- Timestamp:
- Mar 22, 2022 10:35:21 AM (3 years ago)
- Location:
- trunk
- Files:
-
- 3 edited
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TabularUnified trunk/GSASIIplot.py ¶
r5233 r5243 9126 9126 if Add: 9127 9127 Indx = GetSelectedAtoms() 9128 if not getSelection(): #wrong place for doing this 9129 return 9128 9130 if G2frame.phaseDisplay.GetPageText(getSelection()) == 'Map peaks': 9129 9131 peakList = data['Map Peaks'] … … 9142 9144 SetSelectedAtoms(i,Add) 9143 9145 G2frame.G2plotNB.status.SetStatusText( 9144 ' Selected peak: {:.3f} @ ({:.3f},{:.3f},{:.3f})' 9145 .format(*peak[0:4]),1) 9146 ' Selected peak: {:.3f} @ ({:.3f},{:.3f},{:.3f})'.format(*peak[0:4]),1) 9146 9147 return 9147 9148 elif G2frame.phaseDisplay.GetPageText(getSelection()) == 'Draw Atoms': -
TabularUnified trunk/GSASIIrestrGUI.py ¶
r5239 r5243 1462 1462 else: 1463 1463 Volumes.Bind(wg.EVT_GRID_CELL_CHANGE, OnCellChange) 1464 for i in (G2G.wxID_RES RCHANGEVAL,G2G.wxID_RESTCHANGEESD):1464 for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): 1465 1465 G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=True) 1466 1466 G2frame.Bind(wx.EVT_MENU, OnChangeValue, id=G2G.wxID_RESRCHANGEVAL) 1467 1467 G2frame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2G.wxID_RESTCHANGEESD) 1468 G2frame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2G.wxID_RESTDELETE) 1468 1469 mainSizer.Add(wx.StaticText(ChiralRestr,-1, 1469 1470 'Chiral volume restraints: sum(wt*(delt/sig)^2) = %.2f, mean(wt*(delt/sig)^2) = %.2f' \ -
TabularUnified trunk/help/gsasII-phase.html ¶
r5159 r5243 25 25 <o:Author>Von Dreele</o:Author> 26 26 <o:LastAuthor>Von Dreele, Robert B.</o:LastAuthor> 27 <o:Revision>3 1</o:Revision>28 <o:TotalTime> 5325</o:TotalTime>27 <o:Revision>34</o:Revision> 28 <o:TotalTime>6559</o:TotalTime> 29 29 <o:Created>2021-06-20T02:30:00Z</o:Created> 30 <o:LastSaved>202 1-06-22T22:15:00Z</o:LastSaved>30 <o:LastSaved>2022-03-22T15:32:00Z</o:LastSaved> 31 31 <o:Pages>1</o:Pages> 32 <o:Words> 8400</o:Words>33 <o:Characters> 47880</o:Characters>32 <o:Words>9185</o:Words> 33 <o:Characters>52357</o:Characters> 34 34 <o:Company>Argonne National Laboratory</o:Company> 35 <o:Lines> 399</o:Lines>36 <o:Paragraphs>1 12</o:Paragraphs>37 <o:CharactersWithSpaces> 56168</o:CharactersWithSpaces>35 <o:Lines>436</o:Lines> 36 <o:Paragraphs>122</o:Paragraphs> 37 <o:CharactersWithSpaces>61420</o:CharactersWithSpaces> 38 38 <o:Version>16.00</o:Version> 39 39 </o:DocumentProperties> … … 42 42 </o:OfficeDocumentSettings> 43 43 </xml><![endif]--> 44 <link rel=dataStoreItem href="gsasII-phase_files/item005 8.xml"45 target="gsasII-phase_files/props05 9.xml">44 <link rel=dataStoreItem href="gsasII-phase_files/item0054.xml" 45 target="gsasII-phase_files/props055.xml"> 46 46 <link rel=themeData href="gsasII-phase_files/themedata.thmx"> 47 47 <link rel=colorSchemeMapping href="gsasII-phase_files/colorschememapping.xml"> 48 48 <!--[if gte mso 9]><xml> 49 49 <w:WordDocument> 50 <w:Zoom>188</w:Zoom> 51 <w:SpellingState>Clean</w:SpellingState> 52 <w:GrammarState>Clean</w:GrammarState> 50 <w:Zoom>148</w:Zoom> 53 51 <w:TrackMoves>false</w:TrackMoves> 54 52 <w:TrackFormatting/> … … 1308 1306 font-family:"Times New Roman",serif; 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1877 1757 mso-level-number-position:left; … … 1953 1833 1954 1834 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This 1955 is where to find help on the Phase Tree items in GSAS-II. Note that the window displayed1956 for this page has multiple tabs. The help information is broken down by tab 1957 section. <o:p></o:p></span></p>1835 is where to find help on the Phase Tree items in GSAS-II. Note that the window 1836 displayed for this page has multiple tabs. The help information is broken down 1837 by tab section. <o:p></o:p></span></p> 1958 1838 1959 1839 <h2 style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a … … 1978 1858 the unit cell parameters and overall parameters for the atom present in the 1979 1859 phase. It also has the controls for Pawley intensity extraction and for 1980 computing Fourier maps for this phase. It can also be used to compute new 1981 structures based on the unit cell and atom positions. <span class=MsoHyperlink><span 1982 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 1860 computing Fourier maps for this phase. It can also has the controls for Monte 1861 Carlo/Simulated Annealing for solving structures with flexible rigid molecular bodies.. 