minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b> to <b 1612 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1613 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b> 1614 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1615 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> 1616 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1323 1617 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>; 1324 1618 for the peak only refine <b style='mso-bidi-font-weight:normal'><span 1325 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1619 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1326 1620 mso-hansi-theme-font:minor-latin'>int</span></b>. I also set <b 1327 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1328 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span 1329 class=SpellE>coeff</span>.</span></b> <span class=GramE>to</span> <b 1330 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1621 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1622 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. coeff.</span></b> 1623 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1331 1624 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>; 1332 1625 the window shows</p> … … 1337 1630 <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/> 1338 1631 </v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263 1339 src="MCSA%20in%20GSAS_files/image0 37.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>1632 src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p> 1340 1633 1341 1634 <p class=MsoNormal><o:p> </o:p></p> 1342 1635 1343 1636 <p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span 1344 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1345 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span 1346 class=SpellE>Rwp</span> fell to ~8.5%. In <b style='mso-bidi-font-weight:normal'><span 1347 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1348 mso-hansi-theme-font:minor-latin'>Background</span></b> select <span 1349 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1350 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1351 minor-latin'>pos</span></b></span> & <b style='mso-bidi-font-weight:normal'><span 1352 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1353 mso-hansi-theme-font:minor-latin'>sig</span></b> for refinement and in <b 1354 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1355 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument 1356 Parameters</span></b> select <b style='mso-bidi-font-weight:normal'><span 1357 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1358 mso-hansi-theme-font:minor-latin'>X</span></b> & <b style='mso-bidi-font-weight: 1359 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1360 minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> for refinement; then 1361 do <span class=GramE><b style='mso-bidi-font-weight:normal'><span 1362 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1363 mso-hansi-theme-font:minor-latin'>Calculate</span></b></span><b 1364 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1365 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> /Refine</span></b> 1366 again. I got Rwp~7.5% at convergence and the fit looked like</p> 1637 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1638 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my Rwp fell to 1639 ~8.5%. In <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1640 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b> 1641 select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1642 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b> 1643 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1644 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> 1645 for refinement and in <b style='mso-bidi-font-weight:normal'><span 1646 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1647 mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> select <b 1648 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1649 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b> 1650 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1651 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> 1652 for refinement; then do <b style='mso-bidi-font-weight:normal'><span 1653 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1654 mso-hansi-theme-font:minor-latin'>Calculate /Refine</span></b> again. I got 1655 Rwp~7.5% at convergence and the fit looked like</p> 1367 1656 1368 1657 <p class=MsoNormal><span style='mso-no-proof:yes'>c<!--[if gte vml 1]><v:shape … … 1371 1660 <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/> 1372 1661 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1373 src="MCSA%20in%20GSAS_files/image0 38.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>1662 src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_33"><![endif]></span></p> 1374 1663 1375 1664 <p class=MsoNormal><o:p> </o:p></p> … … 1378 1667 Annealing.</p> 1379 1668 1380 <h2> <span class=GramE>Step 6.</span>Setup for Monte Carlo/Simulated Annealing</h2>1381 1382 <p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic rings1383 with one N-substituted position and an amino side group</p>1669 <h2>Step 6. Setup for Monte Carlo/Simulated Annealing</h2> 1670 1671 <p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic 1672 rings with one N-substituted position and an amino side group</p> 1384 1673 1385 1674 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1389 1678 cropbottom="17428f" cropleft="9893f" cropright="13874f"/> 1390 1679 </v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125 1391 src="MCSA%20in%20GSAS_files/image0 39.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>1680 src="MCSA%20in%20GSAS_files/image018.