Changeset 1293 for trunk/help/gsasII.html
- Timestamp:
- Apr 21, 2014 3:15:08 PM (9 years ago)
- File:
-
- 1 edited
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trunk/help/gsasII.html (modified) (231 diffs)
Legend:
- Unmodified
- Added
- Removed
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trunk/help/gsasII.html
r1258 r1293 1 <html xmlns:v="urn:schemas-microsoft-com:vml"1 <html xmlns:v="urn:schemas-microsoft-com:vml" 2 2 xmlns:o="urn:schemas-microsoft-com:office:office" 3 3 xmlns:w="urn:schemas-microsoft-com:office:word" 4 4 xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" 5 xmlns ="http://www.w3.org/TR/REC-html40">5 xmlns:mv="http://macVmlSchemaUri" xmlns="http://www.w3.org/TR/REC-html40"> 6 6 7 7 <head> 8 <meta http-equiv=Content-Type content="text/html; charset=us-ascii"> 8 <meta name=Title content="Help for GSAS-II"> 9 <meta name=Keywords content=""> 10 <meta http-equiv=Content-Type content="text/html; charset=unicode"> 9 11 <meta name=ProgId content=Word.Document> 10 12 <meta name=Generator content="Microsoft Word 14"> … … 24 26 <o:DocumentProperties> 25 27 <o:Author>Von Dreele</o:Author> 26 <o:LastAuthor> Von Dreele</o:LastAuthor>27 <o:Revision>13 5</o:Revision>28 <o:TotalTime>39 79</o:TotalTime>28 <o:LastAuthor>B Toby</o:LastAuthor> 29 <o:Revision>136</o:Revision> 30 <o:TotalTime>3982</o:TotalTime> 29 31 <o:Created>2011-11-28T16:49:00Z</o:Created> 30 <o:LastSaved>2014-0 3-20T17:00:00Z</o:LastSaved>31 <o:Pages>2 7</o:Pages>32 <o:Words>108 04</o:Words>33 <o:Characters>61 589</o:Characters>32 <o:LastSaved>2014-04-21T20:12:00Z</o:LastSaved> 33 <o:Pages>28</o:Pages> 34 <o:Words>10818</o:Words> 35 <o:Characters>61668</o:Characters> 34 36 <o:Company>Argonne National Laboratory</o:Company> 35 37 <o:Lines>513</o:Lines> 36 38 <o:Paragraphs>144</o:Paragraphs> 37 <o:CharactersWithSpaces>72 249</o:CharactersWithSpaces>38 <o:Version>14.0 0</o:Version>39 <o:CharactersWithSpaces>72342</o:CharactersWithSpaces> 40 <o:Version>14.0</o:Version> 39 41 </o:DocumentProperties> 42 <o:OfficeDocumentSettings> 43 <o:AllowPNG/> 44 </o:OfficeDocumentSettings> 40 45 </xml><![endif]--> 41 <link rel=dataStoreItem href="gsasII_files/item0010.xml" 42 target="gsasII_files/props011.xml"> 43 <link rel=themeData href="gsasII_files/themedata.thmx"> 44 <link rel=colorSchemeMapping href="gsasII_files/colorschememapping.xml"> 46 <link rel=themeData href="gsasII_files/themedata.xml"> 45 47 <!--[if gte mso 9]><xml> 46 48 <w:WordDocument> 47 49 <w:View>Print</w:View> 50 <w:Zoom>140</w:Zoom> 48 51 <w:SpellingState>Clean</w:SpellingState> 49 52 <w:GrammarState>Clean</w:GrammarState> … … 71 74 <w:CachedColBalance/> 72 75 </w:Compatibility> 73 <w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel>74 76 <m:mathPr> 75 77 <m:mathFont m:val="Cambria Math"/> … … 84 86 <m:intLim m:val="subSup"/> 85 87 <m:naryLim m:val="undOvr"/> 86 </m:mathPr></w:WordDocument> 88 </m:mathPr> <w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel> 89 </w:WordDocument> 87 90 </xml><![endif]--><!--[if gte mso 9]><xml> 88 91 <w:LatentStyles DefLockedState="false" DefUnhideWhenUsed="true" 89 92 DefSemiHidden="true" DefQFormat="false" DefPriority="99" 90 LatentStyleCount="2 67">93 LatentStyleCount="276"> 91 94 <w:LsdException Locked="false" Priority="0" SemiHidden="false" 92 95 UnhideWhenUsed="false" QFormat="true" Name="Normal"/> … … 347 350 <!-- 348 351 /* Font Definitions */ 349 @font-face 352 @font-face 353 {font-family:"Courier New"; 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1445 1463 mso-ansi-font-size:12.0pt; 1446 font-family:"Times New Roman" ,"serif";1464 font-family:"Times New Roman"; 1447 1465 mso-ansi-font-weight:normal; 1448 1466 mso-ansi-font-style:normal;} … … 1793 1811 text-indent:-.25in; 1794 1812 mso-ansi-font-size:12.0pt; 1795 font-family:"Times New Roman" ,"serif";1813 font-family:"Times New Roman"; 1796 1814 mso-ansi-font-weight:normal; 1797 1815 mso-ansi-font-style:normal;} … … 2229 2247 <style> 2230 2248 /* Style Definitions */ 2231 2249 table.MsoNormalTable 2232 2250 {mso-style-name:"Table Normal"; 2233 2251 mso-tstyle-rowband-size:0; … … 2241 2259 mso-pagination:widow-orphan; 2242 2260 font-size:10.0pt; 2243 font-family:"Times New Roman" ,"serif";}2261 font-family:"Times New Roman";} 2244 2262 </style> 2245 2263 <![endif]--> 2246 <link href=gsasIIfav.png rel="SHORTCUT ICON"> 2264 <link href="file://localhost/Users/toby/software/G2/GSASII/help/gsasIIfav.png" 2265 rel="SHORTCUT ICON"> 2247 2266 <!--[if gte mso 9]><xml> 2248 <o:shapedefaults v:ext="edit" spidmax="10 27"/>2267 <o:shapedefaults v:ext="edit" spidmax="1030"/> 2249 2268 </xml><![endif]--><!--[if gte mso 9]><xml> 2250 2269 <o:shapelayout v:ext="edit"> … … 2279 2298 </v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1026" type="#_x0000_t75" 2280 2299 alt="Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: GSAS-II logo" 2281 style='position:absolute;margin-left: 44.8pt;margin-top:0;width:96pt;height:96pt;2300 style='position:absolute;margin-left:89.6pt;margin-top:0;width:96pt;height:96pt; 2282 2301 z-index:251657728;visibility:visible;mso-wrap-style:square; 2283 2302 mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:0; … … 2287 2306 mso-width-percent:0;mso-height-percent:0;mso-width-relative:page; 2288 2307 mso-height-relative:page' o:allowoverlap="f"> 2289 <v:imagedata src="gsas2logo.png"/> 2290 <w:wrap type="square" anchory="line"/> 2291 </v:shape><![endif]--><![if !vml]><img width=128 height=128 src=gsas2logo.png 2308 <v:imagedata src="help/BHT3%20HD:Users:toby:software:G2:GSASII:help:gsas2logo.png"/> 2309 <w:wrap type="square"/> 2310 </v:shape><![endif]--><![if !vml]><img width=98 height=98 2311 src="help/BHT3%20HD:Users:toby:software:G2:GSASII:help:gsas2logo.png" 2292 2312 align=right 2293 2313 alt="Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: GSAS-II logo" … … 2309 2329 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The 2310 2330 routines and classes used within GSAS-II are documented in a set of <a 2311 href=".. /sphinxdocs/build/html/index.html">web pages</a> and in a <a2312 href=".. /sphinxdocs/build/latex/GSASIIdoc.pdf">PDF document</a>. This2331 href="..:sphinxdocs:build:html:index.html">web pages</a> and in a <a 2332 href="..:sphinxdocs:build:latex:GSASIIdoc.pdf">PDF document</a>. This 2313 2333 documentation is created from the Python source code files using Sphinx. </span></p> 2314 2334 … … 2317 2337 <h2><a name=Tutorials><strong>GSAS-II tutorials</strong></a><strong>:<o:p></o:p></strong></h2> 2318 2338 2319 <p class=MsoNormal><strong><a href="Starting%2 0GSAS.htm"><span2339 <p class=MsoNormal><strong><a href="Starting%2520GSAS.htm"><span 2320 2340 style='font-weight:normal'>Starting GSAS-II</span></a><o:p></o:p></strong></p> 2321 2341 2322 <p class=MsoNormal><strong><a href="Fit%2 0Peaks.htm"><span style='font-weight:2342 <p class=MsoNormal><strong><a href="Fit%2520Peaks.htm"><span style='font-weight: 2323 2343 normal'>Powder pattern peak picking, fitting and indexing</span></a><o:p></o:p></strong></p> 2324 2344 2325 <p class=MsoNormal><strong><a href="Laboratory%2 0X.htm"><span style='font-weight:2326 normal'>Lab X-ray powder pattern Rietveld refinement</span></a><o:p></o:p></strong></p>2327 2328 <p class=MsoNormal><strong><a href="Neutron%2 0CW%20Powder%20Data.htm"><span2345 <p class=MsoNormal><strong><a href="Laboratory%2520X.htm"><span 2346 style='font-weight:normal'>Lab X-ray powder pattern Rietveld refinement</span></a><o:p></o:p></strong></p> 2347 2348 <p class=MsoNormal><strong><a href="Neutron%2520CW%2520Powder%2520Data.htm"><span 2329 2349 style='font-weight:normal'>CW Neutron powder pattern Rietveld refinement with 2330 2350 constraints</span></a><o:p></o:p></strong></p> 2331 2351 2332 <p class=MsoNormal><strong><a href="Combined%2 0refinement.htm"><span2352 <p class=MsoNormal><strong><a href="Combined%2520refinement.htm"><span 2333 2353 style='font-weight:normal'>Combined neutron x-ray Rietveld refinement and 2334 2354 Fourier maps</span></a><o:p></o:p></strong></p> 2335 2355 2336 2356 <p class=MsoNormal><strong><a 2337 href="Calibration%2 0of%20an%20area%20detector%20in%20GSAS.htm"><span2357 href="Calibration%2520of%2520an%2520area%2520detector%2520in%2520GSAS.htm"><span 2338 2358 style='font-weight:normal'>2-D Image calibration</span></a><o:p></o:p></strong></p> 2339 2359 2340 2360 <p class=MsoNormal><strong><a 2341 href="Integration%2 0of%20area%20detector%20data%20in%20GSAS.htm"><span2361 href="Integration%2520of%2520area%2520detector%2520data%2520in%2520GSAS.htm"><span 2342 2362 style='font-weight:normal'>2-D Image integration</span></a><o:p></o:p></strong></p> 2343 2363 2344 2364 <p class=MsoNormal><strong><a 2345 href="Strain%2 0fitting%20of%202D%20data%20in%20GSAS-II.htm"><span2365 href="Strain%2520fitting%2520of%25202D%2520data%2520in%2520GSAS-II.htm"><span 2346 2366 style='font-weight:normal'>2-D Strain data fitting</span></a><o:p></o:p></strong></p> 2347 2367 2368 <p class=MsoNormal><strong><a href="SequentialTutorial.htm"><span 2369 style='font-weight:normal'>Sequential refinement</span></a><o:p></o:p></strong></p> 2370 2371 <p class=MsoNormal><strong><o:p> </o:p></strong></p> 2372 2348 2373 <p class=MsoNormal><strong>Synchrotron X-ray powder pattern Rietveld refinement<o:p></o:p></strong></p> 2349 2374 2350 2375 <p class=MsoNormal><strong><span style='font-weight:normal'>Charge flipping 2351 structure solution</span> – <a href="Charge%20Flipping%20in%20GSAS.htm"><span2376 structure solution</span> – <a href="Charge%2520Flipping%2520in%2520GSAS.htm"><span 2352 2377 class=SpellE><span style='font-weight:normal'>jadarite</span></span></a> & <a 2353 href="Charge%2 0Flipping%20-%20sucrose.htm"><span style='font-weight:normal'>sucrose</span></a><o:p></o:p></strong></p>2378 href="Charge%2520Flipping%2520-%2520sucrose.htm"><span style='font-weight:normal'>sucrose</span></a><o:p></o:p></strong></p> 2354 2379 2355 2380 <p class=MsoNormal><strong><span style='font-weight:normal;mso-bidi-font-weight: 2356 bold'><a href="Small%2 0Angle%20Size%20Distribution.htm"><span style='mso-bidi-font-weight:2357 normal'>Small angle X-ray data size distribution</span></a><o:p></o:p></span></strong></p>2381 bold'><a href="Small%2520Angle%2520Size%2520Distribution.htm"><span 2382 style='mso-bidi-font-weight:normal'>Small angle X-ray data size distribution</span></a><o:p></o:p></span></strong></p> 2358 2383 2359 2384 <p class=MsoNormal><strong><o:p> </o:p></strong></p> … … 2382 2407 Clicking on any item in the tree opens a window where information in that item 2383 2408 can be viewed or edited. For example, the <a href="#Sample_Parameters">"Sample 2384 Parameters"</a> item under a ‘PWDR’ entry contains information2385 about how data were collected, such as the sample temperature <a 2386 href="#Sample_Parameters">(see below)</a>. The arrow keys (up & down) move2387 the selection to successive entries in the data tree; both the data window and 2388 the associated plot (if any)will change.<o:p></o:p></span></p>2409 Parameters"</a> item under a ‘PWDR’ entry contains information about how 2410 data were collected, such as the sample temperature <a href="#Sample_Parameters">(see 2411 below)</a>. The arrow keys (up & down) move the selection to successive 2412 entries in the data tree; both the data window and the associated plot (if any) 2413 will change.<o:p></o:p></span></p> 2389 2414 2390 2415 <h4><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h4> … … 2396 2421 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l14 level1 lfo1'><![if !supportLists]><span 2397 2422 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 2398 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu2399 ‘<b style='mso-bidi-font-weight:normal'>File</b>’ –</p>2423 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu 2424 ‘<b style='mso-bidi-font-weight:normal'>File</b>’ – </p> 2400 2425 2401 2426 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2402 2427 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2403 2428 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 2404 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2405 style='mso-bidi-font-weight:normal'>Open project …</b> - Open a previously2406 saved GSAS-II project file (name.gpx). If you currently have a project file 2407 open, you are asked if it is OK to over write it; Cancel will cancel the 2408 process. <bstyle='mso-bidi-font-weight:normal'>NB</b>: you may open a backup <span2429 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2430 style='mso-bidi-font-weight:normal'>Open project…</b> - Open a previously saved 2431 GSAS-II project file (name.gpx). If you currently have a project file open, you 2432 are asked if it is OK to over write it; Cancel will cancel the process. <b 2433 style='mso-bidi-font-weight:normal'>NB</b>: you may open a backup <span 2409 2434 class=SpellE>gpx</span> file (e.g. name.bak3.gpx) to recover a previous version 2410 of your project. Remember to <b style='mso-bidi-font-weight:normal'>Save As</b> …2435 of your project. Remember to <b style='mso-bidi-font-weight:normal'>Save As</b>… 2411 2436 to e.g. name.gpx to overwrite the current version. Otherwise you will get 2412 2437 backups of your backup file (e.g. name.bak3.bak0.gpx, etc.).</p> … … 2415 2440 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2416 2441 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 2417 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2418 style='mso-bidi-font-weight:normal'>Save project</b> –Save the current2419 project. If a file name is shown after ‘Loaded Data:’ in the data2420 tree<span style='mso-fareast-font-family:"Times New Roman"'>, it will be saved 2421 there. Otherwise, you will be prompted for a new name in a file dialog (you may 2422 changedirectory as well). If the file exists, you will be asked if it OK to2442 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2443 style='mso-bidi-font-weight:normal'>Save project</b> – Save the current 2444 project. If a file name is shown after ‘Loaded Data:’ in the data tree<span 2445 style='mso-fareast-font-family:"Times New Roman"'>, it will be saved there. 2446 Otherwise, you will be prompted for a new name in a file dialog (you may change 2447 directory as well). If the file exists, you will be asked if it OK to 2423 2448 overwrite.</span></p> 2424 2449 … … 2426 2451 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2427 2452 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 2428 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2453 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2429 2454 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Save 2430 As …</span></b><span style='mso-fareast-font-family:"Times New Roman"'> -2431 Save the current project to a new file. A file dialog will be shown to enter 2432 the name (and change directory if desired). If the file exists, you will be 2433 askedif it OK to overwrite.</span></p>2455 As…</span></b><span style='mso-fareast-font-family:"Times New Roman"'> - Save 2456 the current project to a new file. A file dialog will be shown to enter the 2457 name (and change directory if desired). If the file exists, you will be asked 2458 if it OK to overwrite.</span></p> 2434 2459 2435 2460 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2436 2461 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2437 2462 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 2438 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2463 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2439 2464 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Close 2440 project</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 2441 – Close the current project; you will be asked if you want to save it 2442 first.</span></p> 2465 project</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 2466 Close the current project; you will be asked if you want to save it first.</span></p> 2443 2467 2444 2468 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2445 2469 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2446 2470 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span 2447 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2471 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2448 2472 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Exit</span></b><span 2449 style='mso-fareast-font-family:"Times New Roman"'> – Exit the GSAS-II2450 program; if there is a current project you will be asked if you want to save it 2451 first. Pressing the red X in the upper right (Windows) also exits (no save 2452 option)GSAS-II; useful for escaping from GSAS-II if needed.</span></p>2473 style='mso-fareast-font-family:"Times New Roman"'> – Exit the GSAS-II program; 2474 if there is a current project you will be asked if you want to save it first. 2475 Pressing the red X in the upper right (Windows) also exits (no save option) 2476 GSAS-II; useful for escaping from GSAS-II if needed.</span></p> 2453 2477 2454 2478 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l14 level1 lfo1'><![if !supportLists]><b 2455 2479 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 2456 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 2480 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 2457 2481 </span></span></span></b><![endif]><b style='mso-bidi-font-weight:normal'>Menu 2458 ‘Data’ –<o:p></o:p></b></p>2482 ‘Data’ – <o:p></o:p></b></p> 2459 2483 2460 2484 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2461 2485 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2462 2486 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 2463 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2464 style='mso-bidi-font-weight:normal'>Read image data … - </b>Read in 2-D2465 powder diffraction images (multiple patterns can be selected). GSAS-II can read 2466 many different image file formats including MAR345 files, Quantum ADSC files, 2467 and tiff files from Perkin-Elmer, Pilatus, and GE. Although many of these 2468 formats have data fields that should contain relevant information for the2469 exposure (e.g. wavelength), these are rarely filled in correctly by the data 2470 acquisition software. Thus, you should have separately noted this information 2471 as it will beneeded</p>2487 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2488 style='mso-bidi-font-weight:normal'>Read image data… - </b>Read in 2-D powder 2489 diffraction images (multiple patterns can be selected). GSAS-II can read many 2490 different image file formats including MAR345 files, Quantum ADSC files, and 2491 tiff files from Perkin-Elmer, Pilatus, and GE. Although many of these formats 2492 have data fields that should contain relevant information for the exposure 2493 (e.g. wavelength), these are rarely filled in correctly by the data acquisition 2494 software. Thus, you should have separately noted this information as it will be 2495 needed</p> 2472 2496 2473 2497 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2474 2498 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2475 2499 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 2476 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2477 style='mso-bidi-font-weight:normal'>Read Powder Pattern Peaks …</b> - Read2478 in a list of powder pattern peak positions as either a d-spacing table or a set 2479 of 2<span style='font-family:Symbol'>Q</span> positions; these can be used in 2480 GSAS-IIpowder pattern indexing. </p>2500 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2501 style='mso-bidi-font-weight:normal'>Read Powder Pattern Peaks…</b> - Read in a 2502 list of powder pattern peak positions as either a d-spacing table or a set of 2<span 2503 style='font-family:Symbol'>Q</span> positions; these can be used in GSAS-II 2504 powder pattern indexing. </p> 2481 2505 2482 2506 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2483 2507 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2484 2508 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 2485 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2486 style='mso-bidi-font-weight:normal'>Sum powder data</b> –Form the sum of2509 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2510 style='mso-bidi-font-weight:normal'>Sum powder data</b> – Form the sum of 2487 2511 previously read powder patterns; each with a multiplier. Can be used to 2488 2512 accumulate data, subtract background or empty container patterns, etc. Patterns … … 2493 2517 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2494 2518 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 2495 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2496 style='mso-bidi-font-weight:normal'>Sum image data</b> –Form the sum of2519 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2520 style='mso-bidi-font-weight:normal'>Sum image data</b> – Form the sum of 2497 2521 previously read 2-D images; each with a multiplier. Can be used to accumulate 2498 2522 data, subtract background or empty container patterns, etc. Images used to form … … 2503 2527 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2504 2528 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span 2505 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2506 style='mso-bidi-font-weight:normal'>Add phase</b> – This begins the2507 creation of a new phase in the data tree (under Phases). You are first prompted 2508 in a dialog box for a name to be assigned to the new phase. Then the <b 2509 style='mso-bidi-font-weight:normal'><a href="#General">General</a></b> tab is 2510 opened for this phase; you should first select the phase type, enter the space 2511 group symbol and then lattice parameters. Note that nonstandard space group 2512 symbols are permitted; there must be spaces between the axial fields (e.g. use 2513 ‘P n a 21’ not ‘Pna21’).</p>2529 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2530 style='mso-bidi-font-weight:normal'>Add phase</b> – This begins the creation of 2531 a new phase in the data tree (under Phases). You are first prompted in a dialog 2532 box for a name to be assigned to the new phase. Then the <b style='mso-bidi-font-weight: 2533 normal'><a href="#General">General</a></b> tab is opened for this phase; you 2534 should first select the phase type, enter the space group symbol and then 2535 lattice parameters. Note that nonstandard space group symbols are permitted; 2536 there must be spaces between the axial fields (e.g. use ‘P n a 21’ not 2537 ‘Pna21’).</p> 2514 2538 2515 2539 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2516 2540 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2517 2541 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span 2518 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2519 style='mso-bidi-font-weight:normal'>Delete phase</b> – This will remove a2520 phase from the data tree. A dialog box will present the list of phases; pick 2521 one (ormore) to delete.</p>2542 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2543 style='mso-bidi-font-weight:normal'>Delete phase</b> – This will remove a phase 2544 from the data tree. A dialog box will present the list of phases; pick one (or 2545 more) to delete.</p> 2522 2546 2523 2547 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2524 2548 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2525 2549 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span 2526 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2527 style='mso-bidi-font-weight:normal'>Rename data</b> –This might be a bad2528 idea!! Don ’t use this unless the data to be renamed has not been used2529 anywherein GSAS-II, e.g. only rename freshly read data.</p>2550 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2551 style='mso-bidi-font-weight:normal'>Rename data</b> – This might be a bad 2552 idea!! Don’t use this unless the data to be renamed has not been used anywhere 2553 in GSAS-II, e.g. only rename freshly read data.</p> 2530 2554 2531 2555 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2532 2556 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2533 2557 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span 2534 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2535 style='mso-bidi-font-weight:normal'>Delete data</b> – This will remove an2536 itemfrom the data tree. A dialog box with a list of choices is presented.</p>2558 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2559 style='mso-bidi-font-weight:normal'>Delete data</b> – This will remove an item 2560 from the data tree. A dialog box with a list of choices is presented.</p> 2537 2561 2538 2562 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l14 level1 lfo1'><![if !supportLists]><span 2539 2563 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 2540 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu2541 ‘<b style='mso-bidi-font-weight:normal'>Calculate</b>’ –</p>2564 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu 2565 ‘<b style='mso-bidi-font-weight:normal'>Calculate</b>’ – </p> 2542 2566 2543 2567 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2544 2568 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2545 2569 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 2546 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2547 style='mso-bidi-font-weight:normal'>Make new PDFs</b> – This creates the2548 pair distribution function (PDF) controls for each powder pattern selected in 2549 the dialog box. See <b style='mso-bidi-font-weight:normal'><span 2550 style='color:#4F81BD;mso-themecolor:accent1'><a href="#PDF_Controls">PDF 2551 Controls</a></span></b> for furtherdirections.</p>2570 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2571 style='mso-bidi-font-weight:normal'>Make new PDFs</b> – This creates the pair distribution 2572 function (PDF) controls for each powder pattern selected in the dialog box. See 2573 <b style='mso-bidi-font-weight:normal'><span style='color:#4F81BD;mso-themecolor: 2574 accent1'><a href="#PDF_Controls">PDF Controls</a></span></b> for further 2575 directions.</p> 2552 2576 2553 2577 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2554 2578 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2555 2579 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 2556 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2580 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2557 2581 style='mso-bidi-font-weight:normal'>View LS <span class=SpellE>parms</span></b> 2558 – This shows a dialog box with all the parameters for your project; those 2559 to be refined are flagged ‘True’, otherwise ‘False’. 2560 Blanks indicate parameters that are not <span class=SpellE>refinable</span>. 2561 The total number of refined parameters is also shown at the top of the list. 2562 The value of each parameter is also given. The parameter names are of the form 2563 ‘p<span class=GramE>:h:name:id’</span> where ‘p’ is the 2564 phase index, ‘h’ is the histogram index and ‘id’ is the 2565 item index (if needed). Indexes all begin with ‘0’ (zero). Note 2566 that for atom positions the value is not a <span class=SpellE>refinable</span> 2567 parameter, but the shift in the value is. Position names are, e.g. ‘0:<span 2568 class=GramE>:Ax:0’</span> for the x-position of the <span class=SpellE>zeroth</span> 2569 atom in the <span class=SpellE>zeroth</span> phase while shift names have a 2570 ‘d’ in then, e.g. ‘0::dAx:0’. Press the window exit 2582 – This shows a dialog box with all the parameters for your project; those to be 2583 refined are flagged ‘True’, otherwise ‘False’. Blanks indicate parameters that 2584 are not refinable. The total number of refined parameters is also shown at the 2585 top of the list. The value of each parameter is also given. The parameter names 2586 are of the form ‘p<span class=GramE>:h:name:id’</span> where ‘p’ is the phase 2587 index, ‘h’ is the histogram index and ‘id’ is the item index (if needed). 2588 Indexes all begin with ‘0’ (zero). Note that for atom positions the value is 2589 not a refinable parameter, but the shift in the value is. Position names are, 2590 e.g. ‘0<span class=GramE>::</span>Ax:0’ for the x-position of the <span 2591 class=SpellE>zeroth</span> atom in the <span class=SpellE>zeroth</span> phase 2592 while shift names have a ‘d’ in then, e.g. ‘0::dAx:0’. Press the window exit 2571 2593 button to exit this dialog box.</p> 2572 2594 … … 2574 2596 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2575 2597 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 2576 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2577 style='mso-bidi-font-weight:normal'>Refine</b> – This performs the2578 refinement (Pawley/Rietveld or single crystal) according to the controls set in 2579 the <b style='mso-bidi-font-weight:normal'><a href="#Controls">Controls</a></b> 2580 datatree item.</p>2598 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2599 style='mso-bidi-font-weight:normal'>Refine</b> – This performs the refinement 2600 (Pawley/Rietveld or single crystal) according to the controls set in the <b 2601 style='mso-bidi-font-weight:normal'><a href="#Controls">Controls</a></b> data 2602 tree item.</p> 2581 2603 2582 2604 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2583 2605 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2584 2606 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 2585 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2586 style='mso-bidi-font-weight:normal'>Sequential refine</b> –This starts a2607 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2608 style='mso-bidi-font-weight:normal'>Sequential refine</b> – This starts a 2587 2609 sequential refinement with the data sets selected in the <b style='mso-bidi-font-weight: 2588 2610 normal'><a href="#Controls">Controls</a></b> data tree item.</p> … … 2590 2612 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l14 level1 lfo1'><![if !supportLists]><span 2591 2613 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 2592 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu2593 ‘<b style='mso-bidi-font-weight:normal'>Import</b>’ – A sub 2594 menu appears with choices for import of data. Each entry when selected with the 2595 mouse shows further submenus with specific imports that are available. Any of these 2596 filescan be accessed from a zip file.</p>2614 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu 2615 ‘<b style='mso-bidi-font-weight:normal'>Import</b>’ – A sub menu appears with 2616 choices for import of data. Each entry when selected with the mouse shows 2617 further submenus with specific imports that are available. Any of these files 2618 can be accessed from a zip file.</p> 2597 2619 2598 2620 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2599 2621 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2600 2622 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 2601 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2623 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2602 2624 style='mso-bidi-font-weight:normal'>Phase - </b></p> 2603 2625 … … 2605 2627 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><span 2606 2628 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 2607 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span2629 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2608 2630 class=GramE><b style='mso-bidi-font-weight:normal'>from</b></span><b 2609 2631 style='mso-bidi-font-weight:normal'> GSAS .EXP file - </b>This reads one phase … … 2619 2641 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><span 2620 2642 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 2621 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span2643 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2622 2644 class=GramE><b style='mso-bidi-font-weight:normal'>from</b></span><b 2623 style='mso-bidi-font-weight:normal'> PDB file</b> - This reads the 2624 macromolecular phase information from a Protein Data Base file (name.PDB or 2625 name.ENT). The file name is found in a directory dialog; you can change 2626 directories as needed. Only .PDB (or .<span class=SpellE>pdb</span>) or .ENT 2627 (or .<span class=SpellE>ent</span>) file names are shown. Be careful that the 2628 space group symbol on the ‘CRYST1’ record in the PDB file follows2629 the GSAS-II conventions (e.g. with spaces between axial fields). A dialog box 2630 is shown with the proposed phase name. Youcan change it if desired.</p>2645 style='mso-bidi-font-weight:normal'> PDB file</b> - This reads the macromolecular 2646 phase information from a Protein Data Base file (name.PDB or name.ENT). The 2647 file name is found in a directory dialog; you can change directories as needed. 2648 Only .PDB (or .<span class=SpellE>pdb</span>) or .ENT (or .<span class=SpellE>ent</span>) 2649 file names are shown. Be careful that the space group symbol on the ‘CRYST1’ 2650 record in the PDB file follows the GSAS-II conventions (e.g. with spaces 2651 between axial fields). A dialog box is shown with the proposed phase name. You 2652 can change it if desired.