1862 <span class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 1863 text-underline:none'><o:p></o:p></span></span></span></p> 1983 1864 1984 1865 <h5 style='margin-left:.5in'>What can I do here?</h5> … … 2008 1889 map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this 2009 1890 procedure; they will be printed on the console and will be shown in the ‘<a 2010 href="#Phase-Map_peaks">Map peaks</a>’ page. This page will immediately be <span2011 class=GramE>shown</span> and the peaks will be shown on the structure drawing 2012 for this phase aswhite 3-D crosses.<b><o:p></o:p></b></span></p>1891 href="#Phase-Map_peaks">Map peaks</a>’ page. This page will immediately be 1892 shown, and the peaks will be shown on the structure drawing for this phase as 1893 white 3-D crosses.<b><o:p></o:p></b></span></p> 2013 1894 2014 1895 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: … … 2019 1900 style='mso-fareast-font-family:"Times New Roman"'>This performs a charge 2020 1901 flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution 2021 using the method of <span class=SpellE>Oszlanyi</span> & <span 2022 class=SpellE>Suto</span> (Acta <span class=SpellE>Cryst</span>. A60, 134-141, 2023 2004). You will need to select a source for the reflection set and perhaps 2024 select an element for normalization by its form factor, a resolution limit 2025 (usually 0.5A) and a charge flip threshold (usually 0.1); these are found at 2026 the bottom of the <b style='mso-bidi-font-weight:normal'>General</b> window. A 1902 using the method of Oszlanyi & Suto (Acta Cryst. A60, 134-141, 2004). You 1903 will need to select a source for the reflection set and perhaps select an 1904 element for normalization by its form factor, a resolution limit (usually 0.5</span><span 1905 style='font-family:"Calibri",sans-serif;mso-fareast-font-family:"Times New Roman"'>Å</span><span 1906 style='mso-fareast-font-family:"Times New Roman"'>) and a charge flip threshold 1907 (usually 0.1); these are found near the bottom of the <b style='mso-bidi-font-weight: 1908 normal'>General</b> window. There are also Test HKLs to show the progress in 1909 phasing with charge flipping cycles. They show the generally chaotic phase 1910 behavior before a solution is found; after that the phases are essentially 1911 fixed. No use is made of this information; it is just for your edification. A 2027 1912 progress bar showing the charge flip residual is shown while the charge flip is 2028 1913 in operation. When the residual is no longer decreasing (be patient – it 2029 1914 doesn’t necessarily fall continuously), press the <b style='mso-bidi-font-weight: 2030 normal'>Cancel</b> button to stop the charge flipping . The resulting map will2031 be positioned to properly place symmetry operators (<span class=GramE>NB:</span> 2032 depends on the quality of the resulting phases), searched for peaks and the 2033 display shifts to <b style='mso-bidi-font-weight:normal'>Map peaks</b> to show 2034 them.<b><o:p></o:p></b></span></p>1915 normal'>Cancel</b> button to stop the charge flipping, otherwise it will stop 1916 at 10000 cycles. The resulting map will be positioned to properly place 1917 symmetry operators (NB: depends on the quality of the resulting phases; the map 1918 could be still offset by a few steps), searched for peaks and the display 1919 shifts to <b style='mso-bidi-font-weight:normal'>Map peaks</b> to show them.<b><o:p></o:p></b></span></p> 2035 1920 2036 1921 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: … … 2039 1924 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b><span 2040 1925 style='mso-fareast-font-family:"Times New Roman"'>4D Charge flipping – </span></b><span 2041 style='mso-fareast-font-family:"Times New Roman"'> Charge flipping is done for a2042 modulated structure.<o:p></o:p></span></p>1926 style='mso-fareast-font-family:"Times New Roman"'>4-Dimensional<b> </b>charge 1927 flipping is done for a modulated structure.<o:p></o:p></span></p> 2043 1928 2044 1929 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: … … 2057 1942 style='mso-fareast-font-family:"Times New Roman"'> – Perform Monte 2058 1943 Carlo/Simulated Annealing structure solution using the model as set up in the 2059 MC/SA tab .<o:p></o:p></span></p>1944 MC/SA tab and the controls at the bottom of this tab.