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p> 1392 1681 1393 1682 <p class=MsoNormal>MC/SA structure solution consists of optimizing the position … … 1395 1684 freedom. Thus we need to determine essentially six parameters. To do this in 1396 1685 GSAS-II we need to put a model of this molecule in as a rigid body. One must 1397 create the model outside of GSAS-<span class=GramE>II,</span> it has no 1398 facilities for model building. I used the Avogadro (<a 1399 href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>) 1686 create the model outside of GSAS-II, it has no facilities for model building. I 1687 used the Avogadro (<a href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>) 1400 1688 package for this and created a simple xyz Cartesian coordinate file for it (if 1401 1689 you have Avogadro or something equivalent you can try this for yourself). To 1402 1690 start go to <b style='mso-bidi-font-weight:normal'><span style='font-family: 1403 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1691 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1404 1692 minor-latin'>Rigid bodies</span></b> in the main GSAS-II data tree. You will 1405 1693 see a window with two tabs; select <b style='mso-bidi-font-weight:normal'><span 1406 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1694 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1407 1695 mso-hansi-theme-font:minor-latin'>Residue rigid bodies</span></b> and then do <b 1408 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1696 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1409 1697 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Import 1410 1698 XYZ</span></b>. Change the file type to <b style='mso-bidi-font-weight:normal'><span 1411 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1412 mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and select <span 1413 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1414 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1415 minor-latin'>aminoquinoline.xyz</span></b></span>. The <b style='mso-bidi-font-weight: 1416 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1417 minor-latin;mso-hansi-theme-font:minor-latin'>Rigid <span class=GramE>bodies</span></span></b> 1699 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1700 mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and select <b 1701 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1702 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>aminoquinoline.xyz</span></b>. 1703 The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1704 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Rigid bodies</span></b> 1418 1705 window will show</p> 1419 1706 … … 1423 1710 <v:imagedata src="MCSA%20in%20GSAS_files/image019.png" o:title=""/> 1424 1711 </v:shape><![endif]--><![if !vml]><img border=0 width=400 height=427 1425 src="MCSA%20in%20GSAS_files/image0 40.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>1712 src="MCSA%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_35"><![endif]></span></p> 1426 1713 1427 1714 <p class=MsoNormal><o:p> </o:p></p> 1428 1715 1429 <p class=MsoNormal><span class=GramE>If you select the <b style='mso-bidi-font-weight: 1430 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1431 minor-latin;mso-hansi-theme-font:minor-latin'>Plot?</span></b></span> <span 1432 class=GramE>box</span> a drawing will appear</p> 1716 <p class=MsoNormal>If you select the <b style='mso-bidi-font-weight:normal'><span 1717 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1718 mso-hansi-theme-font:minor-latin'>Plot?</span></b> box a drawing will appear</p> 1433 1719 1434 1720 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1438 1724 cropbottom="15961f" cropleft="36898f" cropright="13504f"/> 1439 1725 </v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312 1440 src="MCSA%20in%20GSAS_files/image0 41.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>1726 src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p> 1441 1727 1442 1728 <p class=MsoNormal><o:p> </o:p></p> … … 1454 1740 cropbottom="16027f" cropleft="37724f" cropright="12673f"/> 1455 1741 </v:shape><![endif]--><![if !vml]><img border=0 width=384 height=313 1456 src="MCSA%20in%20GSAS_files/image0 42.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>1742 src="MCSA%20in%20GSAS_files/image024.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p> 1457 1743 1458 1744 <p class=MsoNormal><o:p> </o:p></p> … … 1461 1747 needed for MC/SA and will just make computation times a bit longer than 1462 1748 necessary. You should change the <b style='mso-bidi-font-weight:normal'><span 1463 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1464 mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something meaningful, 1465 I used <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1466 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>.</p> 1749 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1750 mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something 1751 meaningful, I used <b style='mso-bidi-font-weight:normal'><span 1752 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1753 mso-hansi-theme-font:minor-latin'>amino</span></b>.</p> 1467 1754 1468 1755 <p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span 1469 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1756 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1470 1757 mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b> and select 1471 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1758 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1472 1759 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA</span></b> 1473 1760 tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family: 1474 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1761 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1475 1762 minor-latin'>MC/SA/Add rigid body</span></b>; select the only choice (<b 1476 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1763 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1477 1764 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>) 1478 1765 from the popup selection box. The MC/SA window shows</p> … … 1483 1770 <v:imagedata src="MCSA%20in%20GSAS_files/image025.png" o:title=""/> 1484 1771 </v:shape><![endif]--><![if !vml]><img border=0 width=598 height=335 1485 src="MCSA%20in%20GSAS_files/image0 43.