</p> 2631 2653 2632 2654 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 2633 2655 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><span 2634 2656 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 2635 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span2657 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2636 2658 class=GramE><b style='mso-bidi-font-weight:normal'>from</b></span><b 2637 2659 style='mso-bidi-font-weight:normal'> CIF file</b> This reads one phase from a … … 2648 2670 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><span 2649 2671 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 2650 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span2672 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2651 2673 class=GramE><b style='mso-bidi-font-weight:normal'>from</b></span><b 2652 2674 style='mso-bidi-font-weight:normal'> GSAS-II <span class=SpellE>gpx</span> file</b> … … 2663 2685 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><span 2664 2686 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span 2665 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span2687 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2666 2688 class=GramE><b style='mso-bidi-font-weight:normal'>guess</b></span><b 2667 2689 style='mso-bidi-font-weight:normal'> format from file </b>This attempts to read … … 2671 2693 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><b 2672 2694 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 2673 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 2695 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 2674 2696 </span></span></span></b><![endif]><b style='mso-bidi-font-weight:normal'>Powder 2675 Data </b> – results are<b style='mso-bidi-font-weight:normal'> </b>placed2676 in the GSAS-II<b style='mso-bidi-font-weight:normal'> </b>data tree as 2677 ‘PWDR file name’.<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>2697 Data </b>– results are<b style='mso-bidi-font-weight:normal'> </b>placed in the 2698 GSAS-II<b style='mso-bidi-font-weight:normal'> </b>data tree as ‘PWDR file 2699 name’.<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p> 2678 2700 2679 2701 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 2680 2702 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><b 2681 2703 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 2682 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 2704 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 2683 2705 </span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight: 2684 2706 normal'>from</b></span><b style='mso-bidi-font-weight:normal'> CIF file </b>This … … 2686 2708 class=SpellE>name.CIF</span>). The file name is found in a directory dialog; 2687 2709 you can change directories as needed. Only .CIF (or .<span class=SpellE>cif</span>) 2688 file names are <span class=GramE>shown.;</span> only one can be chosen. If you2710 file names are shown<span class=GramE>.;</span> only one can be chosen. If you 2689 2711 want more than one, redo the <b style='mso-bidi-font-weight:normal'>Import/Powder 2690 2712 Data/from CIF</b> <b style='mso-bidi-font-weight:normal'>file</b> command. <b … … 2694 2716 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><b 2695 2717 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 2696 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 2718 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 2697 2719 </span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight: 2698 2720 normal'>from</b></span><b style='mso-bidi-font-weight:normal'> GSAS-II <span … … 2707 2729 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><b 2708 2730 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 2709 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 2731 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 2710 2732 </span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight: 2711 2733 normal'>from</b></span><b style='mso-bidi-font-weight:normal'> GSAS file </b>This 2712 2734 reads powder patterns (histograms) from the defined GSAS format powder data 2713 2735 files. GSAS file types STD, ESD, FXY and FXYE are recognized. Neutron TOF data 2714 with a ‘TIME-MAP’ are also recognized. The file names are found in2715 a directory dialog; you can change directories as needed. If the selected files 2716 have morethan one powder pattern, a dialog is shown with the choices. <b2736 with a ‘TIME-MAP’ are also recognized. The file names are found in a directory 2737 dialog; you can change directories as needed. If the selected files have more 2738 than one powder pattern, a dialog is shown with the choices. <b 2717 2739 style='mso-bidi-font-weight:normal'><o:p></o:p></b></p> 2718 2740 … … 2720 2742 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><b 2721 2743 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 2722 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 2744 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 2723 2745 </span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight: 2724 2746 normal'>from</b></span><b style='mso-bidi-font-weight:normal'> <span … … 2733 2755 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><span 2734 2756 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span 2735 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span2757 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2736 2758 class=GramE><b style='mso-bidi-font-weight:normal'>guess</b></span><b 2737 2759 style='mso-bidi-font-weight:normal'> format from file </b>This attempts to read … … 2742 2764 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><b 2743 2765 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 2744 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 2766 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 2745 2767 </span></span></span></b><![endif]><b style='mso-bidi-font-weight:normal'>Structure 2746 Factor – </b>– results are<b style='mso-bidi-font-weight:normal'> </b>placed2747 in the GSAS-II<b style='mso-bidi-font-weight:normal'> </b>data tree as 2748 ‘HKLF file name’.<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>2768 Factor – </b>– results are<b style='mso-bidi-font-weight:normal'> </b>placed in 2769 the GSAS-II<b style='mso-bidi-font-weight:normal'> </b>data tree as ‘HKLF file 2770 name’.<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p> 2749 2771 2750 2772 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 2751 2773 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><b 2752 2774 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 2753 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 2775 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 2754 2776 </span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight: 2755 2777 normal'>from</b></span><b style='mso-bidi-font-weight:normal'> F**2 HKL file </b>This … … 2763 2785 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><b 2764 2786 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 2765 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 2787 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 2766 2788 </span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight: 2767 2789 normal'>from</b></span><b style='mso-bidi-font-weight:normal'> F HKL file</b> … … 2775 2797 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><b 2776 2798 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 2777 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 2799 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 2778 2800 </span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight: 2779 2801 normal'>from</b></span><b style='mso-bidi-font-weight:normal'> CIF file</b> … … 2787 2809 auto;text-indent:-.25in;mso-list:l14 level3 lfo1;tab-stops:list 1.5in'><![if !supportLists]><b 2788 2810 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 2789 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 2811 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 2790 2812 </span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight: 2791 2813 normal'>guess</b></span><b style='mso-bidi-font-weight:normal'> format from … … 2797 2819 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l14 level1 lfo1'><![if !supportLists]><span 2798 2820 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span 2799 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu2800 ‘<b style='mso-bidi-font-weight:normal'>Export</b>’ –</p>2821 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu 2822 ‘<b style='mso-bidi-font-weight:normal'>Export</b>’ –</p> 2801 2823 2802 2824 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2803 2825 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2804 2826 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 2805 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2806 style='mso-bidi-font-weight:normal'>Export Powder Patterns …</b> - not yet2827 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2828 style='mso-bidi-font-weight:normal'>Export Powder Patterns…</b> - not yet 2807 2829 implemented</p> 2808 2830 … … 2810 2832 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2811 2833 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 2812 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2813 style='mso-bidi-font-weight:normal'>Export All Peak <span class=GramE>Lists</span>…</b>2814 - This writes the contents of the Peak List for all PWDR data onto a simple2815 text file. There will be a heading for each PWDR GSAS-II tree item and columns 2816 of values forposition, intensity, sigma and gamma follow.</p>2834 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2835 style='mso-bidi-font-weight:normal'>Export All Peak Lists…</b> - This writes 2836 the contents of the Peak List for all PWDR data onto a simple text file. There 2837 will be a heading for each PWDR GSAS-II tree item and columns of values for 2838 position, intensity, sigma and gamma follow.</p> 2817 2839 2818 2840 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2819 2841 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2820 2842 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 2821 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2822 style='mso-bidi-font-weight:normal'>Export HKLs…</b> - not yet 2823 implemented</p> 2843 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2844 style='mso-bidi-font-weight:normal'>Export HKLs…</b> - not yet implemented</p> 2824 2845 2825 2846 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2826 2847 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2827 2848 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 2828 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2829 style='mso-bidi-font-weight:normal'>Export PDF …</b> - This writes two2830 simple text files name.gr and <span class=SpellE>name.sq</span> containing g(r) 2831 and s(q), respectively as 2 columns of data; a header on each indicated the2832 source file name and the column headings. The name comes from the PDF entry in 2833 theGSAS-II data tree.</p>2849 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2850 style='mso-bidi-font-weight:normal'>Export PDF…</b> - This writes two simple 2851 text files name.gr and <span class=SpellE>name.sq</span> containing g(r) and 2852 s(q), respectively as 2 columns of data; a header on each indicated the source 2853 file name and the column headings. The name comes from the PDF entry in the 2854 GSAS-II data tree.</p> 2834 2855 2835 2856 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2836 2857 auto;text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2837 2858 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span 2838 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2839 style='mso-bidi-font-weight:normal'>Export Phase…</b> - not yet 2840 implemented</p> 2859 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2860 style='mso-bidi-font-weight:normal'>Export Phase…</b> - not yet implemented</p> 2841 2861 2842 2862 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; 2843 2863 text-indent:-.25in;mso-list:l14 level2 lfo1'><![if !supportLists]><span 2844 2864 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span 2845 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b2846 style='mso-bidi-font-weight:normal'>Export CIF …</b> - not yet implemented</p>2865 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2866 style='mso-bidi-font-weight:normal'>Export CIF…</b> - not yet implemented</p> 2847 2867 2848 2868 <div class=MsoNormal align=center style='text-align:center'><span … … 2898 2918 J. <span class=GramE>More (Argonne National Laboratory, 1980).</span> The 2899 2919 python/numpy version was developed by us based on the material in Numerical 2900 Recipes (Press, Flannery, <span class=SpellE> <span class=GramE>Teulosky</span></span>2901 & <spanclass=SpellE>Vetterling</span>) for the <span class=SpellE>Levenberg</span>-Marquardt2920 Recipes (Press, Flannery, <span class=SpellE>Teulosky</span> & <span 2921 class=SpellE>Vetterling</span>) for the <span class=SpellE>Levenberg</span>-Marquardt 2902 2922 algorithm and is the default.<span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> 2903 2923 … … 2906 2926 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l18 level1 lfo2'><![if !supportLists]><span 2907 2927 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 2908 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span2928 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2909 2929 style='mso-fareast-font-family:"Times New Roman"'>Select whether the refinement 2910 uses ‘analytic <span class=SpellE>Jacobian</span>’, ‘analytic 2911 Hessian’ or ‘numeric’ derivatives. The last is slower and 2912 perhaps a bit less accurate, but may be needed if the analytic functions are 2913 not fully developed. The <span class=SpellE>Jacobian</span> matrix is shaped N 2914 x M (parameters x observations) and is much larger than the Hessian matrix 2915 which is shaped M x M (parameters x parameters). Generally use ‘analytic 2916 Hessian’ for routine work.<o:p></o:p></span></p> 2930 uses ‘analytic <span class=SpellE>Jacobian</span>’, ‘analytic Hessian’ or 2931 ‘numeric’ derivatives. The last is slower and perhaps a bit less accurate, but 2932 may be needed if the analytic functions are not fully developed. The <span 2933 class=SpellE>Jacobian</span> matrix is shaped N x M (parameters x observations) 2934 and is much larger than the Hessian matrix which is shaped M x M (parameters x 2935 parameters). Generally use ‘analytic Hessian’ for routine work.<o:p></o:p></span></p> 2917 2936 2918 2937 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l18 level1 lfo2'><![if !supportLists]><span 2919 2938 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 2920 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span2921 style='mso-fareast-font-family:"Times New Roman"'>Select ‘Min delta-M/M’2922 forconvergence; the refinement will stop when the change in the minimization2939 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2940 style='mso-fareast-font-family:"Times New Roman"'>Select ‘Min delta-M/M’ for 2941 convergence; the refinement will stop when the change in the minimization 2923 2942 function is less than this value. Set Min delta-M/M = 1.0 to force just a 2924 2943 single cycle to be performed. A value less than 10<sup>-4</sup> (the default) … … 2927 2946 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l18 level1 lfo2'><![if !supportLists]><span 2928 2947 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 2929 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2930 style='mso-fareast-font-family:"Times New Roman"'>If ‘analytic 2931 Jacobean’ is chosen then select ‘Initial shift factor’ for 2932 the first cycle of refinement. This value is modified by the least squares 2933 routine. The allowed range is 10<sup>-5</sup> to 100. Smaller values may be 2934 needed if your initial <span class=GramE>refinement</span> trials immediately 2935 diverge, however make sure your starting parameter values are 2936 ‘reasonable’. The selected default (=1.0) normally gives good 2937 performance.<o:p></o:p></span></p> 2948 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2949 style='mso-fareast-font-family:"Times New Roman"'>If ‘analytic Jacobean’ is 2950 chosen then select ‘Initial shift factor’ for the first cycle of refinement. 2951 This value is modified by the least squares routine. The allowed range is 10<sup>-5</sup> 2952 to 100. Smaller values may be needed if your initial refinement trials 2953 immediately diverge, however make sure your starting parameter values are 2954 ‘reasonable’. The selected default (=1.0) normally gives good performance.<o:p></o:p></span></p> 2938 2955 2939 2956 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l18 level1 lfo2'><![if !supportLists]><span 2940 2957 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 2941 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span2942 style='mso-fareast-font-family:"Times New Roman"'>If ‘analytic2943 Hessian’ is chosen then select ‘Max cycles’, the maximum number 2944 of least squares cycles to be performed. Least squares cycles are determined by 2945 the number of times a newHessian matrix is computes; the <span class=SpellE>Levenberg</span>-Marquardt2958 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2959 style='mso-fareast-font-family:"Times New Roman"'>If ‘analytic Hessian’ is 2960 chosen then select ‘Max cycles’, the maximum number of least squares cycles to 2961 be performed. Least squares cycles are determined by the number of times a new 2962 Hessian matrix is computes; the <span class=SpellE>Levenberg</span>-Marquardt 2946 2963 algorithm may compute the function several times between cycles as it finds the 2947 2964 optimal value of the Marquardt coefficient. Choices are given in the pull down … … 2950 2967 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l18 level1 lfo2'><![if !supportLists]><span 2951 2968 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span 2952 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span2969 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2953 2970 style='mso-fareast-font-family:"Times New Roman"'>Select data for sequential 2954 refinement; the data sets may be done in ‘reverse order’. <o:p></o:p></span></p>2971 refinement; the data sets may be done in ‘reverse order’. <o:p></o:p></span></p> 2955 2972 2956 2973 <h4>Covariance<span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4> 2957 2974 2958 2975 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This 2959 window contains final residual information; the GSASII Plots window ‘<a2960 href="#Covariance">Covariance ’</a> shows a graphical representation of2961 thevariance-covariance matrix <o:p></o:p></span></p>2976 window contains final residual information; the GSASII Plots window ‘<a 2977 href="#Covariance">Covariance’</a> shows a graphical representation of the 2978 variance-covariance matrix <o:p></o:p></span></p> 2962 2979 2963 2980 <h4><a name=Constraints><span style='mso-fareast-font-family:"Times New Roman"'>Constraints<o:p></o:p></span></a></h4> … … 2967 2984 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This 2968 2985 window shows the constraints to be used in a refinement. It is organized into 2969 three tabbed pages. ‘Phase constraints’ contain those involving 2970 parameters that describe aspects of the crystalline phases to be used in the 2971 refinement (e.g. atom coordinates, thermal motion and site fraction 2972 parameters). ‘Histogram/Phase constraints’ are those which describe 2973 aspects of the pattern that depend on both the phase and the data set used in 2974 the refinement (e.g. </span><span style='font-family:Symbol;mso-fareast-font-family: 2975 "Times New Roman"'>m</span><span style='mso-fareast-font-family:"Times New Roman"'>strain 2976 and crystallite size parameters). ‘Histogram constraints’ are those 2977 that depend only on the data set (e.g. profile coefficients U<span class=GramE>,V,W,X</span> 2978 and Y).<o:p></o:p></span></p> 2986 three tabbed pages. ‘Phase constraints’ contain those involving parameters that 2987 describe aspects of the crystalline phases to be used in the refinement (e.g. 2988 atom coordinates, thermal motion and site fraction parameters). 2989 ‘Histogram/Phase constraints’ are those which describe aspects of the pattern 2990 that depend on both the phase and the data set used in the refinement (e.g. </span><span 2991 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>m</span><span 2992 style='mso-fareast-font-family:"Times New Roman"'>strain and crystallite size 2993 parameters). ‘Histogram constraints’ are those that depend only on the data set 2994 (e.g. profile coefficients U<span class=GramE>,V,W,X</span> and Y).<o:p></o:p></span></p> 2979 2995 2980 2996 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5> … … 2982 2998 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l21 level1 lfo3'><![if !supportLists]><span 2983 2999 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 2984 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3000 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2985 3001 style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the 2986 3002 parameter types you wish to constrain. Each will have the same possibilities in 2987 the ‘<b style='mso-bidi-font-weight:normal'>Edit’</b> menu.<o:p></o:p></span></p>3003 the ‘<b style='mso-bidi-font-weight:normal'>Edit’</b> menu.<o:p></o:p></span></p> 2988 3004 2989 3005 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l21 level1 lfo3'><![if !supportLists]><span 2990 3006 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 2991 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span2992 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b2993 style='mso-bidi-font-weight:normal'>Edit</b>’ –<o:p></o:p></span></p>3007 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3008 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight: 3009 normal'>Edit</b>’ – <o:p></o:p></span></p> 2994 3010 2995 3011 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2996 3012 auto;text-indent:-.25in;mso-list:l21 level2 lfo3'><![if !supportLists]><span 2997 3013 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 2998 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2999 class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family: 3000 "Times New Roman"'>Add</span></b></span><b style='mso-bidi-font-weight:normal'><span 3001 style='mso-fareast-font-family:"Times New Roman"'> Hold</span></b><span 3002 style='mso-fareast-font-family:"Times New Roman"'> – select a parameter 3003 that you wish to remain fixed although other parameters of the same type may be 3004 selected as a group for refinement. For example, if the space group for a phase 3005 has a polar axis (e.g. the b-axis in P2<sub>1</sub>), then one atom y-parameter 3006 is arbitrary and should be selected for a Hold to keep the structure from 3007 drifting up or down the y-axis during refinement. If selected, a dialog box 3008 will appear showing the list of available parameters; select one and then OK to 3009 implement it, Cancel will cancel the operation. The held parameter will be 3010 shown in the constraint window with the keyword ‘FIXED’. A Delete 3011 button can be used to remove it.<o:p></o:p></span></p> 3014 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3015 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add 3016 Hold</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 3017 select a parameter that you wish to remain fixed although other parameters of 3018 the same type may be selected as a group for refinement. For example, if the 3019 space group for a phase has a polar axis (e.g. the b-axis in P2<sub>1</sub>), 3020 then one atom y-parameter is arbitrary and should be selected for a Hold to 3021 keep the structure from drifting up or down the y-axis during refinement. If 3022 selected, a dialog box will appear showing the list of available parameters; 3023 select one and then OK to implement it, Cancel will cancel the operation. The 3024 held parameter will be shown in the constraint window with the keyword ‘FIXED’. 3025 A Delete button can be used to remove it.<o:p></o:p></span></p> 3012 3026 3013 3027 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3014 3028 auto;text-indent:-.25in;mso-list:l21 level2 lfo3'><![if !supportLists]><span 3015 3029 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 3016 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3030 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3017 3031 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add 3018 3032 equivalence</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 3019 – select a list of parameters that should have the same value (possibly 3020 with a non-unitary multiplier for some). Examples are a list of atoms with the3021 same thermal motion <span class=SpellE>Uiso</span>, sets of profile coefficients 3022 U<span class=GramE>,V,W</span> across multiple data sets. If selected, a dialog 3023 box will appear with a list of the available parameters. Select one and press 3024 OK; asecond dialog box will appear with only those parameters that can be made3033 – select a list of parameters that should have the same value (possibly with a 3034 non-unitary multiplier for some). Examples are a list of atoms with the same 3035 thermal motion <span class=SpellE>Uiso</span>, sets of profile coefficients U<span 3036 class=GramE>,V,W</span> across multiple data sets. If selected, a dialog box will 3037 appear with a list of the available parameters. Select one and press OK; a 3038 second dialog box will appear with only those parameters that can be made 3025 3039 equivalent to the first one. Choose those and press OK. Cancel in either dialog 3026 3040 will cancel the operation. The equivalenced parameters will show as an equation 3027 3041 of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0; usually 3028 M1=1.0 and M2=-1.0, but can be changed via the ‘Edit’ button. The3029 keyword ‘EQUIV’ marks it as <span class=GramE>an equivalence</span>. 3030 A Delete buttoncan be used to remove it.<o:p></o:p></span></p>3042 M1=1.0 and M2=-1.0, but can be changed via the ‘Edit’ button. The keyword 3043 ‘EQUIV’ marks it as <span class=GramE>an equivalence</span>. A Delete button 3044 can be used to remove it.<o:p></o:p></span></p> 3031 3045 3032 3046 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3033 3047 auto;text-indent:-.25in;mso-list:l21 level2 lfo3'><![if !supportLists]><span 3034 3048 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 3035 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3049 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3036 3050 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add 3037 constraint</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 3038 – select a list of parameters whose sum (with possible non-unitary 3039 multipliers) is fixed. For example, the sum of site fractions for atoms on the 3040 same site could be fixed to unity. If selected, a dialog box will appear with a 3041 list of the available parameters. Select one and press OK; a second dialog box 3042 will appear with only those parameters that can be used in a constraint with 3043 the first one. Choose those and press OK. Cancel in either dialog will cancel 3044 the operation. The equivalenced parameters will show as an equation of the form 3045 M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+…=C; the 3046 multipliers M1, <span class=GramE>M2, …</span> and C can be changed via 3047 the ‘Edit’ button. The keyword ‘CONSTR’ marks it as a 3048 constraint. A Delete button can be used to remove it.<o:p></o:p></span></p> 3051 constraint</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 3052 select a list of parameters whose sum (with possible non-unitary multipliers) 3053 is fixed. For example, the sum of site fractions for atoms on the same site 3054 could be fixed to unity. If selected, a dialog box will appear with a list of 3055 the available parameters. Select one and press OK; a second dialog box will 3056 appear with only those parameters that can be used in a constraint with the 3057 first one. Choose those and press OK. Cancel in either dialog will cancel the 3058 operation. The equivalenced parameters will show as an equation of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+…=C; 3059 the multipliers M1, M2, … and C can be changed via the ‘Edit’ button. The 3060 keyword ‘CONSTR’ marks it as a constraint. A Delete button can be used to 3061 remove it.<o:p></o:p></span></p> 3049 3062 3050 3063 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; 3051 3064 text-indent:-.25in;mso-list:l21 level2 lfo3'><![if !supportLists]><span 3052 3065 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 3053 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3066 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3054 3067 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add 3055 function</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 3056 – this is very similar the “Add constraint” type except that 3057 the result of the sum can be varied in the refinement. The keyword 3058 ‘FUNCT’ marks it as a function; the ‘Refine?’ box 3059 indicates your choice to refine the result of the sum. A Delete button can be 3060 used to remove it.<o:p></o:p></span></p> 3068 function</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 3069 this is very similar the “Add constraint” type except that the result of the 3070 sum can be varied in the refinement. The keyword ‘FUNCT’ marks it as a 3071 function; the ‘Refine?’ box indicates your choice to refine the result of the 3072 sum. A Delete button can be used to remove it.<o:p></o:p></span></p> 3061 3073 3062 3074 <h4><a name=Restraints><span style='mso-fareast-font-family:"Times New Roman"'>Restraints</span></a><span … … 3067 3079 several tabbed pages, one page for each type of restraint. Restraints are 3068 3080 developed for an individual phase and act as additional observations to be 3069 “fitted”during the refinement.<o:p></o:p></span></p>3081 “fitted” during the refinement.<o:p></o:p></span></p> 3070 3082 3071 3083 <h5 style='tab-stops:125.25pt'><span style='mso-fareast-font-family:"Times New Roman"'>What 3072 can I do here?<span style='mso-tab-count:1'> </span><o:p></o:p></span></h5>3084 can I do here?<span style='mso-tab-count:1'> </span><o:p></o:p></span></h5> 3073 3085 3074 3086 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l12 level1 lfo4'><![if !supportLists]><span 3075 3087 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 3076 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3088 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3077 3089 style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the 3078 restraint type you wish to use. Each will have the same possibilities in the 3079 ‘<b style='mso-bidi-font-weight:normal'>Edit’</b> menu.<o:p></o:p></span></p>3090 restraint type you wish to use. Each will have the same possibilities in the ‘<b 3091 style='mso-bidi-font-weight:normal'>Edit’</b> menu.<o:p></o:p></span></p> 3080 3092 3081 3093 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l12 level1 lfo4'><![if !supportLists]><span 3082 3094 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 3083 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3095 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3084 3096 style='mso-fareast-font-family:"Times New Roman"'>You can change the <b 3085 style='mso-bidi-font-weight:normal'>Restraint weight factor</b> – this is3086 used to scale the weights for the entire set of restraints of this type. 3087 Defaultvalue for the weight factor is 1.0.<o:p></o:p></span></p>3097 style='mso-bidi-font-weight:normal'>Restraint weight factor</b> – this is used 3098 to scale the weights for the entire set of restraints of this type. Default 3099 value for the weight factor is 1.0.<o:p></o:p></span></p> 3088 3100 3089 3101 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l12 level1 lfo4'><![if !supportLists]><span 3090 3102 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 3091 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3103 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3092 3104 style='mso-fareast-font-family:"Times New Roman"'>You can choose to use or not 3093 3105 use the restraints in subsequent refinements. Default is to use the restraints.<o:p></o:p></span></p> … … 3095 3107 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l12 level1 lfo4'><![if !supportLists]><span 3096 3108 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 3097 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3098 style='mso-fareast-font-family:"Times New Roman"'>You can change the search range3099 used to find the bonds/angles that meet your criteria for restraint.<o:p></o:p></span></p>3109 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3110 style='mso-fareast-font-family:"Times New Roman"'>You can change the search 3111 range used to find the bonds/angles that meet your criteria for restraint.<o:p></o:p></span></p> 3100 3112 3101 3113 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l12 level1 lfo4'><![if !supportLists]><span 3102 3114 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span 3103 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3115 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3104 3116 style='mso-fareast-font-family:"Times New Roman"'>You can examine the table of 3105 3117 restraints and change individual values; grayed out regions cannot be changed. 3106 The ‘<span class=SpellE>calc</span>’ values are determined from the3107 atom positions in your structure, ‘<span class=SpellE>obs</span>’ 3108 values are the target values for the restraint and ‘<span class=SpellE>esd</span>’ 3109 is the uncertainty used to weight the restraint in the refinement (multiplied 3110 by theweight factor).