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>1772 src="MCSA%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_37"><![endif]></span></p> 1486 1773 1487 1774 <p class=MsoNormal><o:p> </o:p></p> … … 1492 1779 id="Picture_x0020_14" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:4in; 1493 1780 height:232.5pt;visibility:visible;mso-wrap-style:square'> 1494 <v:imagedata src="MCSA%20in%20GSAS_files/image0 44.png" o:title="" croptop="17592f"1781 <v:imagedata src="MCSA%20in%20GSAS_files/image027.png" o:title="" croptop="17592f" 1495 1782 cropbottom="12829f" cropleft="38911f" cropright="11642f"/> 1496 1783 </v:shape><![endif]--><![if !vml]><img border=0 width=384 height=310 1497 src="MCSA%20in%20GSAS_files/image0 45.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>1784 src="MCSA%20in%20GSAS_files/image028.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p> 1498 1785 1499 1786 <p class=MsoNormal><o:p> </o:p></p> … … 1501 1788 <p class=MsoNormal>You see the four equivalent molecules for space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub> 1502 1789 whose centers fall within the unit cell; the reference one is that in the lower 1503 left corner with C1 at the origin. You can enter values in the <span 1504 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1505 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1506 minor-latin'>x<span class=GramE>,y,z</span></span></b></span> boxes and see how 1507 the structure changes. Similarly, you can enter an angle in <span class=SpellE><b 1508 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1509 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span> 1510 or a vector in the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span 1511 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1512 mso-hansi-theme-font:minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><span 1790 left corner with C1 at the origin. You can enter values in the <b 1791 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1792 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>x,y,z</span></b> 1793 boxes and see how the structure changes. Similarly, you can enter an angle in <b 1794 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1795 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b> 1796 or a vector in the <b style='mso-bidi-font-weight:normal'><span 1797 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1798 mso-hansi-theme-font:minor-latin'>Oi,Oj,Ok</span></b><span 1513 1799 style='mso-spacerun:yes'> </span>box to see the effects of rotating the 1514 1800 molecule. Each of these parameters has a defined range for the MC/SA … … 1519 1805 with the default. We want to optimize the position and orientation of this 1520 1806 molecule; check the <b style='mso-bidi-font-weight:normal'><span 1521 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1807 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1522 1808 mso-hansi-theme-font:minor-latin'>x</span></b>, <b style='mso-bidi-font-weight: 1523 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1809 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1524 1810 minor-latin;mso-hansi-theme-font:minor-latin'>y</span></b> & <b 1525 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1811 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1526 1812 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b> 1527 1813 boxes and select <b style='mso-bidi-font-weight:normal'><span style='font-family: 1528 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1529 minor-latin'>AV</span></b> from the <span class=SpellE><b style='mso-bidi-font-weight: 1530 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1531 minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>, <span 1532 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1533 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1534 minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><b 1535 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1536 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Vary?</span></b> 1537 <span class=SpellE><span class=GramE>pulldown</span></span>. The MC/SA window 1538 should look like</p> 1814 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1815 minor-latin'>AV</span></b> from the <b style='mso-bidi-font-weight:normal'><span 1816 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1817 mso-hansi-theme-font:minor-latin'>Oa</span></b>, <b style='mso-bidi-font-weight: 1818 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1819 minor-latin;mso-hansi-theme-font:minor-latin'>Oi,Oj,Ok Vary?</span></b> 1820 pulldown. The MC/SA window should look like</p> 1539 1821 1540 1822 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1543 1825 <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/> 1544 1826 </v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258 1545 src="MCSA%20in%20GSAS_files/image0 46.gif" v:shapes="Picture_x0020_39"><![endif]></span><span1827 src="MCSA%20in%20GSAS_files/image030.gif" v:shapes="Picture_x0020_39"><![endif]></span><span 1546 1828 style='mso-spacerun:yes'> </span></p> 1547 1829 … … 1550 1832 <p class=MsoNormal>This completes the set up for MC/SA processing. </p> 1551 1833 1552 <h2> <span class=GramE>Step 7.</span>Monte Carlo/Simulated Annealing</h2>1834 <h2>Step 7. Monte Carlo/Simulated Annealing</h2> 1553 1835 1554 1836 <p class=MsoNormal>Now go to the <b style='mso-bidi-font-weight:normal'><span 1555 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1837 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1556 1838 mso-hansi-theme-font:minor-latin'>General</span></b> tab; the MC/SA controls 1557 1839 are at the bottom of the window. To begin the setup of these controls, select a 1558 1840 source of the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1559 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1841 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1560 1842 minor-latin'>Reflection set</span></b> to be used in the MC/SA runs. The choice 1561 1843 is to use either the Pawley reflections or the Reflection List for the PWDR 1562 1844 data set. If you choose <b style='mso-bidi-font-weight:normal'><span 1563 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1845 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1564 1846 mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> then the 1565 structure factors will be Pawley model values, <span class=SpellE><span 1566 class=GramE>Fsq</span></span><span class=GramE>(</span><span class=SpellE>hkl</span>) 1567 in Pawley table, and the covariance matrix developed from the refinement will 1568 be used for peak overlap effects in the MC/SA calculations. Alternatively, if 1569 you choose <b style='mso-bidi-font-weight:normal'><span style='font-family: 1570 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1571 minor-latin'>PWDR <span class=SpellE>Quinoli.gda</span> Bank 1 </span></b>then 1572 the structure factors will be those, <span class=SpellE>Fosq</span> in 1847 structure factors will be Pawley model values, Fsq(hkl) in Pawley table, and 1848 the covariance matrix developed from the refinement will be used for peak 1849 overlap effects in the MC/SA calculations. Alternatively, if you choose <b 1850 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1851 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR 1852 Quinoli.gda Bank 1 </span></b>then the structure factors will be those, Fosq in 1573 1853 Reflection table, extracted during the Pawley refinement and the peak FWHMs 1574 1854 will be used for peak overlap effects in the MC/SA calculations. Notice that 1575 the Pawley <span class=SpellE><span class=GramE>Fsq</span></span><span 1576 class=GramE>(</span><span class=SpellE>hkl</span>) values are the same as the <span 1577 class=SpellE>Fcsq</span> Reflection List values. Here I chose <b 1578 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1579 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley 1580 reflections</span></b> for the <b style='mso-bidi-font-weight:normal'><span 1581 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1582 mso-hansi-theme-font:minor-latin'>Reflection set</span></b> as it give slightly 1583 better performance in MC/SA.</p> 1855 the Pawley Fsq(hkl) values are the same as the Fcsq Reflection List values. 1856 Here I chose <b style='mso-bidi-font-weight:normal'><span style='font-family: 1857 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1858 minor-latin'>Pawley reflections</span></b> for the <b style='mso-bidi-font-weight: 1859 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1860 minor-latin;mso-hansi-theme-font:minor-latin'>Reflection set</span></b> as it 1861 give slightly better performance in MC/SA.</p> 1584 1862 1585 1863 <p class=MsoNormal>Next, you need to set the minimum d-spacing (<b 1586 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1864 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1587 1865 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>d-min</span></b>). 1588 1866 Smaller values gives minima in the MC/SA minimization surface that are more … … 1591 1869 should have 5-8 reflections for each MC/SA parameter; in this case 35-50 1592 1870 reflections are needed. If you examine the reflection list (either <b 1593 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1871 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1594 1872 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley</span></b> 1595 or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1873 or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1596 1874 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection 1597 1875 List</span></b>) youll see that a <b style='mso-bidi-font-weight:normal'><span 1598 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1876 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1599 1877 mso-hansi-theme-font:minor-latin'>d-min</span></b> of <b style='mso-bidi-font-weight: 1600 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:1878 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1601 1879 minor-latin;mso-hansi-theme-font:minor-latin'>2.5</span></b> will give 1602 1880 sufficient reflections.</p> 1603 1881 1604 1882 <p class=MsoNormal>Lastly, you need to set the run controls. I used <b 1605 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1883 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1606 1884 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>500</span></b> 1607 for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1885 for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1608 1886 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. trials</span></b>; 1609 1887 this is the number of random tries at each temperature in the annealing 1610 1888 schedule. When done the <b style='mso-bidi-font-weight:normal'><span 1611 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1889 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1612 1890 mso-hansi-theme-font:minor-latin'>General</span></b> window should look like</p> 1613 1891 … … 1615 1893 id="Picture_x0020_16" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:7in; 1616 1894 height:375pt;visibility:visible;mso-wrap-style:square'> 1617 <v:imagedata src="MCSA%20in%20GSAS_files/image03 0.png" o:title=""/>1895 <v:imagedata src="MCSA%20in%20GSAS_files/image031.png" o:title=""/> 1618 1896 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500 1619 src="MCSA%20in%20GSAS_files/image0 58.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>1897 src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_16"><![endif]></span></p> 1620 1898 1621 1899 <p class=MsoNormal><o:p> </o:p></p> 1622 1900 1623 1901 <p class=MsoNormal>When ready, you can start the MC/SA calculation by doing <b 1624 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1902 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1625 1903 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b> 1626 from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1904 from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1627 1905 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> 1628 1906 window menu. A progress bar will appear that shows the MC/SA residual (an … … 1630 1908 as indicating which MC/SA run is being done. When it finishes, control is 1631 1909 shifted to the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1632 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:1910 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1633 1911 minor-latin'>MC/SA</span></b> window which gives a list of the solutions it 1634 1912 found at the bottom of the window (scroll down to see them).