<o:p></o:p></span></p>3118 The ‘<span class=SpellE>calc</span>’ values are determined from the atom 3119 positions in your structure, ‘<span class=SpellE>obs</span>’ values are the 3120 target values for the restraint and ‘<span class=SpellE>esd</span>’ is the 3121 uncertainty used to weight the restraint in the refinement (multiplied by the 3122 weight factor).<o:p></o:p></span></p> 3111 3123 3112 3124 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l12 level1 lfo4'><![if !supportLists]><span 3113 3125 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span 3114 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3115 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b3116 style='mso-bidi-font-weight:normal'>Edit</b>’ – some entries may be 3117 grayed out if not appropriate for yourphase or for the selected restraint.<o:p></o:p></span></p>3126 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3127 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight: 3128 normal'>Edit</b>’ – some entries may be grayed out if not appropriate for your 3129 phase or for the selected restraint.<o:p></o:p></span></p> 3118 3130 3119 3131 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3120 3132 auto;text-indent:-.25in;mso-list:l12 level2 lfo4'><![if !supportLists]><span 3121 3133 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 3122 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3134 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3123 3135 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select 3124 phase</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 3125 – active if there is more than one phase in your project. A dialog box 3126 willappear with a list of the phases, select the one you want for restraint3136 phase</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 3137 active if there is more than one phase in your project. A dialog box will 3138 appear with a list of the phases, select the one you want for restraint 3127 3139 development.<o:p></o:p></span></p> 3128 3140 … … 3130 3142 auto;text-indent:-.25in;mso-list:l12 level2 lfo4'><![if !supportLists]><span 3131 3143 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 3132 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3144 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3133 3145 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add 3134 restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 3135 – this takes you through a sequence of dialog boxes which ask for the 3136 identities of the atoms involved in the restraint and the value to be assigned 3137 to the restraint. The <span class=SpellE>esd</span> is given a default value 3138 which canbe changed after the restraints are created.<o:p></o:p></span></p>3146 restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 3147 this takes you through a sequence of dialog boxes which ask for the identities 3148 of the atoms involved in the restraint and the value to be assigned to the 3149 restraint. The <span class=SpellE>esd</span> is given a default value which can 3150 be changed after the restraints are created.<o:p></o:p></span></p> 3139 3151 3140 3152 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3141 3153 auto;text-indent:-.25in;mso-list:l12 level2 lfo4'><![if !supportLists]><span 3142 3154 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 3143 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3155 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3144 3156 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add 3145 3157 residue restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 3146 – if the phase is a ‘macromolecule’ then develop the 3147 restraints from a selected ‘macro’ file based on those used in GSAS 3148 for this purpose. A file dialog box is shown directed to /<span class=SpellE>GSASIImacros</span>; 3149 be sure to selectthe correct file.<o:p></o:p></span></p>3158 – if the phase is a ‘macromolecule’ then develop the restraints from a selected 3159 ‘macro’ file based on those used in GSAS for this purpose. A file dialog box is 3160 shown directed to /<span class=SpellE>GSASIImacros</span>; be sure to select 3161 the correct file.<o:p></o:p></span></p> 3150 3162 3151 3163 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3152 3164 auto;text-indent:-.25in;mso-list:l12 level2 lfo4'><![if !supportLists]><span 3153 3165 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 3154 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3166 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3155 3167 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Plot 3156 3168 residue restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 3157 – if the phase is a ‘macromolecule’ and the restraint type is 3158 either ‘<b style='mso-bidi-font-weight:normal'>Torsion restraints</b>’ 3159 or ‘<spanclass=SpellE><b style='mso-bidi-font-weight:normal'>Ramachandran</b></span><b3160 style='mso-bidi-font-weight:normal'> restraints</b> ’, then a plot will be3161 madeof the restraint distribution; torsions as 1-D plots of angle vs. <span3169 – if the phase is a ‘macromolecule’ and the restraint type is either ‘<b 3170 style='mso-bidi-font-weight:normal'>Torsion restraints</b>’ or ‘<span 3171 class=SpellE><b style='mso-bidi-font-weight:normal'>Ramachandran</b></span><b 3172 style='mso-bidi-font-weight:normal'> restraints</b>’, then a plot will be made 3173 of the restraint distribution; torsions as 1-D plots of angle vs. <span 3162 3174 class=SpellE>pseudopotential</span> energy and <span class=SpellE>Ramachandran</span> 3163 3175 ones as 2-D plot of psi <span class=SpellE>vs</span> phi. In each case a dialog … … 3166 3178 variety of high resolution protein structures and those found (red dots) for 3167 3179 your structure. The restraints are based on a <span class=SpellE>pseudopotential</span> 3168 (red curve or contours –favorable values at the peaks) which has been3180 (red curve or contours – favorable values at the peaks) which has been 3169 3181 developed from the observed distributions for each residue type.<o:p></o:p></span></p> 3170 3182 … … 3172 3184 auto;text-indent:-.25in;mso-list:l12 level2 lfo4'><![if !supportLists]><span 3173 3185 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span 3174 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3186 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3175 3187 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Change 3176 value</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 3177 – this changes the ‘<span class=SpellE>obsd</span>’ value for 3178 selected restraints; adialog box will appear asking for the new value. <o:p></o:p></span></p>3188 value</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – this 3189 changes the ‘<span class=SpellE>obsd</span>’ value for selected restraints; a 3190 dialog box will appear asking for the new value. <o:p></o:p></span></p> 3179 3191 3180 3192 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3181 3193 auto;text-indent:-.25in;mso-list:l12 level2 lfo4'><![if !supportLists]><span 3182 3194 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span 3183 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3195 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3184 3196 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Change 3185 3197 <span class=SpellE>esd</span></span></b><span style='mso-fareast-font-family: 3186 "Times New Roman"'> – this changes the ‘<span class=SpellE>esd</span>’ 3187 value for selected restraints; a dialog box will appear asking for the new 3188 value.<o:p></o:p></span></p> 3198 "Times New Roman"'> – this changes the ‘<span class=SpellE>esd</span>’ value 3199 for selected restraints; a dialog box will appear asking for the new value.<o:p></o:p></span></p> 3189 3200 3190 3201 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; 3191 3202 text-indent:-.25in;mso-list:l12 level2 lfo4'><![if !supportLists]><span 3192 3203 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span 3193 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3204 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3194 3205 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Delete 3195 restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 3196 – this deletes selected restraints from the list. A single click in the 3197 blank box in the upper left corner of the table will select/deselect all 3198 restraints.<o:p></o:p></span></p> 3206 restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 3207 this deletes selected restraints from the list. A single click in the blank box 3208 in the upper left corner of the table will select/deselect all restraints.<o:p></o:p></span></p> 3199 3209 3200 3210 <h4><a name="Rigid_bodies"><span style='mso-fareast-font-family:"Times New Roman"'>Rigid … … 3205 3215 <p class=MsoNormal>This window shows the rigid body models that have been 3206 3216 entered into GSAS-II for this project. There are two tabs; one is for vector 3207 style rigid bodies and the other is for flexible “Residue” rigid3208 bodies. Note that these rigid bodies must be inserted into one of the phases 3209 before it cantake effect in the crystal structure description.</p>3217 style rigid bodies and the other is for flexible “Residue” rigid bodies. Note 3218 that these rigid bodies must be inserted into one of the phases before it can 3219 take effect in the crystal structure description.</p> 3210 3220 3211 3221 <h5 style='tab-stops:125.25pt'><span style='mso-fareast-font-family:"Times New Roman"'>What 3212 can I do here?<span style='mso-tab-count:1'> </span><o:p></o:p></span></h5>3222 can I do here?<span style='mso-tab-count:1'> </span><o:p></o:p></span></h5> 3213 3223 3214 3224 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l25 level1 lfo5'><![if !supportLists]><span 3215 3225 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 3216 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3226 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3217 3227 style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the rigid 3218 body type you wish to use. Each will have the different possibilities in the 3219 ‘<b style='mso-bidi-font-weight:normal'>Edit’</b> menu depending on 3220 whether a rigidbody has been defined.<o:p></o:p></span></p>3228 body type you wish to use. Each will have the different possibilities in the ‘<b 3229 style='mso-bidi-font-weight:normal'>Edit’</b> menu depending on whether a rigid 3230 body has been defined.<o:p></o:p></span></p> 3221 3231 3222 3232 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l25 level1 lfo5'><![if !supportLists]><span 3223 3233 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 3224 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3225 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b3226 style='mso-bidi-font-weight:normal'>Edit</b>’ – the entries listed 3227 below depend on which type of rigid bodyis selected.<o:p></o:p></span></p>3234 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3235 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight: 3236 normal'>Edit</b>’ – the entries listed below depend on which type of rigid body 3237 is selected.<o:p></o:p></span></p> 3228 3238 3229 3239 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3230 3240 auto;text-indent:-.25in;mso-list:l25 level2 lfo5'><![if !supportLists]><b 3231 3241 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'><span 3232 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 3242 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 3233 3243 </span></span></span></b><![endif]><b style='mso-bidi-font-weight:normal'><span 3234 3244 style='mso-fareast-font-family:"Times New Roman"'>Add rigid body</span></b><span 3235 style='mso-fareast-font-family:"Times New Roman"'> – (Vector rigid bodies)3236 this creates a vector description of a rigid body. A dialog box asks the number 3237 of atoms (>2) and the number of vectors required to create the rigid body. 3238 An entry will be created showing a magnitude with the vector set to be applied 3239 foreach vector needed to develop the rigid body.<b style='mso-bidi-font-weight:3245 style='mso-fareast-font-family:"Times New Roman"'> – (Vector rigid bodies) this 3246 creates a vector description of a rigid body. A dialog box asks the number of 3247 atoms (>2) and the number of vectors required to create the rigid body. An 3248 entry will be created showing a magnitude with the vector set to be applied for 3249 each vector needed to develop the rigid body.<b style='mso-bidi-font-weight: 3240 3250 normal'><o:p></o:p></b></span></p> 3241 3251 … … 3243 3253 auto;text-indent:-.25in;mso-list:l25 level2 lfo5'><![if !supportLists]><span 3244 3254 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 3245 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3255 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3246 3256 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Import 3247 XYZ</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –3257 XYZ</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 3248 3258 (Residue rigid bodies) this reads a text file containing a set of Cartesian 3249 3259 coordinates describing a rigid body model. Each line has atom type (e.g. C, Na, … … 3253 3263 auto;text-indent:-.25in;mso-list:l25 level2 lfo5'><![if !supportLists]><span 3254 3264 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 3255 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3265 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3256 3266 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Define 3257 sequence</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 3258 – (Residue rigid bodies) this defines a variable torsion angle in a 3259 sequence of dialog boxes. The first one asks for the origin and the second asks 3260 for the pivot atom for the torsion from the nearest neighbors to the origin 3261 atom ; the atoms that ride on the selected torsion are automatically found from3262 their bondlengths.<o:p></o:p></span></p>3267 sequence</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 3268 (Residue rigid bodies) this defines a variable torsion angle in a sequence of 3269 dialog boxes. The first one asks for the origin and the second asks for the 3270 pivot atom for the torsion from the nearest neighbors to the origin atom; the 3271 atoms that ride on the selected torsion are automatically found from their bond 3272 lengths.<o:p></o:p></span></p> 3263 3273 3264 3274 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3265 3275 auto;text-indent:-.25in;mso-list:l25 level2 lfo5'><![if !supportLists]><span 3266 3276 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 3267 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3277 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3268 3278 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Import 3269 residues</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 3270 – (Residue rigid bodies) this reads a predetermined macro file that 3271 contains standard (<span class=SpellE>Engh</span> & Huber) coordinates for 3272 the amino acids found in natural proteins along with predetermined variable3273 torsion angledefinitions.<o:p></o:p></span></p>3279 residues</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 3280 (Residue rigid bodies) this reads a predetermined macro file that contains 3281 standard (<span class=SpellE>Engh</span> & Huber) coordinates for the amino 3282 acids found in natural proteins along with predetermined variable torsion angle 3283 definitions.<o:p></o:p></span></p> 3274 3284 3275 3285 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l25 level1 lfo5'><![if !supportLists]><span 3276 3286 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 3277 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3278 style='mso-fareast-font-family:"Times New Roman"'>Once a rigid body is defined 3279 you can plot it, change its name or manipulate any torsion angle to see the 3280 effecton the plot.<o:p></o:p></span></p>3287 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3288 style='mso-fareast-font-family:"Times New Roman"'>Once a rigid body is defined you 3289 can plot it, change its name or manipulate any torsion angle to see the effect 3290 on the plot.<o:p></o:p></span></p> 3281 3291 3282 3292 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l25 level1 lfo5'><![if !supportLists]><span 3283 3293 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 3284 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3294 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3285 3295 style='mso-fareast-font-family:"Times New Roman"'>The translation magnitudes in 3286 3296 a vector rigid body can be refined.<o:p></o:p></span></p> … … 3289 3299 style='mso-fareast-font-family:"Times New Roman"'> refinement results<o:p></o:p></span></h4> 3290 3300 3291 <p class=MsoNormal>In this window is tabulated the results of your sequential 3292 refinement. The columns are the parameter names; the naming convention is 3293 ‘p:h:name:n’ where ‘p’ is the phase number,’ 3294 h’ is the histogram number, ‘name’ is the parameter name, and 3295 ‘n’ (if needed) is the item number (e.g. atom number). The rows are 3296 the data sets used in the sequential refinement.</p> 3301 <p class=MsoNormal>In this window is tabulated the results of your sequential refinement. 3302 The columns are the parameter names; the naming convention is ‘p:h:name:n’ 3303 where ‘p’ is the phase number,’ h’ is the histogram number, ‘name’ is the 3304 parameter name, and ‘n’ (if needed) is the item number (e.g. atom number). The 3305 rows are the data sets used in the sequential refinement.</p> 3297 3306 3298 3307 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5> … … 3301 3310 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3302 3311 normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>1.<span 3303 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3312 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3304 3313 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Select a row</span><span 3305 3314 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3306 normal;mso-bidi-font-weight:bold'> – this will display the3307 variance-covariancematrix for the refinement with that data set.<o:p></o:p></span></h5>3315 normal;mso-bidi-font-weight:bold'> – this will display the variance-covariance 3316 matrix for the refinement with that data set.<o:p></o:p></span></h5> 3308 3317 3309 3318 <h5 style='margin-left:.75in;text-indent:-.25in;mso-list:l24 level1 lfo6'><![if !supportLists]><span 3310 3319 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3311 3320 normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>2.<span 3312 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3321 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3313 3322 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Select a 3314 3323 column</span><span style='mso-fareast-font-family:"Times New Roman";color:windowtext; 3315 font-weight:normal;mso-bidi-font-weight:bold'> – this will display a plot3316 of that parameter across the sequence of data sets. Error bars for each value3317 a re also shown.<o:p></o:p></span></h5>3324 font-weight:normal;mso-bidi-font-weight:bold'> – this will display a plot of 3325 that parameter across the sequence of data sets. Error bars for each value are 3326 also shown.<o:p></o:p></span></h5> 3318 3327 3319 3328 <h5 style='margin-left:.75in;text-indent:-.25in;mso-list:l24 level1 lfo6'><![if !supportLists]><span 3320 3329 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3321 3330 normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>3.<span 3322 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3331 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3323 3332 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3324 normal;mso-bidi-font-weight:bold'>Menu ‘</span><span style='mso-fareast-font-family:3325 "Times New Roman";color:windowtext'>File ’ – </span><span3326 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:3327 normal;mso-bidi-font-weight:bold'><o:p></o:p></span></h5>3333 normal;mso-bidi-font-weight:bold'>Menu ‘</span><span style='mso-fareast-font-family: 3334 "Times New Roman";color:windowtext'>File’ – </span><span style='mso-fareast-font-family: 3335 "Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight: 3336 bold'><o:p></o:p></span></h5> 3328 3337 3329 3338 <h5 style='margin-left:1.25in;text-indent:-.25in;mso-list:l24 level2 lfo6'><![if !supportLists]><span 3330 3339 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3331 3340 normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>a.<span 3332 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3341 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3333 3342 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Save</span><span 3334 3343 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3335 normal;mso-bidi-font-weight:bold'> – this will create a text file of3336 selected columns with values and corresponding <span class=SpellE>esds</span>. A 3337 file dialog box will appear; give a suitable file name; you may change 3338 d irectory if desired.<o:p></o:p></span></h5>3344 normal;mso-bidi-font-weight:bold'> – this will create a text file of selected 3345 columns with values and corresponding <span class=SpellE>esds</span>. A file 3346 dialog box will appear; give a suitable file name; you may change directory if 3347 desired.<o:p></o:p></span></h5> 3339 3348 3340 3349 <h3>Histograms</h3> 3341 3350 3342 <p class=MsoNormal>These are shown in the data tree with a prefix of 3343 ‘PWDR’, ’HKLF’, ‘IMG’, or ‘PDF’ 3344 and usually a file name. These constitute the data sets (‘Histograms’) 3345 to be used by GSAS-II for analysis. Selection of these items does not produce 3346 any information in the data window but does display the data in the Plots 3347 Window. They are described below.</p> 3351 <p class=MsoNormal>These are shown in the data tree with a prefix of ‘PWDR’, 3352 ’HKLF’, ‘IMG’, or ‘PDF’ and usually a file name. These constitute the data sets 3353 (‘Histograms’) to be used by GSAS-II for analysis. Selection of these items 3354 does not produce any information in the data window but does display the data 3355 in the Plots Window. They are described below.</p> 3348 3356 3349 3357 <h3><a name="PWD_Analysis"></a>Powder Histograms - PWDR</h3> 3350 3358 3351 3359 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>When 3352 a powder diffraction data set (prefix ‘PWDR’) is selected from the </span><a3360 a powder diffraction data set (prefix ‘PWDR’) is selected from the </span><a 3353 3361 href="#Data_tree"><span style='mso-fareast-font-family:"Times New Roman"'>data 3354 tree</span></a><span style='mso-fareast-font-family:"Times New Roman"'>, a 3355 variety of subcategories in the tree are shown. The items that are shown depend 3356 on thedata set type. Selecting a subcategory raises the window listed below. <o:p></o:p></span></p>3362 tree</span></a><span style='mso-fareast-font-family:"Times New Roman"'>, a variety 3363 of subcategories in the tree are shown. The items that are shown depend on the 3364 data set type. Selecting a subcategory raises the window listed below. <o:p></o:p></span></p> 3357 3365 3358 3366 <h5><a name=Comments></a><a name=""></a><span style='mso-bookmark:Comments'><span … … 3361 3369 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l26 level1 lfo7'><span 3362 3370 style='mso-bookmark:Comments'><![if !supportLists]><span style='mso-fareast-font-family: 3363 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 3371 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 3364 3372 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Menu 3365 ‘<b style='mso-bidi-font-weight:normal'>Analysis</b>’ –<o:p></o:p></span></span></p>3373 ‘<b style='mso-bidi-font-weight:normal'>Analysis</b>’ – <o:p></o:p></span></span></p> 3366 3374 3367 3375 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; 3368 3376 text-indent:-.25in;mso-list:l22 level1 lfo8'><span style='mso-bookmark:Comments'><![if !supportLists]><span 3369 3377 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 3370 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3378 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3371 3379 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Analyze</span></b></span><span 3372 3380 style='mso-bookmark:Comments'><span style='mso-fareast-font-family:"Times New Roman"'> 3373 – this produces a ‘normal probability’ plot for the 3374 refinement result as bounded by the limits. The slope and intercept of the 3375 curve in the central region (-1 < </span></span><span style='mso-bookmark: 3376 Comments'><spanstyle='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>D</span></span><span3381 – this produces a ‘normal probability’ plot for the refinement result as 3382 bounded by the limits. The slope and intercept of the curve in the central 3383 region (-1 < </span></span><span style='mso-bookmark:Comments'><span 3384 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>D</span></span><span 3377 3385 style='mso-bookmark:Comments'><span style='mso-fareast-font-family:"Times New Roman"'>/</span></span><span 3378 3386 style='mso-bookmark:Comments'><span style='font-family:Symbol;mso-fareast-font-family: … … 3385 3393 3386 3394 <p class=MsoNormal><span style='mso-bookmark:Comments'>This window shows 3387 whatever comment lines (preceded by “#”) found when the powder data3388 file was read by GSAS-II. If you are lucky, there will be useful information 3389 here (e.g. sample name, date collected, wavelength used, etc.). If not, this 3390 window willbe blank. The text is read-only.</span></p>3395 whatever comment lines (preceded by “#”) found when the powder data file was 3396 read by GSAS-II. If you are lucky, there will be useful information here (e.g. 3397 sample name, date collected, wavelength used, etc.). If not, this window will 3398 be blank. The text is read-only.</span></p> 3391 3399 3392 3400 <span style='mso-bookmark:Comments'></span> … … 3397 3405 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This 3398 3406 window shows the limits in position to be used in any fitting for this powder 3399 pattern. The ‘original’ values are obtained from the minimum & 3400 maximum values in the powder pattern. You can modify ‘changed’ as 3401 needed.<o:p></o:p></span></p> 3407 pattern. The ‘original’ values are obtained from the minimum & maximum 3408 values in the powder pattern. You can modify ‘changed’ as needed.<o:p></o:p></span></p> 3402 3409 3403 3410 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5> … … 3405 3412 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l5 level1 lfo9'><![if !supportLists]><span 3406 3413 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 3407 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3414 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3408 3415 style='mso-fareast-font-family:"Times New Roman"'>You can change <span 3409 class=SpellE>Tmin</span> and <span class=SpellE>Tmax</span> in the 3410 ‘changed’ row as needed. Use the mouse to select the value to be 3411 changed (the background on the box will be blue or have a black border or a 3412 vertical bar will appear in the value), then enter the new value and press 3413 Enter or click the mouse elsewhere in the Limits window. This will set the new 3414 value.<o:p></o:p></span></p> 3416 class=SpellE>Tmin</span> and <span class=SpellE>Tmax</span> in the ‘changed’ 3417 row as needed. Use the mouse to select the value to be changed (the background 3418 on the box will be blue or have a black border or a vertical bar will appear in 3419 the value), then enter the new value and press Enter or click the mouse 3420 elsewhere in the Limits window. This will set the new value.<o:p></o:p></span></p> 3415 3421 3416 3422 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo9'><![if !supportLists]><span 3417 3423 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 3418 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3424 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3419 3425 style='mso-fareast-font-family:"Times New Roman"'>Modify the values of 3420 ‘changed’; this can be done on the plot by dragging the limit bars 3421 (left – vertical green dashed line, right – vertical red dashed 3422 l ine) into position. A left or right mouse click on a data point on the plot3423 will set the associated limit. In either case the appropriate value on the3424 ‘changed’ row will beupdated immediately.<o:p></o:p></span></p>3426 ‘changed’; this can be done on the plot by dragging the limit bars (left – 3427 vertical green dashed line, right – vertical red dashed line) into position. A 3428 left or right mouse click on a data point on the plot will set the associated 3429 limit. In either case the appropriate value on the ‘changed’ row will be 3430 updated immediately.<o:p></o:p></span></p> 3425 3431 3426 3432 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo9'><![if !supportLists]><span 3427 3433 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 3428 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3429 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b3430 style='mso-bidi-font-weight:normal'>File</b>’ –<o:p></o:p></span></p>3434 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3435 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight: 3436 normal'>File</b>’ – <o:p></o:p></span></p> 3431 3437 3432 3438 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; 3433 3439 text-indent:-.25in;mso-list:l5 level2 lfo9;tab-stops:list 1.0in'><![if !supportLists]><span 3434 3440 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 3435 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3441 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3436 3442 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b><span 3437 style='mso-fareast-font-family:"Times New Roman"'> – this copies the3438 limitsshown to other selected powder patterns. If used, a dialog box (Copy3443 style='mso-fareast-font-family:"Times New Roman"'> – this copies the limits 3444 shown to other selected powder patterns. If used, a dialog box (Copy 3439 3445 Parameters) will appear showing the list of available powder patterns, you can 3440 copy the limits parameters to any or all of them; select ‘All’to3441 copy them to all patterns. Then select ‘OK’ to do the copy; 3442 ‘Cancel’ to cancel theoperation.<o:p></o:p></span></p>3446 copy the limits parameters to any or all of them; select ‘All’ to copy them to 3447 all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the 3448 operation.<o:p></o:p></span></p> 3443 3449 3444 3450 <h4><a name=Background><u><span style='mso-fareast-font-family:"Times New Roman"'>Background<o:p></o:p></span></u></a></h4> … … 3452 3458 3453 3459 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1). 3454 A continuous empirical function (‘<span class=SpellE>chebyschev</span>’, 3455 ‘cosine’, ‘<span class=SpellE><span class=GramE>lin</span></span> 3456 interpolate’, ‘inv interpolate’ & ‘log 3457 interpolate’). The latter three select fixed points with spacing that is 3460 A continuous empirical function (‘<span class=SpellE>chebyschev</span>’, 3461 ‘cosine’, ‘<span class=SpellE>lin</span> interpolate’, ‘inv interpolate’ & 3462 ‘log interpolate’). The latter three select fixed points with spacing that is 3458 3463 equal, inversely equal or equal on a log scale of the x-coordinate. The set of 3459 3464 magnitudes at each point then comprise the background variables. All are … … 3465 3470 3466 3471 <p class=MsoNormal style='tab-stops:0in'><span style='mso-fareast-font-family: 3467 "Times New Roman"'><span style='mso-tab-count:1'> </span></span><!--[if gte msEquation 12]><m:oMath><i3468 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math" ,"serif";3469 mso-fareast-font-family:"Times New Roman"'><span style='mso-tab-count:3'> </span><m:r> B</m:r><m:r>=</m:r><m:r>A</m:r></span></i><m:d><m:dPr><span3470 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";3472 "Times New Roman"'><span style='mso-tab-count:1'> </span></span><!