</p> … … 1637 1915 id="Picture_x0020_19" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:560.25pt; 1638 1916 height:273.75pt;visibility:visible;mso-wrap-style:square'> 1639 <v:imagedata src="MCSA%20in%20GSAS_files/image0 48.png" o:title=""/>1917 <v:imagedata src="MCSA%20in%20GSAS_files/image033.png" o:title=""/> 1640 1918 </v:shape><![endif]--><![if !vml]><img border=0 width=747 height=365 1641 src="MCSA%20in%20GSAS_files/image0 59.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>1919 src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_19"><![endif]></span></p> 1642 1920 1643 1921 <p class=MsoNormal><o:p> </o:p></p> … … 1649 1927 id="Picture_x0020_20" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:279.75pt; 1650 1928 height:243.75pt;visibility:visible;mso-wrap-style:square'> 1651 <v:imagedata src="MCSA%20in%20GSAS_files/image0 50.png" o:title="" croptop="11773f"1929 <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title="" croptop="11773f" 1652 1930 cropbottom="16530f" cropleft="37715f" cropright="13079f"/> 1653 1931 </v:shape><![endif]--><![if !vml]><img border=0 width=373 height=325 1654 src="MCSA%20in%20GSAS_files/image0 60.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>1932 src="MCSA%20in%20GSAS_files/image036.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p> 1655 1933 1656 1934 <p class=MsoNormal><o:p> </o:p></p> … … 1661 1939 molecules clashing), then you should just rerun MC/SA perhaps using more runs 1662 1940 or more trials. Be sure to set the <b style='mso-bidi-font-weight:normal'><span 1663 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;1941 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1664 1942 mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any solutions you 1665 1943 want to retain; the others will be cleared before the next MC/SA run starts. 1666 When you think you have a good one, < span class=GramE><b style='mso-bidi-font-weight:1667 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1668 m inor-latin;mso-hansi-theme-font:minor-latin'>Select</span></b></span> it; the1669 parameters will be copied to the appropriate boxes in the upper part ofthe1670 MC/SA window and the structure is drawn again. Next we want to refine this 1671 solution so go back to the <b style='mso-bidi-font-weight:normal'><span 1672 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1673 mso-hansi-theme-font:minor-latin'>General</span></b>tab.</p>1944 When you think you have a good one, <b style='mso-bidi-font-weight:normal'><span 1945 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1946 mso-hansi-theme-font:minor-latin'>Select</span></b> it; the parameters will be 1947 copied to the appropriate boxes in the upper part of the MC/SA window and the 1948 structure is drawn again. Next we want to refine this solution so go back to 1949 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1950 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> 1951 tab.</p> 1674 1952 1675 1953 <p class=MsoNormal>MC/SA refinement is achieved by narrowing the search ranges 1676 1954 and rerunning the MC/SA calculations. This is done by checking the <b 1677 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1955 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1678 1956 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA Refine</span></b> 1679 1957 box. Using 10% of the ranges reduces the search volume in this case by ~6 1680 1958 orders of magnitude so that the true minimum is much easier to find. Now rerun <b 1681 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";1959 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1682 1960 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>; 1683 1961 be sure to select the best one before starting. The residual should drop to a … … 1688 1966 id="Picture_x0020_22" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:569.25pt; 1689 1967 height:285pt;visibility:visible;mso-wrap-style:square'> 1690 <v:imagedata src="MCSA%20in%20GSAS_files/image0 52.png" o:title=""/>1968 <v:imagedata src="MCSA%20in%20GSAS_files/image037.png" o:title=""/> 1691 1969 </v:shape><![endif]--><![if !vml]><img border=0 width=759 height=380 1692 src="MCSA%20in%20GSAS_files/image0 61.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>1970 src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_22"><![endif]></span></p> 1693 1971 1694 1972 <p class=MsoNormal><o:p> </o:p></p> 1695 1973 1696 <p class=MsoNormal>This is clearly a good result (R ~ <span class=GramE>0.4%</span>!) 1697 and the structure</p> 1974 <p class=MsoNormal>This is clearly a good result (R ~ 0.4%!) and the structure</p> 1698 1975 1699 1976 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1700 1977 id="Picture_x0020_23" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:288.75pt; 1701 1978 height:248.25pt;visibility:visible;mso-wrap-style:square'> 1702 <v:imagedata src="MCSA%20in%20GSAS_files/image0 54.png" o:title="" croptop="11555f"1979 <v:imagedata src="MCSA%20in%20GSAS_files/image039.png" o:title="" croptop="11555f" 1703 1980 cropbottom="16469f" cropleft="37988f" cropright="12498f"/> 1704 1981 </v:shape><![endif]--><![if !vml]><img border=0 width=385 height=331 1705 src="MCSA%20in%20GSAS_files/image0 62.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>1982 src="MCSA%20in%20GSAS_files/image040.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p> 1706 1983 1707 1984 <p class=MsoNormal><o:p> </o:p></p> 1708 1985 1709 <p class=MsoNormal> <span class=GramE>is</span>identical to the published one</p>1986 <p class=MsoNormal>is identical to the published one</p> 1710 1987 1711 1988 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1712 1989 id="Picture_x0020_24" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:288.75pt; 1713 1990 height:225.75pt;visibility:visible;mso-wrap-style:square'> 1714 <v:imagedata src="MCSA%20in%20GSAS_files/image0 56.png" o:title="" croptop="14378f"1991 <v:imagedata src="MCSA%20in%20GSAS_files/image041.png" o:title="" croptop="14378f" 1715 1992 cropbottom="21852f" cropleft="3509f" cropright="49103f"/> 1716 1993 </v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301 1717 src="MCSA%20in%20GSAS_files/image0 63.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>1718 1719 <p class=MsoNormal> <span class=GramE>as</span>drawn by the Mercury program </p>1994 src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p> 1995 1996 <p class=MsoNormal>as drawn by the Mercury program </p> 1720 1997 1721 1998 <p class=MsoNormal>(<a 1722 1999 href="https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx">https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx</a>). 1723 2000 To save this solution to the <b style='mso-bidi-font-weight:normal'><span 1724 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2001 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1725 2002 mso-hansi-theme-font:minor-latin'>Atoms</span></b> list do <b style='mso-bidi-font-weight: 1726 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2003 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1727 2004 minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA/Move MC/SA solution</span></b>; 1728 2005 the drawing will show the new atom positions</p> … … 1731 2008 id="Picture_x0020_25" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:4in; 1732 2009 height:243.75pt;visibility:visible;mso-wrap-style:square'> 1733 <v:imagedata src="MCSA%20in%20GSAS_files/image0 64.png" o:title="" croptop="12581f"2010 <v:imagedata src="MCSA%20in%20GSAS_files/image043.png" o:title="" croptop="12581f" 1734 2011 cropbottom="15938f" cropleft="37111f" cropright="13377f"/> 1735 2012 </v:shape><![endif]--><![if !vml]><img border=0 width=384 height=325 1736 src="MCSA%20in%20GSAS_files/image0 65.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>2013 src="MCSA%20in%20GSAS_files/image044.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p> 1737 2014 1738 2015 <p class=MsoNormal>And they will be listed in the Atoms table.</p> … … 1741 2018 id="Picture_x0020_26" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt; 1742 2019 height:225pt;visibility:visible;mso-wrap-style:square'> 1743 <v:imagedata src="MCSA%20in%20GSAS_files/image0 66.png" o:title=""/>2020 <v:imagedata src="MCSA%20in%20GSAS_files/image045.png" o:title=""/> 1744 2021 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300 1745 src="MCSA%20in%20GSAS_files/image067.gif" v:shapes="Picture_x0020_26"><![endif]></span></p> 1746 1747 <p class=MsoNormal>It is now ready for <span class=SpellE>Rietveld</span> 1748 refinement; this needs to use the rigid body as the data will not support 1749 independent atom position refinement.</p> 1750 1751 <h2><span class=GramE>Step 8.</span> Initial <span class=SpellE>Rietveld</span> 1752 refinement</h2> 2022 src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_26"><![endif]></span></p> 2023 2024 <p class=MsoNormal>It is now ready for Rietveld refinement; this needs to use 2025 the rigid body as the data will not support independent atom position 2026 refinement.</p> 2027 2028 <h2>Step 8. Initial Rietveld refinement</h2> 1753 2029 1754 2030 <p class=MsoNormal>After a few simple steps the 3-aminoquinoline structure will 1755 be ready for the first <span class=SpellE>Rietveld</span> refinement: 1) On the 1756 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1757 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> 1758 tab uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1759 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1760 minor-latin'>Do Pawley refinement?</span></b> box, 2) check the <b 1761 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1762 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram 1763 scale factor</span></b> box in <b style='mso-bidi-font-weight:normal'><span 1764 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1765 mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and 3) zero both 1766 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1767 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b> 1768 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1769 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> 1770 and uncheck their refine boxes in <b style='mso-bidi-font-weight:normal'><span 1771 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1772 mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>. Then do <b 1773 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1774 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> 1775 from the main GSAS-II data tree window; my <span class=SpellE>R<sub>wp</sub></span> 1776 was ~9%. Next check the <b style='mso-bidi-font-weight:normal'><span 1777 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1778 mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> in the <b 1779 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1780 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> 1781 window and in the <b style='mso-bidi-font-weight:normal'><span 1782 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1783 mso-hansi-theme-font:minor-latin'>Data</span></b> window, using the <b 1784 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1785 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>uniaxial</span></b> 1786 model for <span class=SpellE>mustrain</span>, check both <span class=SpellE><b 1787 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1788 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b 1789 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1790 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span 1791 class=GramE>size</span></span></b> & <span class=SpellE><b 1792 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1793 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b></span> 2031 be ready for the first Rietveld refinement: 1) On the <b style='mso-bidi-font-weight: 2032 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2033 minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab uncheck 2034 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2035 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley 2036 refinement?