--[if gte msEquation 12]><m:oMath><i 3473 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 3474 mso-fareast-font-family:"Times New Roman"'><span style='mso-tab-count:3'> </span><m:r><span>B</m:r></span><m:r><span>=</m:r></span><m:r><span>A</m:r></span></span></i><m:d><m:dPr><span 3475 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 3471 3476 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 3472 3477 normal'><m:ctrlPr></m:ctrlPr></span></m:dPr><m:e><m:f><m:fPr><m:type m:val="skw"/><span 3473 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";3478 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 3474 3479 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 3475 3480 normal'><m:ctrlPr></m:ctrlPr></span></m:fPr><m:num><i style='mso-bidi-font-style: 3476 normal'><span style='font-family:"Cambria Math" ,"serif";mso-fareast-font-family:3477 "Times New Roman"'><m:r> sinQR</m:r></span></i></m:num><m:den><i3478 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math" ,"serif";3479 mso-fareast-font-family:"Times New Roman"'><m:r> QR</m:r></span></i></m:den></m:f></m:e></m:d><m:sSup><m:sSupPr><span3480 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";3481 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 3482 "Times New Roman"'><m:r><span>sinQR</m:r></span></span></i></m:num><m:den><i 3483 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 3484 mso-fareast-font-family:"Times New Roman"'><m:r><span>QR</m:r></span></span></i></m:den></m:f></m:e></m:d><m:sSup><m:sSupPr><span 3485 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 3481 3486 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 3482 3487 normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style: 3483 normal'><span style='font-family:"Cambria Math" ,"serif";mso-fareast-font-family:3484 "Times New Roman"'><m:r> e</m:r></span></i></m:e><m:sup><i style='mso-bidi-font-style:3485 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:3486 "Times New Roman"'><m:r>-</m:r><m:r>U</m:r></span></i><m:sSup><m:sSupPr><span3487 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";3488 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 3489 "Times New Roman"'><m:r><span>e</m:r></span></span></i></m:e><m:sup><i 3490 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 3491 mso-fareast-font-family:"Times New Roman"'><m:r><span>-</m:r></span><m:r><span>U</m:r></span></span></i><m:sSup><m:sSupPr><span 3492 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 3488 3493 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 3489 3494 normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style: 3490 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family: 3491 "Times New Roman"'><m:r>Q</m:r></span></i></m:e><m:sup><i 3492 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math","serif"; 3493 mso-fareast-font-family:"Times New Roman"'><m:r>2</m:r></span></i></m:sup></m:sSup></m:sup></m:sSup></m:oMath><![endif]--><![if !msEquation]><span 3494 style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-font-family: 3495 "Times New Roman";mso-fareast-theme-font:minor-fareast;position:relative; 3496 top:16.0pt;mso-text-raise:-16.0pt;mso-ansi-language:EN-US;mso-fareast-language: 3497 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 3498 type="#_x0000_t75" style='width:133.5pt;height:38.25pt'> 3499 <v:imagedata src="gsasII_files/image001.png" o:title="" chromakey="white"/> 3500 </v:shape><![endif]--><![if !vml]><img width=178 height=51 3501 src="gsasII_files/image002.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span 3502 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-tab-count: 3503 1'> </span><o:p></o:p></span></p> 3495 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 3496 "Times New Roman"'><m:r><span>Q</m:r></span></span></i></m:e><m:sup><i 3497 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 3498 mso-fareast-font-family:"Times New Roman"'><m:r><span>2</m:r></span></span></i></m:sup></m:sSup></m:sup></m:sSup></m:oMath><![endif]--><![if !msEquation]><span 3499 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family: 3500 "ＭＳ 明朝";mso-fareast-theme-font:minor-fareast;position:relative;top:7.0pt; 3501 mso-text-raise:-7.0pt;mso-ansi-language:EN-US;mso-fareast-language:EN-US; 3502 mso-bidi-language:AR-SA'><img width=133 height=25 id="_x0000_i1025" 3503 src="gsasII_files/image001.png"></span><![endif]><span style='mso-fareast-font-family: 3504 "Times New Roman"'><span style='mso-tab-count:1'> </span><o:p></o:p></span></p> 3504 3505 3505 3506 <p class=MsoNormal><span class=GramE><span style='mso-fareast-font-family:"Times New Roman"'>where</span></span><span … … 3511 3512 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>3). 3512 3513 A set of individual Bragg peaks using the pseudo-Voigt profile function as 3513 their shapes. Their parameters are ‘<span class=SpellE>pos</span>’,3514 ’<span class=SpellE>int</span>’, ‘sig’ & 3515 ‘gam’; each can be selected for refinement. The default values for 3516 sig & gam (=0.10) are for very sharp peaks, you may adjust them accordingly 3517 to the kind of peak you are trying tofit before trying to refine them.<o:p></o:p></span></p>3514 their shapes. Their parameters are ‘<span class=SpellE>pos</span>’, ’<span 3515 class=SpellE>int</span>’, ‘sig’ & ‘gam’; each can be selected for 3516 refinement. The default values for sig & gam (=0.10) are for very sharp 3517 peaks, you may adjust them accordingly to the kind of peak you are trying to 3518 fit before trying to refine them.<o:p></o:p></span></p> 3518 3519 3519 3520 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5> … … 3521 3522 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l23 level1 lfo10'><![if !supportLists]><span 3522 3523 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 3523 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3524 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b3525 style='mso-bidi-font-weight:normal'>File</b>’ –<o:p></o:p></span></p>3524 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3525 style='mso-fareast-font-family:"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight: 3526 normal'>File</b>’ – <o:p></o:p></span></p> 3526 3527 3527 3528 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3528 3529 auto;text-indent:-.25in;mso-list:l4 level1 lfo11'><![if !supportLists]><span 3529 3530 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 3530 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3531 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3531 3532 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b><span 3532 style='mso-fareast-font-family:"Times New Roman"'> – this copies the3533 background parameters shown to other selected powder patterns. If used, a 3534 dialog box (Copy Parameters) will appear showing the list of available powder 3535 patterns, you can copy the background parameters to any or all of them; select 3536 ‘All’ to copy them to all patterns. Then select ‘OK’ to 3537 do the copy; ‘Cancel’ to cancel theoperation.<o:p></o:p></span></p>3533 style='mso-fareast-font-family:"Times New Roman"'> – this copies the background 3534 parameters shown to other selected powder patterns. If used, a dialog box (Copy 3535 Parameters) will appear showing the list of available powder patterns, you can 3536 copy the background parameters to any or all of them; select ‘All’ to copy them 3537 to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the 3538 operation.<o:p></o:p></span></p> 3538 3539 3539 3540 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3540 3541 auto;text-indent:-.25in;mso-list:l4 level1 lfo11'><![if !supportLists]><span 3541 3542 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 3542 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b3543 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3543 3544 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy 3544 flags </span></b><span style='mso-fareast-font-family:"Times New Roman"'>– 3545 <span class=GramE>this copies</span> only the refinement flags shown to other 3546 selected powder patterns. If used, a dialog box (Copy Refinement Flags) will 3547 appear showing the list of available powder patterns, you can copy the 3548 refinement flags to any or all of them; select ‘All’ to copy them 3549 to all patterns. Then select ‘OK’ to do the copy; 3550 ‘Cancel’ to cancel the operation.<o:p></o:p></span></p> 3545 flags </span></b><span style='mso-fareast-font-family:"Times New Roman"'>– this 3546 copies only the refinement flags shown to other selected powder patterns. If 3547 used, a dialog box (Copy Refinement Flags) will appear showing the list of 3548 available powder patterns, you can copy the refinement flags to any or all of 3549 them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the 3550 copy; ‘Cancel’ to cancel the operation.<o:p></o:p></span></p> 3551 3551 3552 3552 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l23 level1 lfo10'><![if !supportLists]><span 3553 3553 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 3554 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3554 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3555 3555 style='mso-fareast-font-family:"Times New Roman"'>You can select a different 3556 3556 Background function from the pull down tab.<o:p></o:p></span></p> … … 3558 3558 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l23 level1 lfo10'><![if !supportLists]><span 3559 3559 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 3560 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3560 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3561 3561 style='mso-fareast-font-family:"Times New Roman"'>You can choose to refine/not 3562 3562 refine the background coefficients.<o:p></o:p></span></p> … … 3564 3564 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l23 level1 lfo10'><![if !supportLists]><span 3565 3565 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 3566 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3566 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3567 3567 style='mso-fareast-font-family:"Times New Roman"'>You can select the number of 3568 3568 background coefficients to be used (1-36).<o:p></o:p></span></p> … … 3570 3570 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l23 level1 lfo10'><![if !supportLists]><span 3571 3571 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span 3572 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3572 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3573 3573 style='mso-fareast-font-family:"Times New Roman"'>You can change individual 3574 3574 background coefficient values. Enter the value then press Enter or click the … … 3577 3577 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l23 level1 lfo10'><![if !supportLists]><span 3578 3578 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span 3579 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3579 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3580 3580 style='mso-fareast-font-family:"Times New Roman"'>You can introduce one or more 3581 3581 Debye scattering terms into the background. For each one you should enter a 3582 sensible value for ‘R’ – an expected interatomic distance in3583 an amorphous phase is appropriate. Select parameters to refine; usually start 3584 with the ‘A’coefficients.<o:p></o:p></span></p>3582 sensible value for ‘R’ – an expected interatomic distance in an amorphous phase 3583 is appropriate. Select parameters to refine; usually start with the ‘A’ 3584 coefficients.<o:p></o:p></span></p> 3585 3585 3586 3586 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l23 level1 lfo10'><![if !supportLists]><span 3587 3587 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>7.<span 3588 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span3588 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 3589 3589 style='mso-fareast-font-family:"Times New Roman"'>You can introduce single 3590 3590 Bragg peaks into the background. For each you should specify at least the 3591 position. Select parameters to refine; usually start with the ‘<span3592 class=SpellE>int</span> ’coefficients.<o:p></o:p></span></p>3591 position. Select parameters to refine; usually start with the ‘<span 3592 class=SpellE>int</span>’ coefficients.<o:p></o:p></span></p> 3593 3593 3594 3594 <h4><a name="Instrument_Parameters"><u><span style='mso-fareast-font-family: … … 3599 3599 window shows the instrument parameters for the selected powder data set. The 3600 3600 plot window shows the corresponding resolution curves. Solid lines are for the 3601 default values (in parentheses), dashed lines from the refined values and 3602 ‘+’ for individual entries in the ‘<span class=SpellE><span 3603 style='color:#0070C0'>Peak_List</span></span>’. </span><span 3604 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 3605 text-underline:none'><o:p></o:p></span></span></p> 3601 default values (in parentheses), dashed lines from the refined values and ‘+’ 3602 for individual entries in the ‘<span class=SpellE><span style='color:#0070C0'>Peak_List</span></span>’. 3603 </span><span class=MsoHyperlink><span style='color:windowtext;text-decoration: 3604 none;text-underline:none'><o:p></o:p></span></span></p> 3606 3605 3607 3606 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?</span><span … … 3612 3611 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3613 3612 color:windowtext;text-decoration:none;text-underline:none'><span 3614 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 3613 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 3615 3614 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 3616 "Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Operations</b>’3617 –<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 3618 none;text-underline:none'><o:p></o:p></span></span></span></p>3615 "Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Operations</b>’ 3616 –<span class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 3617 text-underline:none'><o:p></o:p></span></span></span></p> 3619 3618 3620 3619 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 3622 3621 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3623 3622 color:windowtext;text-decoration:none;text-underline:none'><span 3624 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 3623 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 3625 3624 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 3626 style='mso-fareast-font-family:"Times New Roman"'>Load profile …</span></b><span3625 style='mso-fareast-font-family:"Times New Roman"'>Load profile… </span></b><span 3627 3626 style='mso-fareast-font-family:"Times New Roman"'>- loads a GSAS-II instrument 3628 3627 parameter file (name.instprm), replacing the existing instrument parameter … … 3635 3634 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3636 3635 color:windowtext;text-decoration:none;text-underline:none'><span 3637 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 3636 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 3638 3637 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 3639 style='mso-fareast-font-family:"Times New Roman"'>Save profile… - </span></b><span 3640 style='mso-fareast-font-family:"Times New Roman"'>saves the current instrument 3641 parameter values in a simple text file (name.instprm); you will be prompted for 3642 the file name – do not change the extension. This file may be edited but 3643 heed the warning to not change the parameter names, the order of the parameter 3644 records or add new parameter records as this will invalidate the file. You may 3645 only change the numeric values if necessary. You can change or add comment 3646 records (begins with ‘#’).<span class=MsoHyperlink><b 3647 style='mso-bidi-font-weight:normal'><span style='color:windowtext;text-decoration: 3648 none;text-underline:none'><o:p></o:p></span></b></span></span></p> 3638 style='mso-fareast-font-family:"Times New Roman"'>Save profile… - </span></b><span 3639 style='mso-fareast-font-family:"Times New Roman"'>saves the current instrument parameter 3640 values in a simple text file (name.instprm); you will be prompted for the file 3641 name – do not change the extension. This file may be edited but heed the 3642 warning to not change the parameter names, the order of the parameter records 3643 or add new parameter records as this will invalidate the file. You may only 3644 change the numeric values if necessary. You can change or add comment records 3645 (begins with ‘#’).<span class=MsoHyperlink><b style='mso-bidi-font-weight:normal'><span 3646 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></b></span></span></p> 3649 3647 3650 3648 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 3652 3650 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3653 3651 color:windowtext;text-decoration:none;text-underline:none'><span 3654 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 3652 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 3655 3653 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 3656 3654 style='mso-fareast-font-family:"Times New Roman"'>Reset profile </span></b><span 3657 style='mso-fareast-font-family:"Times New Roman"'> – resets the values for3658 theinstrument parameters to the default values shown in parentheses for each3655 style='mso-fareast-font-family:"Times New Roman"'>– resets the values for the 3656 instrument parameters to the default values shown in parentheses for each 3659 3657 entry.<span class=MsoHyperlink><b style='mso-bidi-font-weight:normal'><span 3660 3658 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></b></span></span></p> … … 3664 3662 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3665 3663 color:windowtext;text-decoration:none;text-underline:none'><span 3666 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 3664 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 3667 3665 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 3668 3666 style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b><span 3669 style='mso-fareast-font-family:"Times New Roman"'> – this copies the 3670 instrument parameters shown to other selected powder patterns. If used, a 3671 dialog box (Copy parameters) will appear showing the list of available powder patterns, 3672 you can copy the instrument parameters to any or all of them; select 3673 ‘All’ to copy them to all patterns. Then select ‘OK’ to 3674 do the copy; ‘Cancel’ to cancel the operation. The copy will only 3675 work for instrument parameters that are commensurate with the one that is 3667 style='mso-fareast-font-family:"Times New Roman"'> – this copies the instrument 3668 parameters shown to other selected powder patterns. If used, a dialog box (Copy 3669 parameters) will appear showing the list of available powder patterns, you can 3670 copy the instrument parameters to any or all of them; select ‘All’ to copy them 3671 to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the 3672 operation. The copy will only work for instrument parameters that are 3673 commensurate with the one that is shown, e.g. single radiation patterns will 3674 not be updated from K</span><sub><span style='font-family:Symbol;mso-fareast-font-family: 3675 "Times New Roman"'>a</span></sub><sub><span style='mso-fareast-font-family: 3676 "Times New Roman"'>1</span></sub><span style='mso-fareast-font-family:"Times New Roman"'>/K</span><sub><span 3677 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span 3678 style='mso-fareast-font-family:"Times New Roman"'>2</span></sub><span 3679 style='mso-fareast-font-family:"Times New Roman"'> ones.<span 3680 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 3681 text-underline:none'><o:p></o:p></span></span></span></p> 3682 3683 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3684 auto;text-indent:-.25in;mso-list:l19 level2 lfo13;tab-stops:list 1.0in'><![if !supportLists]><span 3685 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3686 color:windowtext;text-decoration:none;text-underline:none'><span 3687 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 3688 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 3689 style='mso-fareast-font-family:"Times New Roman"'>Copy flags </span></b><span 3690 style='mso-fareast-font-family:"Times New Roman"'>- – this copies the 3691 instrument parameter refinement flags shown to other selected powder patterns. 3692 If used, a dialog box (Copy refinement flags) will appear showing the list of 3693 available powder patterns, you can copy the instrument parameter refinement 3694 flags to any or all of them; select ‘All’ to copy them to all patterns. Then 3695 select ‘OK’ to do the copy; ‘Cancel’ to cancel the operation. The copy will 3696 only work for instrument parameters that are commensurate with the one that is 3676 3697 shown, e.g. single radiation patterns will not be updated from K</span><sub><span 3677 3698 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span … … 3684 3705 text-underline:none'><o:p></o:p></span></span></span></p> 3685 3706 3686 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3687 auto;text-indent:-.25in;mso-list:l19 level2 lfo13;tab-stops:list 1.0in'><![if !supportLists]><span 3707 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l10 level1 lfo12'><![if !supportLists]><span 3688 3708 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3689 3709 color:windowtext;text-decoration:none;text-underline:none'><span 3690 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 3691 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 3692 style='mso-fareast-font-family:"Times New Roman"'>Copy flags </span></b><span 3693 style='mso-fareast-font-family:"Times New Roman"'>- – this copies the 3694 instrument parameter refinement flags shown to other selected powder patterns. 3695 If used, a dialog box (Copy refinement flags) will appear showing the list of 3696 available powder patterns, you can copy the instrument parameter refinement 3697 flags to any or all of them; select ‘All’ to copy them to all 3698 patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to 3699 cancel the operation. The copy will only work for instrument parameters that 3700 are commensurate with the one that is shown, e.g. single radiation patterns 3701 will not be updated from K</span><sub><span style='font-family:Symbol; 3702 mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span 3703 style='mso-fareast-font-family:"Times New Roman"'>1</span></sub><span 3704 style='mso-fareast-font-family:"Times New Roman"'>/K</span><sub><span 3705 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span 3706 style='mso-fareast-font-family:"Times New Roman"'>2</span></sub><span 3707 style='mso-fareast-font-family:"Times New Roman"'> ones.<span 3708 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 3709 text-underline:none'><o:p></o:p></span></span></span></p> 3710 3711 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l10 level1 lfo12'><![if !supportLists]><span 3712 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3713 color:windowtext;text-decoration:none;text-underline:none'><span 3714 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 3710 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 3715 3711 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 3716 3712 "Times New Roman"'>You can change any of the profile coefficients<span … … 3721 3717 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3722 3718 color:windowtext;text-decoration:none;text-underline:none'><span 3723 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 3719 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 3724 3720 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 3725 3721 "Times New Roman"'>You can choose to refine any profile coefficients. <b … … 3727 3723 choices are ignored e.g. Zero is not refined during peak fitting. Also some 3728 3724 choices may lead to unstable refinement, e.g. Lam refinement and lattice 3729 parameter refinement. Examine the ‘</span><a href="#Covariance"><span3725 parameter refinement. Examine the ‘</span><a href="#Covariance"><span 3730 3726 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 3731 none;text-underline:none'>Covariance ’</span></a><span style='mso-fareast-font-family:3727 none;text-underline:none'>Covariance’</span></a><span style='mso-fareast-font-family: 3732 3728 "Times New Roman"'> display for highly correlated parameters.<span 3733 3729 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; … … 3759 3755 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration: 3760 3756 none;text-underline:none'><span style='mso-list:Ignore'>1.<span 3761 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span3757 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span 3762 3758 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3763 normal;mso-bidi-font-weight:bold'>Menu ‘</span></span><span3764 style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman";3765 color:windowtext'>File ’</span></span><span style='mso-bookmark:Powder_Peaks'><span3759 normal;mso-bidi-font-weight:bold'>Menu ‘</span></span><span style='mso-bookmark: 3760 Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"; 3761 color:windowtext'>File’</span></span><span style='mso-bookmark:Powder_Peaks'><span 3766 3762 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3767 normal;mso-bidi-font-weight:bold'> –<span class=MsoHyperlink><span3763 normal;mso-bidi-font-weight:bold'> – <span class=MsoHyperlink><span 3768 3764 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5> 3769 3765 … … 3773 3769 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration: 3774 3770 none;text-underline:none'><span style='mso-list:Ignore'>a.<span 3775 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span3771 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span 3776 3772 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Load</span></span><span 3777 3773 style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"; 3778 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this3779 loadssample parameters from a previously saved .<span class=SpellE>samprm</span>3774 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this loads 3775 sample parameters from a previously saved .<span class=SpellE>samprm</span> 3780 3776 file.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 3781 3777 none;text-underline:none'><o:p></o:p></span></span></span></span></h5> … … 3786 3782 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration: 3787 3783 none;text-underline:none'><span style='mso-list:Ignore'>b.<span 3788 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span3784 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span 3789 3785 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Save</span></span><span 3790 3786 style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"; 3791 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this 3792 saves the sample parameters to a file with the extension ’.samprm’. 3793 A file dialog box will appear to ask for the file name.<span 3794 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 3795 text-underline:none'><o:p></o:p></span></span></span></span></h5> 3787 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this saves 3788 the sample parameters to a file with the extension ’.samprm’. A file dialog box 3789 will appear to ask for the file name.<span class=MsoHyperlink><span 3790 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5> 3796 3791 3797 3792 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto; … … 3800 3795 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3801 3796 color:windowtext;text-decoration:none;text-underline:none'><span 3802 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 3797 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 3803 3798 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 3804 3799 style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b></span><span 3805 3800 style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'> 3806 – this copies the sample parameters shown to other selected powder 3807 patterns. If used, a dialog box (Copy parameters) will appear showing the list 3808 of available powder patterns, you can copy the sample parameters to any or all 3809 of them; select ‘All’ to copy them to all patterns. Then select 3810 ‘OK’ to do the copy; ‘Cancel’ to cancel the operation. <span 3811 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 3812 text-underline:none'><o:p></o:p></span></span></span></span></p> 3801 – this copies the sample parameters shown to other selected powder patterns. If 3802 used, a dialog box (Copy parameters) will appear showing the list of available 3803 powder patterns, you can copy the sample parameters to any or all of them; 3804 select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy; 3805 ‘Cancel’ to cancel the operation. <span class=MsoHyperlink><span 3806 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p> 3813 3807 3814 3808 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; … … 3817 3811 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3818 3812 color:windowtext;text-decoration:none;text-underline:none'><span 3819 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 3813 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 3820 3814 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 3821 3815 style='mso-fareast-font-family:"Times New Roman"'>Copy flags</span></b></span><span 3822 3816 style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'> 3823 - – this copies the sample parameter refinement flags shown to other3824 selected powder patterns. If used, a dialog box (Copy refinement flags) will 3825 appearshowing the list of available powder patterns, you can copy the sample3826 parameter refinement flags to any or all of them; select ‘All’to3827 copy them to all patterns. Then select ‘OK’ to do the copy; 3828 ‘Cancel’ to cancel the operation. <span class=MsoHyperlink><span 3829 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>3817 - – this copies the sample parameter refinement flags shown to other selected 3818 powder patterns. If used, a dialog box (Copy refinement flags) will appear 3819 showing the list of available powder patterns, you can copy the sample 3820 parameter refinement flags to any or all of them; select ‘All’ to copy them to 3821 all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to cancel the 3822 operation. <span class=MsoHyperlink><span style='color:windowtext;text-decoration: 3823 none;text-underline:none'><o:p></o:p></span></span></span></span></p> 3830 3824 3831 3825 <h4><span style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family: … … 3837 3831 window shows the list of peaks that will be used by the peak fitting 3838 3832 refinement. It is filled by picking peaks in the powder pattern displayed in 3839 the GSASII Plots window as a sequence of ‘+’ marks.<span 3840 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 3841 text-underline:none'><o:p></o:p></span></span></span></p> 3833 the GSASII Plots window as a sequence of ‘+’ marks.<span class=MsoHyperlink><span 3834 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 3842 3835 3843 3836 <h5><a name="Index_Peaks"><span style='mso-fareast-font-family:"Times New Roman"'>What … … 3851 3844 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3852 3845 normal;mso-bidi-font-weight:bold;text-decoration:none;text-underline:none'><span 3853 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 3846 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 3854 3847 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 3855 3848 "Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight: 3856 bold'>Menu ‘</span></span><span style='mso-bookmark:Index_Peaks'><span3849 bold'>Menu ‘</span></span><span style='mso-bookmark:Index_Peaks'><span 3857 3850 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Peak Fitting</span></span><span 3858 3851 style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman"; 3859 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> ’ –<span3852 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'>’ – <span 3860 3853 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 3861 3854 text-underline:none'><o:p></o:p></span></span></span></span></h5> … … 3866 3859 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration: 3867 3860 none;text-underline:none'><span style='mso-list:Ignore'>a.<span 3868 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span3861 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span 3869 3862 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Auto search</span></span><span 3870 3863 style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman"; 3871 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this3872 fills the table with peak positions. These are selected based on peak tops that 3873 are substantially above background. Noisy data will give spurious peaks and 3874 small peaks or shoulders will not be found. Examine results & modify as 3875 needed.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 3876 none;text-underline:none'><o:p></o:p></span></span></span></span></h5>3864 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this fills 3865 the table with peak positions. These are selected based on peak tops that are 3866 substantially above background. Noisy data will give spurious peaks and small 3867 peaks or shoulders will not be found. Examine results & modify as needed.<span 3868 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 3869 text-underline:none'><o:p></o:p></span></span></span></span></h5> 3877 3870 3878 3871 <h5 style='margin-left:1.0in;text-indent:-.25in;mso-list:l11 level2 lfo15; … … 3881 3874 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration: 3882 3875 none;text-underline:none'><span style='mso-list:Ignore'>b.<span 3883 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span3876 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span 3884 3877 class=SpellE><span style='mso-fareast-font-family:"Times New Roman";color:windowtext'>UnDo</span></span></span><span 3885 3878 style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman"; 3886 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – resets3887 p eak parameters, background and instrument parameter values varied in the last3888 peak fitting refinement back to their original values. Use this to recover from 3889 a failed refinement. Note:<span style='mso-spacerun:yes'> </span>there is 3890 only a single level of recovery available.