</span></b> box, 2) check the <b style='mso-bidi-font-weight:normal'><span 2037 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2038 mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> box in <b 2039 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2040 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample 2041 Parameters</span></b> and 3) zero both <b style='mso-bidi-font-weight:normal'><span 2042 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2043 mso-hansi-theme-font:minor-latin'>X</span></b> & <b style='mso-bidi-font-weight: 2044 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2045 minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> and uncheck their 2046 refine boxes in <b style='mso-bidi-font-weight:normal'><span style='font-family: 2047 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2048 minor-latin'>Instrument Parameters</span></b>. Then do <b style='mso-bidi-font-weight: 2049 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2050 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from 2051 the main GSAS-II data tree window; my R<sub>wp</sub> was ~9%. Next check the <b 2052 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2053 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit 2054 cell</span></b> in the <b style='mso-bidi-font-weight:normal'><span 2055 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2056 mso-hansi-theme-font:minor-latin'>General</span></b> window and in the <b 2057 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2058 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b> 2059 window, using the <b style='mso-bidi-font-weight:normal'><span 2060 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2061 mso-hansi-theme-font:minor-latin'>uniaxial</span></b> model for mustrain, check 2062 both <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2063 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst. size</span></b> 2064 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2065 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b> 1794 2066 boxes and do another <b style='mso-bidi-font-weight:normal'><span 1795 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1796 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I got an <span 1797 class=SpellE>R<sub>wp</sub></span> ~8.5% for this. Weve not refined atom 1798 positions or thermal parameters; to do this we need to describe the structure 1799 as a rigid body.</p> 1800 1801 <h2><span class=GramE>Step 9.</span> Rigid body model</h2> 2067 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2068 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I got an R<sub>wp</sub> 2069 ~8.5% for this. Weve not refined atom positions or thermal parameters; to do 2070 this we need to describe the structure as a rigid body.</p> 2071 2072 <h2>Step 9. Rigid body model</h2> 1802 2073 1803 2074 <p class=MsoNormal>The rigid body itself has already been defined; it was used 1804 2075 for the MC/SA structure solution. Now we have to place it in the unit cell 1805 2076 matching the atom positions obtained from the MC/SA runs. First go to the <b 1806 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2077 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1807 2078 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> 1808 2079 tab and change the <b style='mso-bidi-font-weight:normal'><span 1809 style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;2080 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1810 2081 mso-hansi-theme-font:minor-latin'>Style</span></b> to <b style='mso-bidi-font-weight: 1811 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2082 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1812 2083 minor-latin;mso-hansi-theme-font:minor-latin'>balls & sticks</span></b> and 1813 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2084 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1814 2085 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Label</span></b> 1815 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2086 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1816 2087 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>name</span></b>. 1817 2088 Double click on the column headings and select the item from the popup control. 1818 2089 Next go to the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1819 "Calibri", "sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:2090 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1820 2091 minor-latin'>RB Models</span></b> tab; it will be empty. Do <b 1821 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2092 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1822 2093 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assign 1823 2094 atoms to rigid body</span></b>; then select <b style='mso-bidi-font-weight: 1824 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2095 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1825 2096 minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b> in the <b 1826 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2097 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1827 2098 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select rigid 1828 2099 body model</span></b> pull down (the only choice). The <b style='mso-bidi-font-weight: 1829 normal'><span style='font-family:"Calibri", "sans-serif";mso-ascii-theme-font:2100 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1830 2101 minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window will 1831 2102 show</p> … … 1834 2105 id="Picture_x0020_27" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:337.5pt; 1835 2106 height:218.25pt;visibility:visible;mso-wrap-style:square'> 1836 <v:imagedata src="MCSA%20in%20GSAS_files/image0 68.png" o:title=""/>2107 <v:imagedata src="MCSA%20in%20GSAS_files/image047.png" o:title=""/> 1837 2108 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=291 1838 src="MCSA%20in%20GSAS_files/image0 69.