<span class=MsoHyperlink><span 3891 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>3879 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – resets peak 3880 parameters, background and instrument parameter values varied in the last peak 3881 fitting refinement back to their original values. Use this to recover from a failed 3882 refinement. Note:<span style="mso-spacerun:yes"> </span>there is only a single 3883 level of recovery available.<span class=MsoHyperlink><span style='color:windowtext; 3884 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5> 3892 3885 3893 3886 <h5 style='margin-left:1.0in;text-indent:-.25in;mso-list:l11 level2 lfo15; … … 3896 3889 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration: 3897 3890 none;text-underline:none'><span style='mso-list:Ignore'>c.<span 3898 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span3891 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span 3899 3892 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>LSQ <span 3900 3893 class=SpellE>PeakFit</span></span></span><span style='mso-bookmark:Index_Peaks'><span 3901 3894 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3902 normal;mso-bidi-font-weight:bold'> – perform a least squares fit of the3903 peaksin Peak List to the data. Any peak parameters, background parameters and3895 normal;mso-bidi-font-weight:bold'> – perform a least squares fit of the peaks 3896 in Peak List to the data. Any peak parameters, background parameters and 3904 3897 instrument parameters with refine checked will be varied in this refinement. 3905 3898 The refinement will proceed until convergence. We suggest you vary the 3906 3899 intensity along with the background first (the default), then vary the position 3907 and instrument parameters after. The order will depend on how poor is the 3908 initial estimate of the instrument parameters (U, V, W, X, Y & SH/L). To 3909 determine how to proceed, examine in detail the powder pattern difference curve 3910 displayed in the GSASII Plots window. If individual peaks show peak widths that 3911 are widely different, their individual sigma and gamma parameters may be 3912 refined.If the refinement results in negative peak coefficients, these will be3900 and instrument parameters after. The order will depend on how poor is the initial 3901 estimate of the instrument parameters (U, V, W, X, Y & SH/L). To determine 3902 how to proceed, examine in detail the powder pattern difference curve displayed 3903 in the GSASII Plots window. If individual peaks show peak widths that are 3904 widely different, their individual sigma and gamma parameters may be refined. 3905 If the refinement results in negative peak coefficients, these will be 3913 3906 highlighted in red. If this happens, you should </span></span><span 3914 3907 style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman"; … … 3924 3917 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration: 3925 3918 none;text-underline:none'><span style='mso-list:Ignore'>d.<span 3926 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span3927 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>LSQ one 3928 cycle </span></span><span style='mso-bookmark:Index_Peaks'><span 3929 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:3930 normal;mso-bidi-font-weight:bold'>– perform a single cycle of least 3931 squares refinement. This can be used in difficult cases to get a refinement 3932 started toward convergence.<span class=MsoHyperlink><span style='color:windowtext;3933 text- decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>3919 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span 3920 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>LSQ one cycle 3921 </span></span><span style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family: 3922 "Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight: 3923 bold'>– perform a single cycle of least squares refinement. This can be used in 3924 difficult cases to get a refinement started toward convergence.<span 3925 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 3926 text-underline:none'><o:p></o:p></span></span></span></span></h5> 3934 3927 3935 3928 <h5 style='margin-left:1.0in;text-indent:-.25in;mso-list:l11 level2 lfo15; … … 3938 3931 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration: 3939 3932 none;text-underline:none'><span style='mso-list:Ignore'>e.<span 3940 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span3933 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span 3941 3934 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Reset sig 3942 3935 and gam </span></span><span style='mso-bookmark:Index_Peaks'><span 3943 3936 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3944 normal;mso-bidi-font-weight:bold'> – this resets the values of sigma and3945 gamma to those computed from the instrument parameters U, V, W, <span 3946 class=GramE>X</span> & Y.<span class=MsoHyperlink><span style='color:windowtext; 3947 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>3937 normal;mso-bidi-font-weight:bold'>– this resets the values of sigma and gamma 3938 to those computed from the instrument parameters U, V, W, <span class=GramE>X</span> 3939 & Y.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 3940 none;text-underline:none'><o:p></o:p></span></span></span></span></h5> 3948 3941 3949 3942 <h5 style='margin-left:1.0in;text-indent:-.25in;mso-list:l11 level2 lfo15; … … 3952 3945 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold;text-decoration: 3953 3946 none;text-underline:none'><span style='mso-list:Ignore'>f.<span 3954 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span3947 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span 3955 3948 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Clear peaks </span></span><span 3956 3949 style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman"; 3957 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this3958 removesall the peaks from the Peak List.<span class=MsoHyperlink><span3950 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'>– this removes 3951 all the peaks from the Peak List.<span class=MsoHyperlink><span 3959 3952 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5> 3960 3953 … … 3963 3956 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3964 3957 normal;mso-bidi-font-weight:bold;text-decoration:none;text-underline:none'><span 3965 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 3958 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 3966 3959 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 3967 3960 "Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight: … … 3972 3965 the Zoom/Pan buttons are not selected on the Plot window. We recommend that you 3973 3966 begin picking peaks from the right side of the pattern; that way the tool tip 3974 won ’t be in your way as you select peaks.<span class=MsoHyperlink><span3967 won’t be in your way as you select peaks.<span class=MsoHyperlink><span 3975 3968 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5> 3976 3969 … … 3979 3972 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 3980 3973 normal;mso-bidi-font-weight:bold;text-decoration:none;text-underline:none'><span 3981 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 3974 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 3982 3975 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 3983 3976 "Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight: … … 3994 3987 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 3995 3988 none;text-underline:none'><span style='mso-list:Ignore'>4.<span 3996 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span3989 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span 3997 3990 style='mso-fareast-font-family:"Times New Roman"'>You can change individual 3998 3991 peak coefficient values. Enter the value then press Enter or Tab or click the … … 4005 3998 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4006 3999 color:windowtext;text-decoration:none;text-underline:none'><span 4007 style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> 4000 style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> 4008 4001 </span></span></span></span><![endif]>You can change the refine flags either by 4009 4002 clicking on the box or by selecting one and then selecting the column (a single 4010 click on the column heading; column should show in blue). Then type 4011 ‘y’ to set the refine flags or ‘n’ to clear the flags. </span><span 4012 style='mso-bookmark:Index_Peaks'><span class=MsoHyperlink><span 4013 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 4014 none;text-underline:none'><o:p></o:p></span></span></span></p> 4003 click on the column heading; column should show in blue). Then type ‘y’ to set 4004 the refine flags or ‘n’ to clear the flags. </span><span style='mso-bookmark: 4005 Index_Peaks'><span class=MsoHyperlink><span style='mso-fareast-font-family: 4006 "Times New Roman";color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 4015 4007 4016 4008 <h5 style='margin-left:45.0pt;text-indent:-.25in;mso-list:l11 level1 lfo15'><span … … 4018 4010 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight: 4019 4011 normal;mso-bidi-font-weight:bold;text-decoration:none;text-underline:none'><span 4020 style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'> 4012 style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'> 4021 4013 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4022 4014 "Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight: … … 4042 4034 indexing can proceed. When indexing is completed, this display will show the 4043 4035 resulting hkl values for every indexed reflection along with the calculated 4044 d-spacing ( ‘d-calc’) for the selected unit cell in </span><a4036 d-spacing (‘d-calc’) for the selected unit cell in </span><a 4045 4037 href="#Unit_Cells_List"><span style='mso-fareast-font-family:"Times New Roman"; 4046 4038 color:windowtext;text-decoration:none;text-underline:none'>Unit Cells List</span></a><span … … 4055 4047 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4056 4048 color:windowtext;text-decoration:none;text-underline:none'><span 4057 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 4049 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 4058 4050 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4059 "Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Operations</b>’4060 – <b style='mso-bidi-font-weight:normal'>Load/Reload</b> – loads 4061 the peakpositions & intensities from the </span><a href="#Peak_List"><span4051 "Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Operations</b>’ 4052 – <b style='mso-bidi-font-weight:normal'>Load/Reload</b> – loads the peak 4053 positions & intensities from the </span><a href="#Peak_List"><span 4062 4054 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 4063 4055 none;text-underline:none'>Peak List</span></a><span style='mso-fareast-font-family: 4064 4056 "Times New Roman"'> to make them available for the indexing routine. The d-obs 4065 is obtained from Bragg ’s Law after applying the Zero correction shown on4066 the </span><a href="#Instrument_Parameters"><span style='mso-fareast-font-family: 4067 "Times New Roman";color:windowtext;text-decoration:none;text-underline:none'>Instrument 4068 Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'> 4069 table to the position shown here.<span class=MsoHyperlink><span 4070 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>4057 is obtained from Bragg’s Law after applying the Zero correction shown on the </span><a 4058 href="#Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman"; 4059 color:windowtext;text-decoration:none;text-underline:none'>Instrument Parameters</span></a><span 4060 style='mso-fareast-font-family:"Times New Roman"'> table to the position shown 4061 here.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 4062 none;text-underline:none'><o:p></o:p></span></span></span></p> 4071 4063 4072 4064 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l27 level1 lfo16'><![if !supportLists]><span 4073 4065 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4074 4066 color:windowtext;text-decoration:none;text-underline:none'><span 4075 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 4067 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 4076 4068 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4077 4069 "Times New Roman"'>You may deselect individual peaks from indexing by 4078 unchecking the corresponding ‘use’box.<span class=MsoHyperlink><span4070 unchecking the corresponding ‘use’ box.<span class=MsoHyperlink><span 4079 4071 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 4080 4072 … … 4096 4088 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 4097 4089 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 4098 field-begin'></span><span style='mso-spacerun:yes'> </span>REF 4099 Index_Peak_List \h </span><![endif]--><span style='mso-fareast-font-family: 4100 "Times New Roman"'><!--[if gte mso 9]><xml> 4090 field-begin'></span><span style="mso-spacerun:yes"> </span>REF Index_Peak_List 4091 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 4101 4092 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 4102 4093 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 4103 4094 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 4104 4095 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 4105 field-begin'></span><span style='mso-spacerun:yes'> </span>REF 4106 Index_Peak_List \h </span><![endif]--><span style='mso-fareast-font-family: 4107 "Times New Roman"'><!--[if gte mso 9]><xml> 4096 field-begin'></span><span style="mso-spacerun:yes"> </span>REF Index_Peak_List 4097 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 4108 4098 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 4109 4099 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 4110 4100 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 4111 4101 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 4112 field-begin'></span><span style='mso-spacerun:yes'> </span>REF 4113 Index_Peak_List \h </span><![endif]--><span style='mso-fareast-font-family: 4114 "Times New Roman"'><!--[if gte mso 9]><xml> 4102 field-begin'></span><span style="mso-spacerun:yes"> </span>REF Index_Peak_List 4103 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 4115 4104 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 4116 4105 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 4117 4106 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 4118 4107 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 4119 field-begin'></span><span style='mso-spacerun:yes'> </span>REF 4120 Index_Peak_List \h </span><![endif]--><span style='mso-fareast-font-family: 4121 "Times New Roman"'><!--[if gte mso 9]><xml> 4108 field-begin'></span><span style="mso-spacerun:yes"> </span>REF Index_Peak_List 4109 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 4122 4110 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 4123 4111 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 4124 4112 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 4125 4113 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 4126 field-begin'></span><span style='mso-spacerun:yes'> </span>REF 4127 Index_Peak_List \h </span><![endif]--><span style='mso-fareast-font-family: 4128 "Times New Roman"'><!--[if gte mso 9]><xml> 4114 field-begin'></span><span style="mso-spacerun:yes"> </span>REF Index_Peak_List 4115 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 4129 4116 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 4130 4117 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 4131 4118 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 4132 4119 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 4133 field-begin'></span><span style='mso-spacerun:yes'> </span>REF 4134 Index_Peak_List \h </span><![endif]--><span style='mso-fareast-font-family: 4135 "Times New Roman"'><!--[if gte mso 9]><xml> 4120 field-begin'></span><span style="mso-spacerun:yes"> </span>REF Index_Peak_List 4121 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 4136 4122 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 4137 4123 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: … … 4148 4134 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4149 4135 color:windowtext;text-decoration:none;text-underline:none'><span 4150 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 4136 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 4151 4137 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4152 4138 style='mso-fareast-font-family:"Times New Roman"'>Select <span class=SpellE>Bravais</span> 4153 4139 Lattices</span></b></span><span style='mso-bookmark:Reflection_List'><span 4154 style='mso-fareast-font-family:"Times New Roman"'> – the selected are4155 tried for indexing the powder pattern. <span class=MsoHyperlink><span 4156 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>4140 style='mso-fareast-font-family:"Times New Roman"'> – the selected are tried for 4141 indexing the powder pattern. <span class=MsoHyperlink><span style='color:windowtext; 4142 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p> 4157 4143 4158 4144 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l16 level1 lfo17'><span … … 4160 4146 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4161 4147 color:windowtext;text-decoration:none;text-underline:none'><span 4162 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 4148 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 4163 4149 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4164 4150 style='mso-fareast-font-family:"Times New Roman"'>Max <span class=SpellE>Nc</span>/Nobs 4165 4151 </span></b></span><span style='mso-bookmark:Reflection_List'><span 4166 style='mso-fareast-font-family:"Times New Roman"'> – this controls the extent4167 ofthe search for the correct indexing. This may need to be increased if an4152 style='mso-fareast-font-family:"Times New Roman"'>– this controls the extent of 4153 the search for the correct indexing. This may need to be increased if an 4168 4154 indexing trial terminates too quickly. It rarely needs to be changed.<span 4169 4155 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; … … 4174 4160 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4175 4161 color:windowtext;text-decoration:none;text-underline:none'><span 4176 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 4177 </span></span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight: 4178 normal'><span style='mso-fareast-font-family:"Times New Roman"'>Start</span></b></span></span><span 4179 style='mso-bookmark:Reflection_List'><b style='mso-bidi-font-weight:normal'><span 4180 style='mso-fareast-font-family:"Times New Roman"'> Volume </span></b></span><span 4181 style='mso-bookmark:Reflection_List'><span style='mso-fareast-font-family:"Times New Roman"'>– 4162 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 4163 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4164 style='mso-fareast-font-family:"Times New Roman"'>Start Volume </span></b></span><span 4165 style='mso-bookmark:Reflection_List'><span style='mso-fareast-font-family:"Times New Roman"'>– 4182 4166 this sets an initial unit cell volume for the indexing. It rarely needs to be 4183 4167 changed.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: … … 4188 4172 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4189 4173 color:windowtext;text-decoration:none;text-underline:none'><span 4190 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 4174 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 4191 4175 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4192 "Times New Roman"'>Menu<b style='mso-bidi-font-weight:normal'> ‘Cell4193 Index/Refine ’ </b>– <span class=MsoHyperlink><span4194 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>4176 "Times New Roman"'>Menu<b style='mso-bidi-font-weight:normal'> ‘Cell 4177 Index/Refine’ </b>– <span class=MsoHyperlink><span style='color:windowtext; 4178 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p> 4195 4179 4196 4180 <p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space: … … 4199 4183 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 4200 4184 none;text-underline:none'><span style='mso-list:Ignore'>a.<span 4201 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b4185 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b 4202 4186 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Index 4203 4187 Cell</span></b></span><span style='mso-bookmark:Reflection_List'><span 4204 style='mso-fareast-font-family:"Times New Roman"'> – this starts the4205 indexing process. Output will appear on the console and a progress bar dialog 4206 willappear which tracks trial volume. A <b style='mso-bidi-font-weight:normal'>Cancel</b>4188 style='mso-fareast-font-family:"Times New Roman"'> – this starts the indexing 4189 process. Output will appear on the console and a progress bar dialog will 4190 appear which tracks trial volume. A <b style='mso-bidi-font-weight:normal'>Cancel</b> 4207 4191 button will terminate indexing; it may need to be pressed more than once to 4208 4192 fully terminate the indexing process. Console output shows possible solutions … … 4210 4194 solutions are indicated by high <b style='mso-bidi-font-weight:normal'>M20</b> 4211 4195 values. <b style='mso-bidi-font-weight:normal'>X20</b> gives number of 4212 unindexed lines out of the 1<sup>st</sup> 20 lines and < span class=GramE><b4213 style='mso-bidi-font-weight:normal'>Nc</b></span> gives total number of 4214 reflections generated for each solution.<span class=MsoHyperlink><span 4215 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>4196 unindexed lines out of the 1<sup>st</sup> 20 lines and <b style='mso-bidi-font-weight: 4197 normal'>Nc</b> gives total number of reflections generated for each solution.<span 4198 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 4199 text-underline:none'><o:p></o:p></span></span></span></span></p> 4216 4200 4217 4201 <p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space: … … 4220 4204 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 4221 4205 none;text-underline:none'><span style='mso-list:Ignore'>b.<span 4222 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b4206 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b 4223 4207 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy 4224 4208 Cell</span></b></span><span style='mso-bookmark:Reflection_List'><span 4225 style='mso-fareast-font-family:"Times New Roman"'> –this copies selected4209 style='mso-fareast-font-family:"Times New Roman"'> – this copies selected 4226 4210 solution to the Unit cell values; attention is paid to the Bravais lattice 4227 4211 shown for the choice and you may select a <b style='mso-bidi-font-weight:normal'>Space … … 4237 4221 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 4238 4222 none;text-underline:none'><span style='mso-list:Ignore'>c.<span 4239 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b4223 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b 4240 4224 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Refine 4241 4225 cell</span></b></span><span style='mso-bookmark:Reflection_List'><span 4242 style='mso-fareast-font-family:"Times New Roman"'> – this refines the4243 copied lattice parameters and optionally the <b style='mso-bidi-font-weight: 4244 normal'>Zerooffset. </b>The results will be placed in the <b style='mso-bidi-font-weight:4245 normal'>Indexing Result</b> table with ‘<b style='mso-bidi-font-weight:4246 normal'>use’</b> selected.<span class=MsoHyperlink><span 4247 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>4226 style='mso-fareast-font-family:"Times New Roman"'> – this refines the copied 4227 lattice parameters and optionally the <b style='mso-bidi-font-weight:normal'>Zero 4228 offset. </b>The results will be placed in the <b style='mso-bidi-font-weight: 4229 normal'>Indexing Result</b> table with ‘<b style='mso-bidi-font-weight:normal'>use’</b> 4230 selected.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 4231 none;text-underline:none'><o:p></o:p></span></span></span></span></p> 4248 4232 4249 4233 <p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space: … … 4252 4236 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 4253 4237 none;text-underline:none'><span style='mso-list:Ignore'>d.<span 4254 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b4238 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b 4255 4239 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Make 4256 4240 new phase</span></b></span><span style='mso-bookmark:Reflection_List'><span 4257 style='mso-fareast-font-family:"Times New Roman"'> – this creates a new4258 phase from the selected unit cell and chosen space group. A dialog box will 4259 a ppear asking for a name for this phase. See the new entry under Phases and the4260 newlattice parameters will be in the </span></span><a href="#General"><span4241 style='mso-fareast-font-family:"Times New Roman"'> – this creates a new phase 4242 from the selected unit cell and chosen space group. A dialog box will appear 4243 asking for a name for this phase. See the new entry under Phases and the new 4244 lattice parameters will be in the </span></span><a href="#General"><span 4261 4245 style='mso-bookmark:Reflection_List'><span style='mso-fareast-font-family:"Times New Roman"; 4262 4246 color:windowtext;text-decoration:none;text-underline:none'>General</span></span><span … … 4270 4254 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4271 4255 color:windowtext;text-decoration:none;text-underline:none'><span 4272 style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> 4256 style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> 4273 4257 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4274 style='mso-fareast-font-family:"Times New Roman"'>Select another solution 4275 – </span></b></span><span style='mso-bookmark:Reflection_List'><span 4276 style='mso-fareast-font-family:"Times New Roman"'>the plot will show (red 4277 dashed lines) the<b style='mso-bidi-font-weight:normal'> </b>generated 4258 style='mso-fareast-font-family:"Times New Roman"'>Select another solution – </span></b></span><span 4259 style='mso-bookmark:Reflection_List'><span style='mso-fareast-font-family:"Times New Roman"'>the 4260 plot will show (red dashed lines) the<b style='mso-bidi-font-weight:normal'> </b>generated 4278 4261 reflection positions for the choice; compare them to the peak positions (blue 4279 4262 lines) and any unfitted peaks for conformation.<span class=MsoHyperlink><span … … 4284 4267 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4285 4268 color:windowtext;text-decoration:none;text-underline:none'><span 4286 style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'> 4269 style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'> 4287 4270 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4288 style='mso-fareast-font-family:"Times New Roman"'>Select ‘keep’ 4289 –</span></b></span><span style='mso-bookmark:Reflection_List'><span 4290 style='mso-fareast-font-family:"Times New Roman"'> this preserves this solution 4291 for a subsequent indexing run; otherwise all solutions are erased before the 4292 indexing trial begins.<span class=MsoHyperlink><span style='color:windowtext; 4293 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p> 4271 style='mso-fareast-font-family:"Times New Roman"'>Select ‘keep’ –</span></b></span><span 4272 style='mso-bookmark:Reflection_List'><span style='mso-fareast-font-family:"Times New Roman"'> 4273 this preserves this solution for a subsequent indexing run; otherwise all 4274 solutions are erased before the indexing trial begins.<span class=MsoHyperlink><span 4275 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p> 4294 4276 4295 4277 <h4><span style='mso-bookmark:Reflection_List'><span style='mso-fareast-font-family: … … 4300 4282 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This 4301 4283 window shows the reflections for the selected phase found in this powder data 4302 set. It is generated by a <span class=SpellE>Rietveld</span> or Pawley4303 refinement. <span class=MsoHyperlink><span style='color:windowtext;text-decoration: 4304 none;text-underline:none'><o:p></o:p></span></span></span></p>4284 set. It is generated by a Rietveld or Pawley refinement. <span 4285 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 4286 text-underline:none'><o:p></o:p></span></span></span></p> 4305 4287 4306 4288 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<span … … 4311 4293 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4312 4294 color:windowtext;text-decoration:none;text-underline:none'><span 4313 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 4295 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 4314 4296 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4315 "Times New Roman"'>Menu<b style='mso-bidi-font-weight:normal'> 4316 ‘Reflection List’ </b>– <span class=MsoHyperlink><span 4317 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>4297 "Times New Roman"'>Menu<b style='mso-bidi-font-weight:normal'> ‘Reflection 4298 List’ </b>– <span class=MsoHyperlink><span style='color:windowtext;text-decoration: 4299 none;text-underline:none'><o:p></o:p></span></span></span></p> 4318 4300 4319 4301 <p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto; … … 4321 4303 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4322 4304 color:windowtext;text-decoration:none;text-underline:none'><span 4323 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4305 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4324 4306 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4325 "Times New Roman"'>Select phase – if there is more than one phase; you4326 canselect another phase; the window title will show which phase is shown. <span4307 "Times New Roman"'>Select phase – if there is more than one phase; you can 4308 select another phase; the window title will show which phase is shown. <span 4327 4309 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 4328 4310 text-underline:none'><o:p></o:p></span></span></span></p> 4329 4311 4330 <h3>Single Crystal Histograms –HKLF</h3>4312 <h3>Single Crystal Histograms – HKLF</h3> 4331 4313 4332 4314 <h4>Instrument Parameters</h4> … … 4338 4320 4339 4321 <p class=MsoNormal>This controls the display of the single crystal reflections 4340 on the plot. If available a green ring is shown for F-observed, a blue ring for 4341 F-calculated and a central disk for <span style='font-family:"Calibri","sans-serif"'>Δ</span>F 4342 (green for <span class=GramE>Fo></span>Fc and red for Fo<Fc).</p> 4322 on the plot. <span class=GramE>If available a green ring is shown for 4323 F-observed, a blue ring for F-calculated and a central disk for <span 4324 style='font-family:Calibri'>Δ</span>F (green for Fo>Fc and red for 4325 Fo<Fc).</span></p> 4343 4326 4344 4327 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5> … … 4346 4329 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo19'><![if !supportLists]><span 4347 4330 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 4348 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b4331 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 4349 4332 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Change 4350 the scale</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 4351 –move the slider, the rings will change their radius accordingly.<o:p></o:p></span></p>4333 the scale</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 4334 move the slider, the rings will change their radius accordingly.<o:p></o:p></span></p> 4352 4335 4353 4336 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo19'><![if !supportLists]><span 4354 4337 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 4355 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b4338 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 4356 4339 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select 4357 the zone</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 4358 –select between 100, 010 or 001; plot axes will be labeled accordingly.<o:p></o:p></span></p>4340 the zone</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 4341 select between 100, 010 or 001; plot axes will be labeled accordingly.<o:p></o:p></span></p> 4359 4342 4360 4343 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo19'><![if !supportLists]><span 4361 4344 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 4362 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b4345 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 4363 4346 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select 4364 plot type</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 4365 – the choices are either F or F<sup>2</sup>, </span><span 4366 style='font-family:"Calibri","sans-serif";mso-fareast-font-family:"Times New Roman"'>Δ</span><span4347 plot type</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 4348 the choices are either F or F<sup>2</sup>, </span><span style='font-family: 4349 Calibri;mso-fareast-font-family:"Times New Roman"'>Δ</span><span 4367 4350 style='mso-fareast-font-family:"Times New Roman"'>F<sup>2</sup>/</span><span 4368 class=GramE><span style='font-family:"Calibri","sans-serif";mso-fareast-font-family: 4369 "Times New Roman"'>σ(</span></span><span style='font-family:"Calibri","sans-serif"; 4370 mso-fareast-font-family:"Times New Roman"'>F<sup>2</sup>)</span><span 4351 class=GramE><span style='font-family:Calibri;mso-fareast-font-family:"Times New Roman"'>σ(</span></span><span 4352 style='font-family:Calibri;mso-fareast-font-family:"Times New Roman"'>F<sup>2</sup>)</span><span 4371 4353 style='mso-fareast-font-family:"Times New Roman"'>, </span><span 4372 style='font-family: "Calibri","sans-serif";mso-fareast-font-family:"Times New Roman"'>Δ</span><span4354 style='font-family:Calibri;mso-fareast-font-family:"Times New Roman"'>Δ</span><span 4373 4355 style='mso-fareast-font-family:"Times New Roman"'>F<sup>2</sup>></span><span 4374 style='font-family: "Calibri","sans-serif";mso-fareast-font-family:"Times New Roman"'>σ(F<sup>2</sup>)</span><span4356 style='font-family:Calibri;mso-fareast-font-family:"Times New Roman"'>σ(F<sup>2</sup>)</span><span 4375 4357 style='mso-fareast-font-family:"Times New Roman"'> or </span><span 4376 style='font-family: "Calibri","sans-serif";mso-fareast-font-family:"Times New Roman"'>Δ</span><span4358 style='font-family:Calibri;mso-fareast-font-family:"Times New Roman"'>Δ</span><span 4377 4359 style='mso-fareast-font-family:"Times New Roman"'>F<sup>2</sup>>3</span><span 4378 style='font-family: "Calibri","sans-serif";mso-fareast-font-family:"Times New Roman"'>σ(F<sup>2</sup>)</span><span4360 style='font-family:Calibri;mso-fareast-font-family:"Times New Roman"'>σ(F<sup>2</sup>)</span><span 4379 4361 style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></p> 4380 4362 4381 4363 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo19'><![if !supportLists]><span 4382 4364 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 4383 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b4365 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 4384 4366 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select 4385 layer </span></b><span style='mso-fareast-font-family:"Times New Roman"'> –4386 movethe slider for upper layers for the selected zone.<o:p></o:p></span></p>4367 layer </span></b><span style='mso-fareast-font-family:"Times New Roman"'>– move 4368 the slider for upper layers for the selected zone.<o:p></o:p></span></p> 4387 4369 4388 4370 <h4><span style='mso-fareast-font-family:"Times New Roman"'>Reflection List</span><span … … 4415 4397 none;text-underline:none'><o:p></o:p></span></span></span></p> 4416 4398 4417 <h3><span style='mso-fareast-font-family:"Times New Roman"'>2-D Images –4418 IMG<spanclass=MsoHyperlink><span style='color:windowtext;text-decoration:none;4399 <h3><span style='mso-fareast-font-family:"Times New Roman"'>2-D Images – IMG<span 4400 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 4419 4401 text-underline:none'><o:p></o:p></span></span></span></h3> 4420 4402 … … 4422 4404 4423 4405 <p class=MsoNormal>This window shows whatever comment lines found in a 4424 “metadata” file when the image data file was read by GSAS-II. If 4425 you are lucky, there will be useful information here (e.g. sample name, date 4426 collected, wavelength used, etc.). If not, this window will be blank. The text 4427 isread-only.</p>4406 “metadata” file when the image data file was read by GSAS-II. If you are lucky, 4407 there will be useful information here (e.g. sample name, date collected, 4408 wavelength used, etc.). If not, this window will be blank. The text is 4409 read-only.</p> 4428 4410 4429 4411 <h4>Image Controls<a name="Image_Controls"></a></h4> … … 4467 4449 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4468 4450 color:windowtext;text-decoration:none;text-underline:none'><span 4469 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 4451 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 4470 4452 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4471 "Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Compute’</b>4472 –The compute menu shows computations that are possible for this phase.<span4453 "Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Compute’</b> – 4454 The compute menu shows computations that are possible for this phase.<span 4473 4455 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 4474 4456 text-underline:none'><o:p></o:p></span></span></span></p> … … 4478 4460 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4479 4461 color:windowtext;text-decoration:none;text-underline:none'><span 4480 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4462 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4481 4463 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4482 4464 style='mso-fareast-font-family:"Times New Roman"'>Fourier maps</span></b><span 4483 style='mso-fareast-font-family:"Times New Roman"'> –compute Fourier maps4465 style='mso-fareast-font-family:"Times New Roman"'> – compute Fourier maps 4484 4466 according to the controls set at bottom of General page.<span 4485 4467 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; … … 4490 4472 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4491 4473 color:windowtext;text-decoration:none;text-underline:none'><span 4492 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4474 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4493 4475 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4494 4476 style='mso-fareast-font-family:"Times New Roman"'>Search maps </span></b><span 4495 style='mso-fareast-font-family:"Times New Roman"'>– search the computed 4496 Fourier map. Peaks that are above ‘Peak cutoff’ % of the maximum 4497 will be found in this procedure; they will be printed on the console and will 4498 be shown in the ‘<a name="Map_peaks"></a><a href="gsasII.html"><span 4499 style='mso-bookmark:Map_peaks'><span style='color:windowtext;text-decoration: 4500 none;text-underline:none'>Map peaks</span></span></a><span style='mso-bookmark: 4501 Map_peaks'></span>’ page. This page will immediately be shown and the 4502 peaks will be shown on the structure drawing for this phase as white 3-D 4503 crosses.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 4504 none;text-underline:none'><o:p></o:p></span></span></span></p> 4477 style='mso-fareast-font-family:"Times New Roman"'>– search the computed Fourier 4478 map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this 4479 procedure; they will be printed on the console and will be shown in the ‘<a 4480 name="Map_peaks"></a><a href="gsasII.html"><span style='mso-bookmark:Map_peaks'><span 4481 style='color:windowtext;text-decoration:none;text-underline:none'>Map peaks</span></span></a><span 4482 style='mso-bookmark:Map_peaks'></span>’ page. This page will immediately be 4483 shown and the peaks will be shown on the structure drawing for this phase as 4484 white 3-D crosses.<span class=MsoHyperlink><span style='color:windowtext; 4485 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 4505 4486 4506 4487 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 4508 4489 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4509 4490 color:windowtext;text-decoration:none;text-underline:none'><span 4510 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4491 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4511 4492 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4512 4493 style='mso-fareast-font-family:"Times New Roman"'>Charge flipping </span></b><span 4513 style='mso-fareast-font-family:"Times New Roman"'>– This performs a 4514 charge flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure 4515 solution using the method of Oszlanyi & Suto (Acta Cryst. A60, 134-141, 4516 2004). You will need to select a source for the reflection set and perhaps 4517 select an element for normalization by its form factor, a resolution limit 4518 (usually 0.5A) and a charge flip threshold (usually 0.1); these are found at 4519 the bottom of the <b style='mso-bidi-font-weight:normal'>General</b> window. A 4520 progress bar showing the charge flip residual is shown while the charge flip is 4521 in operation. When the residual is no longer decreasing (be patient – it 4522 doesn’t necessarily fall continuously), press the <b style='mso-bidi-font-weight: 4523 normal'>Cancel</b> button to stop the charge flipping. The resulting map will 4524 be positioned to properly place symmetry operators (NB: depends on the quality 4525 of the resulting phases), searched for peaks and the display shifts to <b 4526 style='mso-bidi-font-weight:normal'>Map peaks</b> to show them.<span 4527 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 4528 text-underline:none'><o:p></o:p></span></span></span></p> 4494 style='mso-fareast-font-family:"Times New Roman"'>– This performs a charge 4495 flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution 4496 using the method of Oszlanyi & Suto (Acta Cryst. A60, 134-141, 2004). You 4497 will need to select a source for the reflection set and perhaps select an 4498 element for normalization by its form factor, a resolution limit (usually 0.5A) 4499 and a charge flip threshold (usually 0.1); these are found at the bottom of the 4500 <b style='mso-bidi-font-weight:normal'>General</b> window. A progress bar 4501 showing the charge flip residual is shown while the charge flip is in 4502 operation. When the residual is no longer decreasing (be patient – it doesn’t 4503 necessarily fall continuously), press the <b style='mso-bidi-font-weight:normal'>Cancel</b> 4504 button to stop the charge flipping. The resulting map will be positioned to 4505 properly place symmetry operators (NB: depends on the quality of the resulting 4506 phases), searched for peaks and the display shifts to <b style='mso-bidi-font-weight: 4507 normal'>Map peaks</b> to show them.<span class=MsoHyperlink><span 4508 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 4529 4509 4530 4510 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 4532 4512 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4533 4513 color:windowtext;text-decoration:none;text-underline:none'><span 4534 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 4514 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 4535 4515 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4536 4516 style='mso-fareast-font-family:"Times New Roman"'>Clear map </span></b><span 4537 style='mso-fareast-font-family:"Times New Roman"'> –This clears any4517 style='mso-fareast-font-family:"Times New Roman"'>– This clears any 4538 4518 Fourier/charge flip map from memory; the Fourier map controls are also cleared.<span 4539 4519 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; … … 4543 4523 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4544 4524 color:windowtext;text-decoration:none;text-underline:none'><span 4545 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 4525 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 4546 4526 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4547 4527 "Times New Roman"'>The items in the upper part of the General page that can be … … 4554 4534 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4555 4535 color:windowtext;text-decoration:none;text-underline:none'><span 4556 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4536 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4557 4537 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4558 4538 style='mso-fareast-font-family:"Times New Roman"'>Phase name</span></b><span 4559 style='mso-fareast-font-family:"Times New Roman"'> – this is the name4560 assigned to this phase. It should only be changed when the phase is initialized 4561 orimported.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>4539 style='mso-fareast-font-family:"Times New Roman"'> – this is the name assigned 4540 to this phase. It should only be changed when the phase is initialized or 4541 imported.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p> 4562 4542 4563 4543 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 4565 4545 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4566 4546 color:windowtext;text-decoration:none;text-underline:none'><span 4567 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4547 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4568 4548 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4569 style='mso-fareast-font-family:"Times New Roman"'>Phase type –</span></b><span4570 style='mso-fareast-font-family:"Times New Roman"'>this can only be set when 4571 thereare no atoms in the Atoms page for this phase. Select it when the phase is4549 style='mso-fareast-font-family:"Times New Roman"'>Phase type – </span></b><span 4550 style='mso-fareast-font-family:"Times New Roman"'>this can only be set when there 4551 are no atoms in the Atoms page for this phase. Select it when the phase is 4572 4552 initialized.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p> 4573 4553 … … 4576 4556 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4577 4557 color:windowtext;text-decoration:none;text-underline:none'><span 4578 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4558 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4579 4559 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4580 4560 style='mso-fareast-font-family:"Times New Roman"'>Space group</span></b><span 4581 style='mso-fareast-font-family:"Times New Roman"'> – this should be set4582 when the phase is initialized; it can be changed later. Be careful about the 4583 impact on Atom site symmetry and multiplicity if you do. GSAS-II will recognize 4584 anylegal space group symbol using the short Hermann-Mauguin forms; put a space4585 between the axial fields (e.g. ‘F d 3 m’ not ‘Fd3m’).4586 For space groups with a choice of origin (e.g. F d 3 m), GSAS-II always uses 4587 the 2<sup>nd</sup> setting where the center of inversion is located at the4588 origin. The choice of space group will set the available unit cell parameters.<span4589 class=MsoHyperlink><spanstyle='color:windowtext'><o:p></o:p></span></span></span></p>4561 style='mso-fareast-font-family:"Times New Roman"'> – this should be set when 4562 the phase is initialized; it can be changed later. Be careful about the impact 4563 on Atom site symmetry and multiplicity if you do. GSAS-II will recognize any 4564 legal space group symbol using the short Hermann-Mauguin forms; put a space 4565 between the axial fields (e.g. ‘F d 3 m’ not ‘Fd3m’). For space groups with a 4566 choice of origin (e.g. F d 3 m), GSAS-II always uses the 2<sup>nd</sup> setting 4567 where the center of inversion is located at the origin. The choice of space 4568 group will set the available unit cell parameters.<span class=MsoHyperlink><span 4569 style='color:windowtext'><o:p></o:p></span></span></span></p> 4590 4570 4591 4571 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 4592 4572 auto;text-indent:-.25in;mso-list:l1 level2 lfo20'><![if !supportLists]><span 4593 4573 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 4594 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b4574 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 4595 4575 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Refine 4596 unit cell</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 4597 – set this flag to refine the unit cell parameters in a Rietveld or 4598 Pawley refinement. The actual parameters refined are the symmetry allowed terms 4599 (A<sub>0</sub>-A<sub>5</sub>) in the expression</span><i style='mso-bidi-font-style: 4600 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family: 4601 "Times New Roman"'><br> 4576 unit cell</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 4577 set this flag to refine the unit cell parameters in a Rietveld or Pawley 4578 refinement. The actual parameters refined are the symmetry allowed terms (A<sub>0</sub>-A<sub>5</sub>) 4579 in the expression</span><i style='mso-bidi-font-style:normal'><span 4580 style='font-family:"Cambria Math";mso-fareast-font-family:"Times New Roman"'><br> 4602 4581 </span></i><!--[if gte msEquation 12]><m:oMathPara><m:oMath><m:sSup><m:sSupPr><span 4603 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";4582 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 4604 4583 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 4605 4584 normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style: 4606 normal'><span style='font-family:"Cambria Math" ,"serif";mso-fareast-font-family:4607 "Times New Roman"'><m:r> d</m:r></span></i></m:e><m:sup><i style='mso-bidi-font-style:4608 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:4609 "Times New Roman"'><m:r>*2</m:r></span></i></m:sup></m:sSup><i4610 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math" ,"serif";4611 mso-fareast-font-family:"Times New Roman"'><m:r> =</m:r></span></i><m:sSub><m:sSubPr><span4612 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";4585 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 4586 "Times New Roman"'><m:r><span>d</m:r></span></span></i></m:e><m:sup><i 4587 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4588 mso-fareast-font-family:"Times New Roman"'><m:r><span>*2</m:r></span></span></i></m:sup></m:sSup><i 4589 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4590 mso-fareast-font-family:"Times New Roman"'><m:r><span>=</m:r></span></span></i><m:sSub><m:sSubPr><span 4591 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 4613 4592 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 4614 4593 normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style: 4615 normal'><span style='font-family:"Cambria Math" ,"serif";mso-fareast-font-family:4616 "Times New Roman"'><m:r> A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style:4617 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:4618 "Times New Roman"'><m:r>0</m:r></span></i></m:sub></m:sSub><m:sSup><m:sSupPr><span4619 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";4594 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 4595 "Times New Roman"'><m:r><span>A</m:r></span></span></i></m:e><m:sub><i 4596 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4597 mso-fareast-font-family:"Times New Roman"'><m:r><span>0</m:r></span></span></i></m:sub></m:sSub><m:sSup><m:sSupPr><span 4598 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 4620 4599 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 4621 4600 normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style: 4622 normal'><span style='font-family:"Cambria Math" ,"serif";mso-fareast-font-family:4623 "Times New Roman"'><m:r> h</m:r></span></i></m:e><m:sup><i style='mso-bidi-font-style:4624 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:4625 "Times New Roman"'><m:r>2</m:r></span></i></m:sup></m:sSup><i4626 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math" ,"serif";4627 mso-fareast-font-family:"Times New Roman"'><m:r> +</m:r></span></i><m:sSub><m:sSubPr><span4628 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";4601 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 4602 "Times New Roman"'><m:r><span>h</m:r></span></span></i></m:e><m:sup><i 4603 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4604 mso-fareast-font-family:"Times New Roman"'><m:r><span>2</m:r></span></span></i></m:sup></m:sSup><i 4605 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4606 mso-fareast-font-family:"Times New Roman"'><m:r><span>+</m:r></span></span></i><m:sSub><m:sSubPr><span 4607 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 4629 4608 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 4630 4609 normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style: 4631 normal'><span style='font-family:"Cambria Math" ,"serif";mso-fareast-font-family:4632 "Times New Roman"'><m:r> A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style:4633 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:4634 "Times New Roman"'><m:r>1</m:r></span></i></m:sub></m:sSub><m:sSup><m:sSupPr><span4635 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";4610 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 4611 "Times New Roman"'><m:r><span>A</m:r></span></span></i></m:e><m:sub><i 4612 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4613 mso-fareast-font-family:"Times New Roman"'><m:r><span>1</m:r></span></span></i></m:sub></m:sSub><m:sSup><m:sSupPr><span 4614 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 4636 4615 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 4637 4616 normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style: 4638 normal'><span style='font-family:"Cambria Math" ,"serif";mso-fareast-font-family:4639 "Times New Roman"'><m:r> k</m:r></span></i></m:e><m:sup><i style='mso-bidi-font-style:4640 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:4641 "Times New Roman"'><m:r>2</m:r></span></i></m:sup></m:sSup><i4642 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math" ,"serif";4643 mso-fareast-font-family:"Times New Roman"'><m:r> +</m:r></span></i><m:sSub><m:sSubPr><span4644 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";4617 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 4618 "Times New Roman"'><m:r><span>k</m:r></span></span></i></m:e><m:sup><i 4619 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4620 mso-fareast-font-family:"Times New Roman"'><m:r><span>2</m:r></span></span></i></m:sup></m:sSup><i 4621 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4622 mso-fareast-font-family:"Times New Roman"'><m:r><span>+</m:r></span></span></i><m:sSub><m:sSubPr><span 4623 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 4645 4624 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 4646 4625 normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style: 4647 normal'><span style='font-family:"Cambria Math" ,"serif";mso-fareast-font-family:4648 "Times New Roman"'><m:r> A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style:4649 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:4650 "Times New Roman"'><m:r>2</m:r></span></i></m:sub></m:sSub><m:sSup><m:sSupPr><span4651 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";4626 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 4627 "Times New Roman"'><m:r><span>A</m:r></span></span></i></m:e><m:sub><i 4628 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4629 mso-fareast-font-family:"Times New Roman"'><m:r><span>2</m:r></span></span></i></m:sub></m:sSub><m:sSup><m:sSupPr><span 4630 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 4652 4631 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 4653 4632 normal'><m:ctrlPr></m:ctrlPr></span></m:sSupPr><m:e><i style='mso-bidi-font-style: 4654 normal'><span style='font-family:"Cambria Math" ,"serif";mso-fareast-font-family:4655 "Times New Roman"'><m:r> l</m:r></span></i></m:e><m:sup><i style='mso-bidi-font-style:4656 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:4657 "Times New Roman"'><m:r>2</m:r></span></i></m:sup></m:sSup><i4658 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math" ,"serif";4659 mso-fareast-font-family:"Times New Roman"'><m:r> +</m:r></span></i><m:sSub><m:sSubPr><span4660 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";4633 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 4634 "Times New Roman"'><m:r><span>l</m:r></span></span></i></m:e><m:sup><i 4635 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4636 mso-fareast-font-family:"Times New Roman"'><m:r><span>2</m:r></span></span></i></m:sup></m:sSup><i 4637 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4638 mso-fareast-font-family:"Times New Roman"'><m:r><span>+</m:r></span></span></i><m:sSub><m:sSubPr><span 4639 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 4661 4640 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 4662 4641 normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style: 4663 normal'><span style='font-family:"Cambria Math" ,"serif";mso-fareast-font-family:4664 "Times New Roman"'><m:r> A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style:4665 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:4666 "Times New Roman"'><m:r>3</m:r></span></i></m:sub></m:sSub><i4667 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math" ,"serif";4668 mso-fareast-font-family:"Times New Roman"'><m:r> h</m:r><m:r>k</m:r><m:r>+</m:r></span></i><m:sSub><m:sSubPr><span4669 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";4642 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 4643 "Times New Roman"'><m:r><span>A</m:r></span></span></i></m:e><m:sub><i 4644 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4645 mso-fareast-font-family:"Times New Roman"'><m:r><span>3</m:r></span></span></i></m:sub></m:sSub><i 4646 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4647 mso-fareast-font-family:"Times New Roman"'><m:r><span>h</m:r></span><m:r><span>k</m:r></span><m:r><span>+</m:r></span></span></i><m:sSub><m:sSubPr><span 4648 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 4670 4649 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 4671 4650 normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style: 4672 normal'><span style='font-family:"Cambria Math" ,"serif";mso-fareast-font-family:4673 "Times New Roman"'><m:r> A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style:4674 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:4675 "Times New Roman"'><m:r>4</m:r></span></i></m:sub></m:sSub><i4676 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math" ,"serif";4677 mso-fareast-font-family:"Times New Roman"'><m:r> h</m:r><m:r>l</m:r><m:r>+</m:r></span></i><m:sSub><m:sSubPr><span4678 style='font-family:"Cambria Math" ,"serif";mso-ascii-font-family:"Cambria Math";4651 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 4652 "Times New Roman"'><m:r><span>A</m:r></span></span></i></m:e><m:sub><i 4653 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4654 mso-fareast-font-family:"Times New Roman"'><m:r><span>4</m:r></span></span></i></m:sub></m:sSub><i 4655 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4656 mso-fareast-font-family:"Times New Roman"'><m:r><span>h</m:r></span><m:r><span>l</m:r></span><m:r><span>+</m:r></span></span></i><m:sSub><m:sSubPr><span 4657 style='font-family:"Cambria Math";mso-ascii-font-family:"Cambria Math"; 4679 4658 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: 4680 4659 normal'><m:ctrlPr></m:ctrlPr></span></m:sSubPr><m:e><i style='mso-bidi-font-style: 4681 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family: 4682 "Times New Roman"'><m:r>A</m:r></span></i></m:e><m:sub><i style='mso-bidi-font-style: 4683 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family: 4684 "Times New Roman"'><m:r>5</m:r></span></i></m:sub></m:sSub><i 4685 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math","serif"; 4686 mso-fareast-font-family:"Times New Roman"'><m:r>kl</m:r></span></i></m:oMath></m:oMathPara><![endif]--><![if !msEquation]><span 4687 style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-font-family: 4688 "Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US; 4689 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape 4690 id="_x0000_i1025" type="#_x0000_t75" style='width:251.25pt;height:14.25pt'> 4691 <v:imagedata src="gsasII_files/image003.png" o:title="" chromakey="white"/> 4692 </v:shape><![endif]--><![if !vml]><img width=335 height=19 4693 src="gsasII_files/image004.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]></p> 4660 normal'><span style='font-family:"Cambria Math";mso-fareast-font-family: 4661 "Times New Roman"'><m:r><span>A</m:r></span></span></i></m:e><m:sub><i 4662 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4663 mso-fareast-font-family:"Times New Roman"'><m:r><span>5</m:r></span></span></i></m:sub></m:sSub><i 4664 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4665 mso-fareast-font-family:"Times New Roman"'><m:r><span>kl</m:r></span></span></i></m:oMath></m:oMathPara><![endif]--><![if !msEquation]><span 4666 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family: 4667 "ＭＳ 明朝";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US; 4668 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><img width=254 height=16 4669 id="_x0000_i1025" src="gsasII_files/image002.png"></span><![endif]></p> 4694 4670 4695 4671 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 4697 4673 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4698 4674 color:windowtext;text-decoration:none;text-underline:none'><span 4699 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 4675 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 4700 4676 </span></span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight: 4701 4677 normal'><span style='mso-fareast-font-family:"Times New Roman"'>a</span></b></span><b 4702 4678 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>, 4703 4679 b, c, alpha, beta, gamma</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 4704 – lattice parameters; only those permitted by the space group are shown. 4705 The <span class=GramE>volume<span style='mso-spacerun:yes'> </span>is</span> 4706 computed from the values entered.</span><span class=MsoHyperlink><span 4707 style='color:windowtext'><o:p></o:p></span></span></p>4680 – lattice parameters; only those permitted by the space group are shown. The <span 4681 class=GramE>volume<span style="mso-spacerun:yes"> </span>is</span> computed 4682 from the values entered.</span><span class=MsoHyperlink><span style='color: 4683 windowtext'><o:p></o:p></span></span></p> 4708 4684 4709 4685 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l1 level1 lfo20'><![if !supportLists]><span 4710 4686 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4711 4687 color:windowtext;text-decoration:none;text-underline:none'><span 4712 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 4688 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 4713 4689 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4714 4690 "Times New Roman"'>If there are entries in the Atoms page then the Elements … … 4722 4698 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4723 4699 color:windowtext;text-decoration:none;text-underline:none'><span 4724 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 4700 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 4725 4701 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4726 4702 "Times New Roman"'>Next are the Pawley controls.<span class=MsoHyperlink><span … … 4731 4707 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4732 4708 color:windowtext;text-decoration:none;text-underline:none'><span 4733 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4709 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4734 4710 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4735 4711 style='mso-fareast-font-family:"Times New Roman"'>Do Pawley refinement?</span></b><span 4736 style='mso-fareast-font-family:"Times New Roman"'> – This must be chosen 4737 to perform a Pawley refinement as opposed to a Rietveld refinement for this 4738 phase. <b style='mso-bidi-font-weight:normal'>NB:</b> you probably should clear 4739 the <b style='mso-bidi-font-weight:normal'>Histogram scale factor</b> 4740 refinement flag (found in <b style='mso-bidi-font-weight:normal'>Sample 4741 parameters</b> for the powder data set) as it cannot be refined simultaneously 4742 with the Pawley reflection intensities.<span class=MsoHyperlink><span 4743 style='color:windowtext'><o:p></o:p></span></span></span></p> 4712 style='mso-fareast-font-family:"Times New Roman"'> – This must be chosen to 4713 perform a Pawley refinement as opposed to a Rietveld refinement for this phase. 4714 <b style='mso-bidi-font-weight:normal'>NB:</b> you probably should clear the <b 4715 style='mso-bidi-font-weight:normal'>Histogram scale factor</b> refinement flag 4716 (found in <b style='mso-bidi-font-weight:normal'>Sample parameters</b> for the 4717 powder data set) as it cannot be refined simultaneously with the Pawley 4718 reflection intensities.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p> 4744 4719 4745 4720 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 4747 4722 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4748 4723 color:windowtext;text-decoration:none;text-underline:none'><span 4749 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4724 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4750 4725 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4751 4726 style='mso-fareast-font-family:"Times New Roman"'>Pawley <span class=SpellE>dmin</span></span></b><span 4752 style='mso-fareast-font-family:"Times New Roman"'> –This is the minimum4727 style='mso-fareast-font-family:"Times New Roman"'> – This is the minimum 4753 4728 d-spacing to be used in a Pawley refinement. <b style='mso-bidi-font-weight: 4754 4729 normal'>NB:</b> be sure to set this to match the minimum d-spacing indicated by … … 4760 4735 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4761 4736 color:windowtext;text-decoration:none;text-underline:none'><span 4762 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4737 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4763 4738 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4764 4739 style='mso-fareast-font-family:"Times New Roman"'>Pawley neg. wt.</span></b><span 4765 style='mso-fareast-font-family:"Times New Roman"'> – This is the weight4766 for apenalty function applied during a Pawley refinement on resulting negative4740 style='mso-fareast-font-family:"Times New Roman"'> – This is the weight for a 4741 penalty function applied during a Pawley refinement on resulting negative 4767 4742 intensities. Use with caution; initially try very small values (e.g. .01). A 4768 4743 value of zero means no penalty is applied.