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>2109 src="MCSA%20in%20GSAS_files/image048.gif" v:shapes="Picture_x0020_27"><![endif]></span></p> 1839 2110 1840 2111 <p class=MsoNormal><o:p> </o:p></p> … … 1842 2113 <p class=MsoNormal>You will orient the rigid body against the atoms by matching 1843 2114 up the 3 reference atoms in the rigid body (C1, C2 & C5) to the 1844 corresponding atoms in the structure (C(2), C(3) & C(6)). Do <span1845 class=GramE>these in order</span>; the drawing will show the shift of molecular 1846 origin and then its reorientation as the three atoms are selected. Press <span 1847 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:1848 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1849 minor-latin'>Ready</span></b></span> when done; the structure will be drawn 1850 with yellow bonds indicating that it is now a rigid body and not independent 1851 atoms. The <b style='mso-bidi-font-weight:normal'><span style='font-family: 1852 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1853 minor-latin'>RB Models</span></b> window shows the newrigid body</p>2115 corresponding atoms in the structure (C(2), C(3) & C(6)). Do these in 2116 order; the drawing will show the shift of molecular origin and then its 2117 reorientation as the three atoms are selected. Press <b style='mso-bidi-font-weight: 2118 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2119 minor-latin;mso-hansi-theme-font:minor-latin'>Ready</span></b> when done; the 2120 structure will be drawn with yellow bonds indicating that it is now a rigid 2121 body and not independent atoms. The <b style='mso-bidi-font-weight:normal'><span 2122 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2123 mso-hansi-theme-font:minor-latin'>RB Models</span></b> window shows the new 2124 rigid body</p> 1854 2125 1855 2126 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1856 2127 id="Picture_x0020_29" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:474.75pt; 1857 2128 height:210pt;visibility:visible;mso-wrap-style:square'> 1858 <v:imagedata src="MCSA%20in%20GSAS_files/image0 70.png" o:title=""/>2129 <v:imagedata src="MCSA%20in%20GSAS_files/image049.png" o:title=""/> 1859 2130 </v:shape><![endif]--><![if !vml]><img border=0 width=633 height=280 1860 src="MCSA%20in%20GSAS_files/image0 71.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>2131 src="MCSA%20in%20GSAS_files/image050.gif" v:shapes="Picture_x0020_29"><![endif]></span></p> 1861 2132 1862 2133 <p class=MsoNormal>To refine the rigid body parameters check the <b 1863 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri", "sans-serif";2134 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1864 2135 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b> 1865 <span class=GramE>box</span>, select <b style='mso-bidi-font-weight:normal'><span 1866 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1867 mso-hansi-theme-font:minor-latin'>AV</span></b> from the pull down, choose <span 1868 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1869 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1870 minor-latin'>Uiso</span></b></span> from the thermal parameter model and check 1871 its <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1872 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b> 1873 <span class=GramE>box</span>. Then do <b style='mso-bidi-font-weight:normal'><span 1874 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1875 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; after a couple 1876 of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span> ~7.9% and 1877 the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span 1878 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1879 mso-hansi-theme-font:minor-latin'>RBModels</span></b></span> window shows the 1880 new parameters</p> 2136 box, select <b style='mso-bidi-font-weight:normal'><span style='font-family: 2137 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2138 minor-latin'>AV</span></b> from the pull down, choose <b style='mso-bidi-font-weight: 2139 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 2140 minor-latin;mso-hansi-theme-font:minor-latin'>Uiso</span></b> from the thermal 2141 parameter model and check its <b style='mso-bidi-font-weight:normal'><span 2142 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 2143 mso-hansi-theme-font:minor-latin'>Refine?</span></b> box. Then do <b 2144 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2145 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; 2146 after a couple of refinement runs I got an R<sub>wp</sub> ~7.9% and the <b 2147 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2148 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>RBModels</span></b> 2149 window shows the new parameters</p> 1881 2150 1882 2151 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1883 2152 id="Picture_x0020_32" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:474.75pt; 1884 2153 height:225.75pt;visibility:visible;mso-wrap-style:square'> 1885 <v:imagedata src="MCSA%20in%20GSAS_files/image0 73.png" o:title=""/>2154 <v:imagedata src="MCSA%20in%20GSAS_files/image051.png" o:title=""/> 1886 2155 </v:shape><![endif]--><![if !vml]><img border=0 width=633 height=301 1887 src="MCSA%20in%20GSAS_files/image0 75.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>1888 1889 <p class=MsoNormal> <span class=GramE>and</span>the profile shows the fit</p>2156 src="MCSA%20in%20GSAS_files/image052.gif" v:shapes="Picture_x0020_32"><![endif]></span></p> 2157 2158 <p class=MsoNormal>and the profile shows the fit</p> 1890 2159 1891 2160 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1892 2161 id="Picture_x0020_31" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt; 1893 2162 height:450pt;visibility:visible;mso-wrap-style:square'> 1894 <v:imagedata src="MCSA%20in%20GSAS_files/image0 74.png" o:title=""/>2163 <v:imagedata src="MCSA%20in%20GSAS_files/image053.png" o:title=""/> 1895 2164 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1896 src="MCSA%20in%20GSAS_files/image0 81.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>2165 src="MCSA%20in%20GSAS_files/image054.gif" v:shapes="Picture_x0020_31"><![endif]></span></p> 1897 2166 1898 2167 <p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline. 1899 2168 Next is a more complex case involving some internal degrees of freedom in the 1900 molecule of a-d- <span class=GramE>lactose.</span></p>2169 molecule of a-d-lactose.</p> 1901 2170 1902 2171 </div>
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