<span class=MsoHyperlink><span … … 4772 4747 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4773 4748 color:windowtext;text-decoration:none;text-underline:none'><span 4774 style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> 4749 style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> 4775 4750 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4776 4751 "Times New Roman"'>Fourier map controls are shown next on the General page. A … … 4784 4759 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4785 4760 color:windowtext;text-decoration:none;text-underline:none'><span 4786 style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'> 4761 style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'> 4787 4762 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 4788 4763 "Times New Roman"'>Charge flip controls are below the Fourier map controls.<span … … 4794 4769 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4795 4770 color:windowtext;text-decoration:none;text-underline:none'><span 4796 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4771 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4797 4772 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4798 4773 style='mso-fareast-font-family:"Times New Roman"'>Reflection set from</span></b><span 4799 style='mso-fareast-font-family:"Times New Roman"'> – This is the source 4800 of structure factors to be used in a charge flip calculation. These may be 4801 either a single crystal data set, or structure factors extracted from a powder 4802 pattern via a Pawley refinement or a <span class=SpellE>Rietveld</span> 4803 refinement.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 4804 none;text-underline:none'><o:p></o:p></span></span></span></p> 4774 style='mso-fareast-font-family:"Times New Roman"'> – This is the source of 4775 structure factors to be used in a charge flip calculation. These may be either 4776 a single crystal data set, or structure factors extracted from a powder pattern 4777 via a Pawley refinement or a Rietveld refinement.<span class=MsoHyperlink><span 4778 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 4805 4779 4806 4780 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 4808 4782 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4809 4783 color:windowtext;text-decoration:none;text-underline:none'><span 4810 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4784 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4811 4785 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4812 4786 style='mso-fareast-font-family:"Times New Roman"'>Normalizing element </span></b><span 4813 style='mso-fareast-font-family:"Times New Roman"'> – This is an element4814 f orm factor chosen to normalize the structure factors before charge flipping. <b4787 style='mso-fareast-font-family:"Times New Roman"'>– This is an element form 4788 factor chosen to normalize the structure factors before charge flipping. <b 4815 4789 style='mso-bidi-font-weight:normal'>None</b> (the default) can be selected from 4816 4790 the lower right of the Periodic Table display shown when this is selected.<span … … 4822 4796 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4823 4797 color:windowtext;text-decoration:none;text-underline:none'><span 4824 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4798 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4825 4799 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4826 4800 style='mso-fareast-font-family:"Times New Roman"'>Resolution </span></b><span 4827 style='mso-fareast-font-family:"Times New Roman"'> – This is the4828 resolution of the charge flip map; default is 0.5A. The set of reflections is 4829 expanded to a full sphere and zero filled to this resolution limit; this suite 4830 of reflectionsis then used for charge flipping.<span class=MsoHyperlink><span4801 style='mso-fareast-font-family:"Times New Roman"'>– This is the resolution of 4802 the charge flip map; default is 0.5A. The set of reflections is expanded to a 4803 full sphere and zero filled to this resolution limit; this suite of reflections 4804 is then used for charge flipping.<span class=MsoHyperlink><span 4831 4805 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 4832 4806 … … 4834 4808 auto;text-indent:-.25in;mso-list:l1 level2 lfo20'><![if !supportLists]><span 4835 4809 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 4836 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span4810 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 4837 4811 class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family: 4838 "Times New Roman"'>k-Factor</span></b></span><span style='mso-fareast-font-family: 4839 "Times New Roman"'> – This is the threshold on the density map, all 4840 densities below this are charge flipped.</span></p> 4812 "Times New Roman"'>k</span></b></span><b style='mso-bidi-font-weight:normal'><span 4813 style='mso-fareast-font-family:"Times New Roman"'>-Factor</span></b><span 4814 style='mso-fareast-font-family:"Times New Roman"'> – This is the threshold on 4815 the density map, all densities below this are charge flipped.</span></p> 4841 4816 4842 4817 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 4843 4818 auto;text-indent:-.25in;mso-list:l1 level2 lfo20'><![if !supportLists]><span 4844 4819 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span 4845 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span4820 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 4846 4821 class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family: 4847 "Times New Roman"'>k-Max</span></b></span><span style='mso-fareast-font-family: 4848 "Times New Roman"'> – This is an upper threshold on the density may; all 4849 densities above this are charge flipped. In this way the “uranium 4850 solution” problem is avoided. Use k-Max = 10-12 for equal atom problems 4851 and larger for heavy atom ones.<o:p></o:p></span></p> 4822 "Times New Roman"'>k</span></b></span><b style='mso-bidi-font-weight:normal'><span 4823 style='mso-fareast-font-family:"Times New Roman"'>-Max</span></b><span 4824 style='mso-fareast-font-family:"Times New Roman"'> – This is an upper threshold 4825 on the density may; all densities above this are charge flipped. In this way 4826 the “uranium solution” problem is avoided. Use k-Max = 10-12 for equal atom 4827 problems and larger for heavy atom ones.<o:p></o:p></span></p> 4852 4828 4853 4829 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l1 level1 lfo20'><![if !supportLists]><span 4854 4830 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>7.<span 4855 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span4831 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 4856 4832 style='mso-fareast-font-family:"Times New Roman"'>Monte Carlo/Simulated 4857 4833 Annealing controls are at the bottom of the window. (Future capability & … … 4861 4837 auto;text-indent:-.25in;mso-list:l1 level2 lfo20'><![if !supportLists]><span 4862 4838 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 4863 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b4839 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 4864 4840 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Reflection 4865 set from</span></b><span style='mso-fareast-font-family:"Times New Roman"'> 4866 –This is the source of structure factors to be used in a charge flip4841 set from</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – 4842 This is the source of structure factors to be used in a charge flip 4867 4843 calculation. These may be either a single crystal data set, or structure 4868 factors extracted from a powder pattern via a Pawley refinement or a <span4869 class=SpellE>Rietveld</span>refinement.<o:p></o:p></span></p>4844 factors extracted from a powder pattern via a Pawley refinement or a Rietveld 4845 refinement.<o:p></o:p></span></p> 4870 4846 4871 4847 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 4873 4849 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4874 4850 color:windowtext;text-decoration:none;text-underline:none'><span 4875 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4851 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4876 4852 </span></span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight: 4877 normal'><span style='mso-fareast-font-family:"Times New Roman"'>d -min</span></b></span><b4878 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'> 4853 normal'><span style='mso-fareast-font-family:"Times New Roman"'>d</span></b></span><b 4854 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>-min 4879 4855 </span></b><span style='mso-fareast-font-family:"Times New Roman"'>- This 4880 4856 restricts the set of reflections to be used in the MC/SA run.</span><span … … 4886 4862 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4887 4863 color:windowtext;text-decoration:none;text-underline:none'><span 4888 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4864 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4889 4865 </span></span></span></span><![endif]><span class=MsoHyperlink><b 4890 4866 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"; 4891 4867 color:windowtext;text-decoration:none;text-underline:none'>MC/SA algorithm</span></b></span><span 4892 4868 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4893 color:windowtext;text-decoration:none;text-underline:none'> – This selects4894 t he type of jump to be used for each MC/SA trial.<o:p></o:p></span></span></p>4869 color:windowtext;text-decoration:none;text-underline:none'> – This selects the 4870 type of jump to be used for each MC/SA trial.<o:p></o:p></span></span></p> 4895 4871 4896 4872 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 4898 4874 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4899 4875 color:windowtext;text-decoration:none;text-underline:none'><span 4900 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 4876 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 4901 4877 </span></span></span></span><![endif]><span class=MsoHyperlink><b 4902 4878 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"; 4903 4879 color:windowtext;text-decoration:none;text-underline:none'>Annealing schedule</span></b></span><span 4904 4880 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4905 color:windowtext;text-decoration:none;text-underline:none'> – This4906 selects the beginning MC/SA “temperature”, final 4907 “temperature”, slope and number of trialsat each step.<o:p></o:p></span></span></p>4881 color:windowtext;text-decoration:none;text-underline:none'> – This selects the 4882 beginning MC/SA “temperature”, final “temperature”, slope and number of trials 4883 at each step.<o:p></o:p></span></span></p> 4908 4884 4909 4885 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; … … 4911 4887 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4912 4888 color:windowtext;text-decoration:none;text-underline:none'><span 4913 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 4889 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 4914 4890 </span></span></span></span><![endif]><span class=MsoHyperlink><b 4915 4891 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"; 4916 4892 color:windowtext;text-decoration:none;text-underline:none'>A-jump & B-jump</span></b></span><span 4917 4893 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4918 color:windowtext;text-decoration:none;text-underline:none'> – If the 4919 “Tremayne” algorithm is chosen these determine the jump components 4920 for each trial.<o:p></o:p></span></span></p> 4894 color:windowtext;text-decoration:none;text-underline:none'> – If the “Tremayne” 4895 algorithm is chosen these determine the jump components for each trial.<o:p></o:p></span></span></p> 4921 4896 4922 4897 <h4><a name=Data></a><u><span style='mso-fareast-font-family:"Times New Roman"'>Data … … 4924 4899 4925 4900 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?</span><i 4926 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math" ,"serif";4901 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math"; 4927 4902 mso-fareast-font-family:"Times New Roman"'><br style='mso-special-character: 4928 4903 line-break'> … … 4932 4907 4933 4908 <h4><a name=Atoms></a><u>Atoms</u><span class=MsoHyperlink><span 4934 style='font-size:12.0pt;font-family:"Times New Roman" ,"serif";mso-fareast-font-family:4909 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family: 4935 4910 "Times New Roman";color:#4F4FFF;font-style:normal;text-decoration:none; 4936 4911 text-underline:none'><o:p></o:p></span></span></h4> … … 4948 4923 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4949 4924 color:windowtext;text-decoration:none;text-underline:none'><span 4950 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 4925 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 4951 4926 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Atom</b><b 4952 4927 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'> … … 4960 4935 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4961 4936 color:windowtext;text-decoration:none;text-underline:none'><span 4962 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4937 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 4963 4938 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4964 4939 style='mso-fareast-font-family:"Times New Roman"'>Left Mouse Button (LMB)</span></b><span 4965 style='mso-fareast-font-family:"Times New Roman"'> – on a row number4966 selects the atom.<span class=MsoHyperlink><span style='color:windowtext; 4967 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>4940 style='mso-fareast-font-family:"Times New Roman"'> – on a row number selects 4941 the atom.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 4942 none;text-underline:none'><o:p></o:p></span></span></span></p> 4968 4943 4969 4944 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 4971 4946 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4972 4947 color:windowtext;text-decoration:none;text-underline:none'><span 4973 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4948 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 4974 4949 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4975 4950 style='mso-fareast-font-family:"Times New Roman"'>Shift LMB</span></b><span 4976 style='mso-fareast-font-family:"Times New Roman"'> – on a row number4977 selects all atoms from last selection to the selected row (or top is none 4978 previously selected).<span class=MsoHyperlink><span style='color:windowtext; 4979 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>4951 style='mso-fareast-font-family:"Times New Roman"'> – on a row number selects 4952 all atoms from last selection to the selected row (or top is none previously 4953 selected).<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 4954 none;text-underline:none'><o:p></o:p></span></span></span></p> 4980 4955 4981 4956 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 4983 4958 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4984 4959 color:windowtext;text-decoration:none;text-underline:none'><span 4985 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4960 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 4986 4961 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4987 4962 style='mso-fareast-font-family:"Times New Roman"'>Ctrl LMB</span></b><span 4988 style='mso-fareast-font-family:"Times New Roman"'> –on a row number4963 style='mso-fareast-font-family:"Times New Roman"'> – on a row number 4989 4964 selects/deselects the atom.<span class=MsoHyperlink><span style='color:windowtext; 4990 4965 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> … … 4994 4969 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 4995 4970 color:windowtext;text-decoration:none;text-underline:none'><span 4996 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 4971 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 4997 4972 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 4998 4973 style='mso-fareast-font-family:"Times New Roman"'>Alt LMB</span></b><span 4999 style='mso-fareast-font-family:"Times New Roman"'> – on a row number5000 selects that atom for moving; the status line at bottom of window will show 5001 name of atom selected. Use <b style='mso-bidi-font-weight:normal'>Alt LMB</b> 5002 again to select a target row for this atom; insertion will be before this row 5003 and thetable will be updated to show the change. NB: the <b style='mso-bidi-font-weight:4974 style='mso-fareast-font-family:"Times New Roman"'> – on a row number selects 4975 that atom for moving; the status line at bottom of window will show name of 4976 atom selected. Use <b style='mso-bidi-font-weight:normal'>Alt LMB</b> again to 4977 select a target row for this atom; insertion will be before this row and the 4978 table will be updated to show the change. NB: the <b style='mso-bidi-font-weight: 5004 4979 normal'>Draw Atoms</b> list is not updated by this change.<span 5005 4980 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; … … 5009 4984 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 5010 4985 color:windowtext;text-decoration:none;text-underline:none'><span 5011 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 4986 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 5012 4987 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Double 5013 4988 left click a Type column heading</b>: a dialog box is shown that allows you to … … 5019 4994 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 5020 4995 color:windowtext;text-decoration:none;text-underline:none'><span 5021 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 4996 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 5022 4997 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Double 5023 4998 click a refine or I/A column heading</b><span style='mso-fareast-font-family: … … 5029 5004 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 5030 5005 color:windowtext;text-decoration:none;text-underline:none'><span 5031 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 5006 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 5032 5007 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 5033 5008 style='mso-fareast-font-family:"Times New Roman"'>Atom data item editing tools</span></b><span 5034 style='mso-fareast-font-family:"Times New Roman"'> – These are controlled5035 bythe mouse (<b style='mso-bidi-font-weight:normal'>Alt</b> ignored, <b5009 style='mso-fareast-font-family:"Times New Roman"'> – These are controlled by 5010 the mouse (<b style='mso-bidi-font-weight:normal'>Alt</b> ignored, <b 5036 5011 style='mso-bidi-font-weight:normal'>Shift</b> & <b style='mso-bidi-font-weight: 5037 5012 normal'>Ctrl</b> allow selection of multiple cells but no use is made of them). 5038 An individual data item can be cup/pasted anywhere including from/to another 5039 document. Bad entries are rejected. If any entry is changed, press <b 5040 style='mso-bidi-font-weight:normal'>Enter</b> key or select another atom entry 5041 to apply the change.<span class=MsoHyperlink><span style='color:windowtext;5042 text- decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>5013 An individual data item can be cup/pasted anywhere including from/to another document. 5014 Bad entries are rejected. If any entry is changed, press <b style='mso-bidi-font-weight: 5015 normal'>Enter</b> key or select another atom entry to apply the change.<span 5016 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 5017 text-underline:none'><o:p></o:p></span></span></span></p> 5043 5018 5044 5019 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 5046 5021 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 5047 5022 color:windowtext;text-decoration:none;text-underline:none'><span 5048 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 5023 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 5049 5024 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 5050 5025 style='mso-fareast-font-family:"Times New Roman"'>Name</span></b><span 5051 style='mso-fareast-font-family:"Times New Roman"'> – can change to any5052 textstring. <span class=MsoHyperlink><span style='color:windowtext;text-decoration:5026 style='mso-fareast-font-family:"Times New Roman"'> – can change to any text 5027 string. <span class=MsoHyperlink><span style='color:windowtext;text-decoration: 5053 5028 none;text-underline:none'><o:p></o:p></span></span></span></p> 5054 5029 … … 5057 5032 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 5058 5033 color:windowtext;text-decoration:none;text-underline:none'><span 5059 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 5034 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 5060 5035 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 5061 5036 style='mso-fareast-font-family:"Times New Roman"'>Type</span></b><span 5062 style='mso-fareast-font-family:"Times New Roman"'> – causes a popup5063 display of the Periodic Table of the elements; select the element/valence5064 desired; the atom will be renamed as well.<span class=MsoHyperlink><span 5065 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>5037 style='mso-fareast-font-family:"Times New Roman"'> – causes a popup display of 5038 the Periodic Table of the elements; select the element/valence desired; the 5039 atom will be renamed as well.<span class=MsoHyperlink><span style='color:windowtext; 5040 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 5066 5041 5067 5042 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: … … 5069 5044 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 5070 5045 color:windowtext;text-decoration:none;text-underline:none'><span 5071 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 5046 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 5072 5047 </span></span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight: 5073 5048 normal'><span style='mso-fareast-font-family:"Times New Roman"'>refine</span></b></span><span 5074 style='mso-fareast-font-family:"Times New Roman"'> –shows a pulldown of5049 style='mso-fareast-font-family:"Times New Roman"'> – shows a pulldown of 5075 5050 allowed refinement flag choices to be shown; select one (top entry is blank for 5076 5051 no refinement).<span class=MsoHyperlink><span style='color:windowtext; … … 5081 5056 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 5082 5057 color:windowtext;text-decoration:none;text-underline:none'><span 5083 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 5058 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 5084 5059 </span></span></span></span><![endif]><span class=SpellE><span class=GramE><b 5085 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>x ,</span></b></span><b5086 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'> y,z</span></b></span><span5087 style='mso-fareast-font-family:"Times New Roman"'> – change atom5088 coordinate.Fractions (e.g. 1/3, 1/4) are allowed.<span class=MsoHyperlink><span5060 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>x</span></b></span><b 5061 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>,y,z</span></b></span><span 5062 style='mso-fareast-font-family:"Times New Roman"'> – change atom coordinate. 5063 Fractions (e.g. 1/3, 1/4) are allowed.<span class=MsoHyperlink><span 5089 5064 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 5090 5065 … … 5093 5068 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 5094 5069 color:windowtext;text-decoration:none;text-underline:none'><span 5095 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 5070 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 5096 5071 </span></span></span></span><![endif]><span class=SpellE><span class=GramE><b 5097 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>frac,</span></b></span><b 5098 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Uiso,Uij</span></b></span><span 5099 style='mso-fareast-font-family:"Times New Roman"'> – change these values; 5072 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>frac,Uiso,Uij</span></b></span></span><span 5073 style='mso-fareast-font-family:"Times New Roman"'> – change these values; 5100 5074 numeric entry only.<span class=MsoHyperlink><span style='color:windowtext; 5101 5075 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> … … 5105 5079 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 5106 5080 color:windowtext;text-decoration:none;text-underline:none'><span 5107 style='mso-list:Ignore'>f.<span style='font:7.0pt "Times New Roman"'> 5081 style='mso-list:Ignore'>f.<span style='font:7.0pt "Times New Roman"'> 5108 5082 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 5109 5083 style='mso-fareast-font-family:"Times New Roman"'>I/A</span></b><span 5110 style='mso-fareast-font-family:"Times New Roman"'> –select one of <span5084 style='mso-fareast-font-family:"Times New Roman"'> – select one of <span 5111 5085 class=GramE><b style='mso-bidi-font-weight:normal'>I</b>(</span><span 5112 5086 class=SpellE>sotropic</span>) or <b style='mso-bidi-font-weight:normal'>A</b>(<span … … 5120 5094 name=Texture></a><a name="Draw_Options"></a><![if !supportLists]><span 5121 5095 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span 5122 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu5123 ‘<b style='mso-bidi-font-weight:normal'>Edit’ - </b>The edit menu 5124 shows operations that can be performed on your selected atoms. You must select 5125 one ormore atoms before using many of the menu items.</p>5096 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu 5097 ‘<b style='mso-bidi-font-weight:normal'>Edit’ - </b>The edit menu shows 5098 operations that can be performed on your selected atoms. You must select one or 5099 more atoms before using many of the menu items.</p> 5126 5100 5127 5101 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5128 5102 auto;text-indent:-.25in;mso-list:l3 level2 lfo21'><![if !supportLists]><span 5129 5103 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 5130 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5131 style='mso-bidi-font-weight:normal'>Append atom</b> – add an H atom5132 (name= Unk) at 0<span class=GramE>,0,0</span> to the end of the atom table, it 5133 is also drawn as an H atom in thestructure plot.</p>5104 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5105 style='mso-bidi-font-weight:normal'>Append atom</b> – add an H atom (name= Unk) 5106 at 0,0,0 to the end of the atom table, it is also drawn as an H atom in the 5107 structure plot.</p> 5134 5108 5135 5109 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5136 5110 auto;text-indent:-.25in;mso-list:l3 level2 lfo21'><![if !supportLists]><span 5137 5111 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 5138 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5139 style='mso-bidi-font-weight:normal'>Append view point</b> –add an H atom5112 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5113 style='mso-bidi-font-weight:normal'>Append view point</b> – add an H atom 5140 5114 (name= Unk) to the end of the atom table with coordinates matching the location 5141 5115 of the view point, it is drawn as an H atom in the structure plot</p> … … 5144 5118 auto;text-indent:-.25in;mso-list:l3 level2 lfo21'><![if !supportLists]><span 5145 5119 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 5146 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5147 style='mso-bidi-font-weight:normal'>Insert atom</b> – insert an H atom5148 (name= Unk) at 0<span class=GramE>,0,0</span> before the selected atom, it is 5149 also drawn as an H atom in thestructure plot.</p>5120 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5121 style='mso-bidi-font-weight:normal'>Insert atom</b> – insert an H atom (name= 5122 Unk) at 0,0,0 before the selected atom, it is also drawn as an H atom in the 5123 structure plot.</p> 5150 5124 5151 5125 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5152 5126 auto;text-indent:-.25in;mso-list:l3 level2 lfo21'><![if !supportLists]><span 5153 5127 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 5154 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5155 style='mso-bidi-font-weight:normal'>Insert view point</b> – insert an H 5156 atom (name= Unk) before the selected atom with coordinates matching the 5157 location of the view point, it is also drawn as an H atom in the structure 5158 plot.</p> 5128 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5129 style='mso-bidi-font-weight:normal'>Insert view point</b> – insert an H atom 5130 (name= Unk) before the selected atom with coordinates matching the location of 5131 the view point, it is also drawn as an H atom in the structure plot.</p> 5159 5132 5160 5133 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5161 5134 auto;text-indent:-.25in;mso-list:l3 level2 lfo21'><![if !supportLists]><span 5162 5135 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span 5163 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5164 style='mso-bidi-font-weight:normal'>Delete atom</b> – selected atoms will5165 be deleted from the atom <span class=GramE>list,</span> they should also vanish 5166 fromthe structure drawing.</p>5136 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5137 style='mso-bidi-font-weight:normal'>Delete atom</b> – selected atoms will be 5138 deleted from the atom <span class=GramE>list,</span> they should also vanish from 5139 the structure drawing.</p> 5167 5140 5168 5141 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5169 5142 auto;text-indent:-.25in;mso-list:l3 level2 lfo21'><![if !supportLists]><span 5170 5143 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span 5171 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5172 style='mso-bidi-font-weight:normal'>Set atom refinement flags</b> –A popup5144 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5145 style='mso-bidi-font-weight:normal'>Set atom refinement flags</b> – A popup 5173 5146 dialog box appears; select refinement flags to apply to all selected atoms.</p> 5174 5147 … … 5176 5149 auto;text-indent:-.25in;mso-list:l3 level2 lfo21'><![if !supportLists]><span 5177 5150 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span 5178 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5179 style='mso-bidi-font-weight:normal'>Modify atom parameters</b> – A popup5180 dialog box appears with a list of atom parameter names; select one to apply to 5181 all atoms. <b style='mso-bidi-font-weight:normal'>Name</b> will rename selected 5182 a toms according to position in table (e.g. Na(1) for Na atom as 1<sup>st</sup>5183 atom in list in row ‘0’). <b style='mso-bidi-font-weight:normal'>Type</b> 5184 will give periodic table popup; selected element valence will be used for all 5185 selected atoms and atoms names will be changed. <b style='mso-bidi-font-weight: 5186 normal'>I/A</b> will give popup with choices to be used for all selected atoms. 5187 <b style='mso-bidi-font-weight:normal'>x,y,z</b> will give popup for shift to 5188 beapplied to the parameter for all selected atoms. <span class=SpellE><b5151 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5152 style='mso-bidi-font-weight:normal'>Modify atom parameters</b> – A popup dialog 5153 box appears with a list of atom parameter names; select one to apply to all atoms. 5154 <b style='mso-bidi-font-weight:normal'>Name</b> will rename selected atoms 5155 according to position in table (e.g. Na(1) for Na atom as 1<sup>st</sup> atom 5156 in list in row ‘0’). <b style='mso-bidi-font-weight:normal'>Type</b> will give 5157 periodic table popup; selected element valence will be used for all selected 5158 atoms and atoms names will be changed. <b style='mso-bidi-font-weight:normal'>I/A</b> 5159 will give popup with choices to be used for all selected atoms. <b 5160 style='mso-bidi-font-weight:normal'>x,y,z</b> will give popup for shift to be 5161 applied to the parameter for all selected atoms. <span class=SpellE><b 5189 5162 style='mso-bidi-font-weight:normal'>Uiso</b></span> and <span class=SpellE><b 5190 5163 style='mso-bidi-font-weight:normal'>frac</b></span> will give popup for new … … 5194 5167 auto;text-indent:-.25in;mso-list:l3 level2 lfo21'><![if !supportLists]><span 5195 5168 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span 5196 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5197 style='mso-bidi-font-weight:normal'>Transform atoms</b> – A popup dialog5198 boxappears; select space group operator/unit cell translation to apply to the5169 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5170 style='mso-bidi-font-weight:normal'>Transform atoms</b> – A popup dialog box 5171 appears; select space group operator/unit cell translation to apply to the 5199 5172 selected atoms. You can optionally force the result to be within the unit cell 5200 5173 and optionally generate a new set of atom positions.</p> … … 5203 5176 auto;text-indent:-.25in;mso-list:l3 level2 lfo21'><![if !supportLists]><span 5204 5177 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span 5205 style='font:7.0pt "Times New Roman"'> 5206 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Reload 5207 draw atoms</b> – </p> 5178 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5179 style='mso-bidi-font-weight:normal'>Reload draw atoms</b> – </p> 5208 5180 5209 5181 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo21'><![if !supportLists]><span 5210 5182 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span 5211 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu<b5212 style='mso-bidi-font-weight:normal'> ‘Compute’ –</b></p>5183 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu<b 5184 style='mso-bidi-font-weight:normal'> ‘Compute’ – </b></p> 5213 5185 5214 5186 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; 5215 5187 text-indent:-.25in;mso-list:l3 level2 lfo21'><![if !supportLists]><span 5216 5188 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 5217 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5218 style='mso-bidi-font-weight:normal'>Distances & Angles –</b>compute5189 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5190 style='mso-bidi-font-weight:normal'>Distances & Angles – </b>compute 5219 5191 distances and angles with esds (if possible) for selected atoms. A popup dialog 5220 5192 box will appear with distance angle controls. NB: if atoms have been added or … … 5243 5215 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l13 level1 lfo22'><![if !supportLists]><span 5244 5216 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 5245 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5246 style='mso-bidi-font-weight:normal'>Atom Selection from table</b>: select 5247 individual atoms by a left click of the mouse when pointed at the left most 5248 column (atom numbers) of the atom display; hold down the Ctrl key to add to 5249 your selection; a previously selected atom will be deselected; hold down Shift5250 key to select from last in list selected to current selection. A selected atom 5251 will behighlighted (in grey) and the atoms will be shown in green on the plot.5217 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5218 style='mso-bidi-font-weight:normal'>Atom Selection from table</b>: select individual 5219 atoms by a left click of the mouse when pointed at the left most column (atom 5220 numbers) of the atom display; hold down the Ctrl key to add to your selection; 5221 a previously selected atom will be deselected; hold down Shift key to select 5222 from last in list selected to current selection. A selected atom will be 5223 highlighted (in grey) and the atoms will be shown in green on the plot. 5252 5224 Selection without the Ctrl key will clear previous selections. A double left 5253 5225 click in the (empty) upper left box will select or deselect all atoms.</p> … … 5255 5227 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l13 level1 lfo22'><![if !supportLists]><span 5256 5228 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 5257 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5229 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5258 5230 style='mso-bidi-font-weight:normal'>Atom Selection from plot</b>: select an 5259 5231 atom by a left click of the mouse while holding down the Shift key and pointed 5260 at the center of the displayed atom, it will turn green if successful and the 5261 corresponding entry in the table will be highlighted (in grey); any previous 5262 selections will be cleared. To add to .your selection use the right mouse 5263 button (Shift down); if a previously selection is reselected it is removed from 5264 the selection list. <b style='mso-bidi-font-weight:normal'>NB</b>: beware of 5265 atoms that are hiding behind the one you are trying to select, they may be 5266 selected inadvertently. You can rotate the structure anytime during the 5267 selection process.</p> 5232 at the center of the displayed atom, it will turn green if successful and the corresponding 5233 entry in the table will be highlighted (in grey); any previous selections will 5234 be cleared. To add to .your selection use the right mouse button (Shift down); 5235 if a previously selection is reselected it is removed from the selection list. <b 5236 style='mso-bidi-font-weight:normal'>NB</b>: beware of atoms that are hiding 5237 behind the one you are trying to select, they may be selected inadvertently. 5238 You can rotate the structure anytime during the selection process.</p> 5268 5239 5269 5240 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l13 level1 lfo22'><![if !supportLists]><span 5270 5241 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 5271 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5242 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5272 5243 style='mso-bidi-font-weight:normal'>Double left click a Name, Type and Sym Op 5273 5244 column heading</b>: a dialog box is shown that allows you to select all atoms … … 5277 5248 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l13 level1 lfo22'><![if !supportLists]><span 5278 5249 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 5279 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5250 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5280 5251 style='mso-bidi-font-weight:normal'>Double left click a Style, Label or Color 5281 5252 column</b>: a dialog box is shown that allows you to select a rendering option 5282 5253 for all the atoms. For Color a color choice dialog is displayed that covers the 5283 5254 entire color spectrum. Choose a color by any of the means available, press the 5284 “Add to Custom Colors”, select that color in the Custom colors 5285 display and then press OK. <b style='mso-bidi-font-weight:normal'>NB</b>: 5286 selecting Color will make all atoms have the same color and for Style 5287 “blank” means the atoms aren’t rendered and thus the plot 5288 will not show any atoms or bonds!</p> 5255 “Add to Custom Colors”, select that color in the Custom colors display and then 5256 press OK. <b style='mso-bidi-font-weight:normal'>NB</b>: selecting Color will 5257 make all atoms have the same color and for Style “blank” means the atoms aren’t 5258 rendered and thus the plot will not show any atoms or bonds!</p> 5289 5259 5290 5260 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l13 level1 lfo22'><![if !supportLists]><span 5291 5261 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span 5292 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu5293 ‘<b style='mso-bidi-font-weight:normal'>Edit’ - </b>The edit menu 5294 shows operations that can be performed on your selected atoms. You must select 5295 one ormore atoms before using any of the menu items.</p>5262 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu 5263 ‘<b style='mso-bidi-font-weight:normal'>Edit’ - </b>The edit menu shows 5264 operations that can be performed on your selected atoms. You must select one or 5265 more atoms before using any of the menu items.</p> 5296 5266 5297 5267 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5298 5268 auto;text-indent:-.25in;mso-list:l17 level1 lfo23'><![if !supportLists]><span 5299 5269 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 5300 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5301 style='mso-bidi-font-weight:normal'>Atom style</b> – select the rendering5302 stylefor the selected atoms</p>5270 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5271 style='mso-bidi-font-weight:normal'>Atom style</b> – select the rendering style 5272 for the selected atoms</p> 5303 5273 5304 5274 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5305 5275 auto;text-indent:-.25in;mso-list:l17 level1 lfo23'><![if !supportLists]><span 5306 5276 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 5307 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5308 style='mso-bidi-font-weight:normal'>Atom label</b> – select the item to5309 be shown as a label for each atom in selection. The choices are: none, type, 5310 nameor number.</p>5277 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5278 style='mso-bidi-font-weight:normal'>Atom label</b> – select the item to be 5279 shown as a label for each atom in selection. The choices are: none, type, name 5280 or number.</p> 5311 5281 5312 5282 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5313 5283 auto;text-indent:-.25in;mso-list:l17 level1 lfo23'><![if !supportLists]><span 5314 5284 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 5315 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5316 style='mso-bidi-font-weight:normal'>Atom color</b> – select the color for 5317 the atom; a color choice dialog is displayed that covers the entire color 5318 spectrum. Choose a color by any of the means available, press the “Add to 5319 Custom Colors”, select that color in the Custom colors display and then 5320 press OK.</p> 5285 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5286 style='mso-bidi-font-weight:normal'>Atom color</b> – select the color for the 5287 atom; a color choice dialog is displayed that covers the entire color spectrum. 5288 Choose a color by any of the means available, press the “Add to Custom Colors”, 5289 select that color in the Custom colors display and then press OK.</p> 5321 5290 5322 5291 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5323 5292 auto;text-indent:-.25in;mso-list:l17 level1 lfo23'><![if !supportLists]><span 5324 5293 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 5325 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5326 style='mso-bidi-font-weight:normal'>Reset atom colors</b> – return the5327 atomcolor back to their defaults for the selected atoms.</p>5294 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5295 style='mso-bidi-font-weight:normal'>Reset atom colors</b> – return the atom 5296 color back to their defaults for the selected atoms.</p> 5328 5297 5329 5298 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5330 5299 auto;text-indent:-.25in;mso-list:l17 level1 lfo23'><![if !supportLists]><span 5331 5300 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span 5332 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5333 style='mso-bidi-font-weight:normal'>View point</b> – position the plot5334 viewpoint to the first atom in the selection.</p>5301 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5302 style='mso-bidi-font-weight:normal'>View point</b> – position the plot view 5303 point to the first atom in the selection.</p> 5335 5304 5336 5305 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5337 5306 auto;text-indent:-.25in;mso-list:l17 level1 lfo23'><![if !supportLists]><span 5338 5307 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span 5339 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5340 style='mso-bidi-font-weight:normal'>Add atoms</b> – using the selected5341 atoms, new ones are added to the bottom of the list after applying your choice 5342 ofsymmetry operator and unit cell translation selected via a dialog display.5308 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5309 style='mso-bidi-font-weight:normal'>Add atoms</b> – using the selected atoms, 5310 new ones are added to the bottom of the list after applying your choice of 5311 symmetry operator and unit cell translation selected via a dialog display. 5343 5312 Duplicate atom positions are not retained. Any anisotropic thermal displacement 5344 5313 parameters (Uij) will be transformed as appropriate.</p> … … 5347 5316 auto;text-indent:-.25in;mso-list:l17 level1 lfo23'><![if !supportLists]><span 5348 5317 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span 5349 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5350 style='mso-bidi-font-weight:normal'>Transform atoms</b> – apply a5351 symmetry operator and unit cell translation to the set of selected atoms; they 5352 will be changed in place. Any anisotropic thermal displacement parameters (Uij) 5353 will betransformed as appropriate.</p>5318 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5319 style='mso-bidi-font-weight:normal'>Transform atoms</b> – apply a symmetry 5320 operator and unit cell translation to the set of selected atoms; they will be 5321 changed in place. Any anisotropic thermal displacement parameters (Uij) will be 5322 transformed as appropriate.</p> 5354 5323 5355 5324 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5356 5325 auto;text-indent:-.25in;mso-list:l17 level1 lfo23'><![if !supportLists]><span 5357 5326 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span 5358 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5359 style='mso-bidi-font-weight:normal'>Fill CN-sphere</b> –using the atoms5327 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5328 style='mso-bidi-font-weight:normal'>Fill CN-sphere</b> – using the atoms 5360 5329 currently in the draw atom table, find all atoms that belong in the 5361 5330 coordination sphere around the selected atoms via unit cell translations. NB: … … 5365 5334 auto;text-indent:-.25in;mso-list:l17 level1 lfo23'><![if !supportLists]><span 5366 5335 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span 5367 style='font:7.0pt "Times New Roman"'> 5368 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Fill unit 5369 c ell</b> - using the atoms currently selected from the draw atom table, find5370 all atoms that fall inside or on the edge/surface/corners of the unit cell. 5371 This operation is frequentlyperformed before Fill CN-sphere.</p>5336 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5337 style='mso-bidi-font-weight:normal'>Fill unit cell</b> - using the atoms 5338 currently selected from the draw atom table, find all atoms that fall inside or 5339 on the edge/surface/corners of the unit cell. This operation is frequently 5340 performed before Fill CN-sphere.</p> 5372 5341 5373 5342 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5374 5343 auto;text-indent:-.25in;mso-list:l17 level1 lfo23'><![if !supportLists]><span 5375 5344 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span 5376 style='font:7.0pt "Times New Roman"'> 5377 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Delete 5378 atoms</b> – clear the entire draw atom table; it is then refilled from 5379 the Atoms table. You should do this operation after any changes in the Atoms 5380 table, e.g. by a structure refinement.</p> 5345 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5346 style='mso-bidi-font-weight:normal'>Delete atoms</b> – clear the entire draw 5347 atom table; it is then refilled from the Atoms table. You should do this 5348 operation after any changes in the Atoms table, e.g. by a structure refinement.</p> 5381 5349 5382 5350 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l13 level1 lfo22'><![if !supportLists]><span 5383 5351 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span 5384 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu5385 ‘<b style='mso-bidi-font-weight:normal'>Compute’</b> - The compute 5386 menu gives a choice of geometric calculations to be performed with the selected 5387 atoms. You must select the appropriate number of atoms for these to work and 5388 thecomputation is done for the atoms in selection order.</p>5352 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu 5353 ‘<b style='mso-bidi-font-weight:normal'>Compute’</b> - The compute menu gives a 5354 choice of geometric calculations to be performed with the selected atoms. You 5355 must select the appropriate number of atoms for these to work and the 5356 computation is done for the atoms in selection order.</p> 5389 5357 5390 5358 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5391 5359 auto;text-indent:-.25in;mso-list:l13 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span 5392 5360 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 5393 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5394 style='mso-bidi-font-weight:normal'>View pt. dist.</b> - this calculates distance5395 from view point to all selected draw atoms; result is given on the console5396 window.</p>5361 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5362 style='mso-bidi-font-weight:normal'>View pt. dist.</b> - this calculates 5363 distance from view point to all selected draw atoms; result is given on the 5364 console window.</p> 5397 5365 5398 5366 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5399 5367 auto;text-indent:-.25in;mso-list:l13 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span 5400 5368 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 5401 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5369 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5402 5370 style='mso-bidi-font-weight:normal'>Dist. Ang.</b> <b style='mso-bidi-font-weight: 5403 normal'>Tors. </b> – when 2-4 atoms are selected, a distance, angle or5404 torsion angle will be found for them. The angles are computed for the atoms in 5405 their selection order. The torsion angle is a right hand angle about the A2-A3 5406 vector for the sequence of atoms A1-A2-A3-A4. An estimated standard deviation5407 is given for the calculated value if a current variance-covariance matrix is 5408 available. The result is shown on the console window; it may be cut & 5409 pasted toanother application (e.g. Microsoft Word).</p>5371 normal'>Tors. </b>– when 2-4 atoms are selected, a distance, angle or torsion 5372 angle will be found for them. The angles are computed for the atoms in their 5373 selection order. The torsion angle is a right hand angle about the A2-A3 vector 5374 for the sequence of atoms A1-A2-A3-A4. An estimated standard deviation is given 5375 for the calculated value if a current variance-covariance matrix is available. 5376 The result is shown on the console window; it may be cut & pasted to 5377 another application (e.g. Microsoft Word).</p> 5410 5378 5411 5379 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; 5412 5380 text-indent:-.25in;mso-list:l13 level2 lfo22;tab-stops:list 1.0in'><![if !supportLists]><span 5413 5381 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 5414 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b5415 style='mso-bidi-font-weight:normal'>Best plane</b> – when 4 or more atoms5416 areselected, a best plane is determined for them. The result is shown on the5382 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5383 style='mso-bidi-font-weight:normal'>Best plane</b> – when 4 or more atoms are 5384 selected, a best plane is determined for them. The result is shown on the 5417 5385 console window; it may be cut & pasted to another application (e.g. 5418 5386 Microsoft Word). Shown are the atom coordinates transformed to Cartesian best … … 5433 5401 mso-style-textfill-fill-themecolor:accent1;mso-style-textfill-fill-alpha:100.0%; 5434 5402 mso-style-textfill-fill-colortransforms:lumm=75000'><a 5435 href=".. /../pyGSAS/help/gsasII.html#Rigid_bodies"><!--[if supportFields]><span5403 href="..:..:pyGSAS:help:gsasII.html#Rigid_bodies"><!--[if supportFields]><span 5436 5404 style='color:black;mso-style-textfill-fill-color:black;mso-style-textfill-fill-alpha: 5437 5405 100.0%'><span style='mso-element:field-begin'></span></span><span … … 5439 5407 100.0%'><span style='color:black;mso-style-textfill-fill-color:black; 5440 5408 mso-style-textfill-fill-alpha:100.0%'><span 5441 style='mso-spacerun:yes'> </span>REF _Ref355170529 \h </span></span><span 5409 style="mso-spacerun:yes"> </span>REF _Ref35<span style='color:black;mso-style-textfill-fill-color: 5410 black;mso-style-textfill-fill-alpha:100.0%'>5170529 \h </span></span></span><span 5442 5411 style='color:black;mso-style-textfill-fill-color:black;mso-style-textfill-fill-alpha: 5443 5412 100.0%'><span style='mso-element:field-separator'></span></span><![endif]--><span … … 5462 5431 5463 5432 <p class=MsoNormal><span style='mso-bookmark:Pawley'>This gives the list 5464 (magnitude, x y & z) of all peaks found within the unit cell from the last 5465 Fourier/charge flip map search sorted in order of decreasing peak magnitude. 5466 The crystal structure plot shows each peak position as a white to dark gray cross; 5467 theshade is determined from the magnitude for the peak relative to the maximum5433 (magnitude, x y & z) of all peaks found within the unit cell from the last Fourier/charge 5434 flip map search sorted in order of decreasing peak magnitude. The crystal 5435 structure plot shows each peak position as a white to dark gray cross; the 5436 shade is determined from the magnitude for the peak relative to the maximum 5468 5437 peak magnitude.</span></p> 5469 5438 … … 5472 5441 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l28 level1 lfo24'><span 5473 5442 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5474 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 5443 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 5475 5444 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Peak 5476 5445 Selection from table</b>: select individual atoms by a left click of the mouse … … 5485 5454 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l28 level1 lfo24'><span 5486 5455 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5487 "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 5456 "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 5488 5457 </span></span></span><![endif]>Select the <b style='mso-bidi-font-weight:normal'>mag</b> 5489 column –the entries will be sorted with the largest at the top.</span></p>5458 column – the entries will be sorted with the largest at the top.</span></p> 5490 5459 5491 5460 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l28 level1 lfo24'><span 5492 5461 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5493 "Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 5462 "Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 5494 5463 </span></span></span><![endif]>Select the <span class=SpellE><b 5495 style='mso-bidi-font-weight:normal'>dzero</b></span> column – the entries5496 willbe sorted with the smallest (distance from origin) at the top.</span></p>5464 style='mso-bidi-font-weight:normal'>dzero</b></span> column – the entries will 5465 be sorted with the smallest (distance from origin) at the top.</span></p> 5497 5466 5498 5467 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l28 level1 lfo24'><span 5499 5468 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5500 "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 5501 </span></span></span><![endif]>Menu <b style='mso-bidi-font-weight:normal'> ‘Map5502 peaks ’ </b><span style='mso-spacerun:yes'> </span>–</span></p>5469 "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 5470 </span></span></span><![endif]>Menu <b style='mso-bidi-font-weight:normal'>‘Map 5471 peaks’ </b><span style="mso-spacerun:yes"> </span>–</span></p> 5503 5472 5504 5473 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5505 5474 auto;text-indent:-.25in;mso-list:l28 level2 lfo24;tab-stops:list 1.0in'><span 5506 5475 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5507 "Times New Roman"'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 5476 "Times New Roman"'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 5508 5477 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Move 5509 peaks</b> –this copies selected peaks to the </span><a href="gsasII.html"><span5478 peaks</b> – this copies selected peaks to the </span><a href="gsasII.html"><span 5510 5479 style='mso-bookmark:Pawley'><span style='color:windowtext;text-decoration:none; 5511 5480 text-underline:none'>Atoms</span></span></a><span style='mso-bookmark:Pawley'> … … 5513 5482 style='color:windowtext;text-decoration:none;text-underline:none'>Draw Atoms</span></span></a><span 5514 5483 style='mso-bookmark:Pawley'> list. They will be appended to the end of each 5515 list each with the name ‘UNK’ and the atom type as ‘H’. 5516 They will also be drawn as small white spheres at their respective positions in 5517 the structure drawing. You should next go to the </span><a href="gsasII.html"><span 5518 style='mso-bookmark:Pawley'><span style='color:windowtext;text-decoration:none; 5519 text-underline:none'>Atoms</span></span></a><span style='mso-bookmark:Pawley'> 5520 page and change the atom type to whatever element you desire; it will be 5521 renamed automatically.</span></p> 5484 list each with the name ‘UNK’ and the atom type as ‘H’. They will also be drawn 5485 as small white spheres at their respective positions in the structure drawing. 5486 You should next go to the </span><a href="gsasII.html"><span style='mso-bookmark: 5487 Pawley'><span style='color:windowtext;text-decoration:none;text-underline:none'>Atoms</span></span></a><span 5488 style='mso-bookmark:Pawley'> page and change the atom type to whatever element 5489 you desire; it will be renamed automatically.</span></p> 5522 5490 5523 5491 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5524 5492 auto;text-indent:-.25in;mso-list:l28 level2 lfo24;tab-stops:list 1.0in'><span 5525 5493 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5526 "Times New Roman"'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 5494 "Times New Roman"'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 5527 5495 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>View 5528 point </b> –this positions the view point (large 3D RGB cross) at the 1<sup>st</sup>5496 point </b>– this positions the view point (large 3D RGB cross) at the 1<sup>st</sup> 5529 5497 selected peak.</span></p> 5530 5498 … … 5532 5500 auto;text-indent:-.25in;mso-list:l28 level2 lfo24;tab-stops:list 1.0in'><span 5533 5501 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5534 "Times New Roman"'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 5502 "Times New Roman"'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 5535 5503 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>View pt</b>. 5536 <b style='mso-bidi-font-weight:normal'>dist</b>. – this calculates5537 distancefrom view point to all selected map peaks.</span></p>5504 <b style='mso-bidi-font-weight:normal'>dist</b>. – this calculates distance 5505 from view point to all selected map peaks.</span></p> 5538 5506 5539 5507 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5540 5508 auto;text-indent:-.25in;mso-list:l28 level2 lfo24;tab-stops:list 1.0in'><span 5541 5509 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5542 "Times New Roman"'><span style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 5510 "Times New Roman"'><span style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 5543 5511 </span></span></span><![endif]><span class=SpellE><b style='mso-bidi-font-weight: 5544 5512 normal'>Calc</b></span><b style='mso-bidi-font-weight:normal'> <span 5545 class=SpellE>dist</span>/<span class=SpellE>ang</span> </b>– if 2 peaks 5546 are selected, this calculates the distance between them. If 3 peaks are 5547 selected this calculates the angle between them; NB: selection order matters. 5548 If selection is not 2 or 3 peaks this is ignored. Output is on the console 5549 window.</span></p> 5513 class=SpellE>dist</span>/<span class=SpellE>ang</span> </b>– if 2 peaks are 5514 selected, this calculates the distance between them. If 3 peaks are selected 5515 this calculates the angle between them; NB: selection order matters. If 5516 selection is not 2 or 3 peaks this is ignored. Output is on the console window.</span></p> 5550 5517 5551 5518 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5552 5519 auto;text-indent:-.25in;mso-list:l28 level2 lfo24;tab-stops:list 1.0in'><span 5553 5520 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5554 "Times New Roman"'><span style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 5521 "Times New Roman"'><span style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 5555 5522 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Equivalent 5556 peaks </b> –this selects all peaks related to selection by space group5523 peaks </b>– this selects all peaks related to selection by space group 5557 5524 symmetry.</span></p> 5558 5525 … … 5560 5527 auto;text-indent:-.25in;mso-list:l28 level2 lfo24;tab-stops:list 1.0in'><span 5561 5528 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5562 "Times New Roman"'><span style='mso-list:Ignore'>f.<span style='font:7.0pt "Times New Roman"'> 5529 "Times New Roman"'><span style='mso-list:Ignore'>f.<span style='font:7.0pt "Times New Roman"'> 5563 5530 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Unique 5564 peaks </b>– this selects only the unique peak positions amongst those 5565 selected.</span></p> 5531 peaks </b>– this selects only the unique peak positions amongst those selected.</span></p> 5566 5532 5567 5533 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5568 5534 auto;text-indent:-.25in;mso-list:l28 level2 lfo24;tab-stops:list 1.0in'><span 5569 5535 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5570 "Times New Roman"'><span style='mso-list:Ignore'>g.<span style='font:7.0pt "Times New Roman"'> 5536 "Times New Roman"'><span style='mso-list:Ignore'>g.<span style='font:7.0pt "Times New Roman"'> 5571 5537 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Delete 5572 peaks </b> – this deletes selected peaks. The shading on the remaining5573 peaks ischanged to reflect any change in the maximum after deletion.</span></p>5538 peaks </b>– this deletes selected peaks. The shading on the remaining peaks is 5539 changed to reflect any change in the maximum after deletion.</span></p> 5574 5540 5575 5541 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; 5576 5542 text-indent:-.25in;mso-list:l28 level2 lfo24;tab-stops:list 1.0in'><span 5577 5543 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5578 "Times New Roman"'><span style='mso-list:Ignore'>h.<span style='font:7.0pt "Times New Roman"'> 5544 "Times New Roman"'><span style='mso-list:Ignore'>h.<span style='font:7.0pt "Times New Roman"'> 5579 5545 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Clear 5580 peaks </b> – this deletes all the peaks in the map peak list; they are5581 alsoremoved from the crystal structure drawing plot.</span></p>5546 peaks </b>– this deletes all the peaks in the map peak list; they are also 5547 removed from the crystal structure drawing plot.</span></p> 5582 5548 5583 5549 <h4><span style='mso-bookmark:Pawley'>Pawley reflections<span 5584 5550 class=MsoHyperlink><span style='color:#4F81BD;mso-themecolor:accent1'><o:p></o:p></span></span></span></h4> 5585 5551 5586 <p class=MsoNormal><span style='mso-bookmark:Pawley'>This gives the list of reflections5587 used in a Pawley refinement and can only be seen if the phase type is 5588 ‘Pawley’ (see </span><a href="#General"><span style='mso-bookmark: 5589 Pawley'><spanstyle='color:windowtext;text-decoration:none;text-underline:none'>General</span></span></a><span5552 <p class=MsoNormal><span style='mso-bookmark:Pawley'>This gives the list of 5553 reflections used in a Pawley refinement and can only be seen if the phase type 5554 is ‘Pawley’ (see </span><a href="#General"><span style='mso-bookmark:Pawley'><span 5555 style='color:windowtext;text-decoration:none;text-underline:none'>General</span></span></a><span 5590 5556 style='mso-bookmark:Pawley'>).</span></p> 5591 5557 … … 5594 5560 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l7 level1 lfo25'><span 5595 5561 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5596 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 5597 </span></span></span><![endif]>Menu <b style='mso-bidi-font-weight:normal'> ‘Operations’</b>5598 –</span></p>5562 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 5563 </span></span></span><![endif]>Menu <b style='mso-bidi-font-weight:normal'>‘Operations’</b> 5564 –</span></p> 5599 5565 5600 5566 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5601 5567 auto;text-indent:-.25in;mso-list:l15 level2 lfo26'><span style='mso-bookmark: 5602 5568 Pawley'><![if !supportLists]><span style='mso-fareast-font-family:"Times New Roman"'><span 5603 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 5569 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> 5604 5570 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Pawley 5605 create</b> – this creates a new set of Pawley reflections, over writing 5606 any preexisting Pawley set. They are generated with d-spacings larger than the 5607 limit set as ‘Pawley dmin’ in the General tab for this phase. By 5608 default the refine flags are not set and the <span class=SpellE><span 5609 class=GramE>Fsq</span></span><span class=GramE>(</span><span class=SpellE>hkl</span>) 5610 = 100.0.</span></p> 5571 create</b> – this creates a new set of Pawley reflections, over writing any 5572 preexisting Pawley set. They are generated with d-spacings larger than the 5573 limit set as ‘Pawley dmin’ in the General tab for this phase. By default the 5574 refine flags are not set and the <span class=SpellE><span class=GramE>Fsq</span></span><span 5575 class=GramE>(</span><span class=SpellE>hkl</span>) = 100.0.</span></p> 5611 5576 5612 5577 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5613 5578 auto;text-indent:-.25in;mso-list:l15 level2 lfo26'><span style='mso-bookmark: 5614 5579 Pawley'><![if !supportLists]><span style='mso-fareast-font-family:"Times New Roman"'><span 5615 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 5580 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 5616 5581 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Pawley 5617 estimate</b> –this attempts an estimate of <span class=GramE>Fsq(</span>hkl)5582 estimate</b> – this attempts an estimate of <span class=GramE>Fsq(</span>hkl) 5618 5583 from the peak heights of the reflection as seen in the 1<sup>st</sup> powder 5619 5584 pattern of those selected in the </span><a href="#Data"><span style='mso-bookmark: … … 5624 5589 auto;text-indent:-.25in;mso-list:l15 level2 lfo26'><span style='mso-bookmark: 5625 5590 Pawley'><![if !supportLists]><span style='mso-fareast-font-family:"Times New Roman"'><span 5626 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> &nb