<o:p></o:p></span></p> 2060 1945 2061 1946 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: … … 2084 1969 </span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Compare 2085 1970 – </span></b><span style='mso-fareast-font-family:"Times New Roman"'>Compares 2086 idealized <span class=SpellE>polyhedra</span> (tetrahedron & octahedron) to2087 those obtained from a Reverse Monte Carlo run.<b><o:p></o:p></b></span></p>1971 idealized polyhedra (tetrahedron & octahedron) to those obtained from a 1972 Reverse Monte Carlo run in RMCProfile.<b><o:p></o:p></b></span></p> 2088 1973 2089 1974 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: … … 2105 1990 style='mso-fareast-font-family:"Times New Roman"'>Protein quality</span></b><span 2106 1991 style='mso-fareast-font-family:"Times New Roman"'> – evaluate protein quality 2107 by python versions of <span class=SpellE>errat</span> & errat2 codes by <span 2108 class=SpellE>Colovos</span>, C. & <span class=SpellE>Yeates</span>, T.O. Protein 2109 Science 2, 1511-1519 (1991).<b><o:p></o:p></b></span></p> 1992 by python versions of errat & errat2 codes by Colovos, C. & Yeates, 1993 T.O. Protein Science 2, 1511-1519 (1991).<b><o:p></o:p></b></span></p> 2110 1994 2111 1995 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span … … 2153 2037 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 2154 2038 style='mso-fareast-font-family:"Times New Roman"'>Space group</span></b><span 2155 style='mso-fareast-font-family:"Times New Roman"'> – this should be set when 2156 the phase is initialized; it can be changed later. Be careful about the impact 2157 on Atom site symmetry and multiplicity if you do. GSAS-II will recognize any 2158 legal space group symbol using the short Hermann-<span class=SpellE>Mauguin</span> 2159 forms; put a space between the axial fields (e.g. ‘F d 3 m’ not ‘Fd3m’; ‘F d 3 2160 m’ is understood as well as ‘F d -3 m’). For space groups with a choice of 2161 origin (e.g. F d 3 m), GSAS-II always uses the 2<sup>nd</sup> setting where the 2162 center of inversion is located at the origin. The choice of space group will 2163 set the available unit cell parameters.<span class=MsoHyperlink><span 2164 style='color:windowtext'><o:p></o:p></span></span></span></p> 2039 style='mso-fareast-font-family:"Times New Roman"'> – this should be set when the 2040 phase is initialized; it can be changed later. Be careful about the impact on 2041 Atom site symmetry and multiplicity if you do. GSAS-II will recognize any legal 2042 space group symbol using the short Hermann-Mauguin forms; put a space between 2043 the axial fields (e.g. ‘F d 3 m’ not ‘Fd3m’; ‘F d 3 m’ is understood as well as 2044 ‘F d -3 m’). For space groups with a choice of origin (e.g. F d 3 m), GSAS-II 2045 always uses the 2<sup>nd</sup> setting where the center of inversion is located 2046 at the origin. The choice of space group will set the available unit cell 2047 parameters.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p> 2165 2048 2166 2049 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: … … 2290 2173 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 2291 2174 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 2292 "Times New Roman"'>If there are entries in the Atoms <span class=GramE>page</span>2293 t hen the Elements table is shown next on the General page; you may select the2294 isotope (only relevant for neutron diffraction experiments). The density (just 2295 above the Elements) is computed depending on this choice, the unit cell volume2296 a nd the atom fractions/site multiplicities in the entries on the Atoms page.<span2175 "Times New Roman"'>If there are entries in the Atoms tab, then the Elements 2176 table is shown next on the General page; you may select the isotope (only 2177 relevant for neutron diffraction experiments). The density (just above the 2178 Elements) is computed depending on this choice, the unit cell volume and the 2179 atom fractions/site multiplicities in the entries on the Atoms page.<span 2297 2180 class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p> 2298 2181 … … 2323 2206 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: 2324 2207 auto;text-indent:-.25in;mso-list:l0 level2 lfo2;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 2325 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 2326 color:windowtext;text-decoration:none;text-underline:none'><span 2327 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 2328 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 2329 style='mso-fareast-font-family:"Times New Roman"'>Pawley <span class=SpellE>dmin</span></span></b><span 2330 style='mso-fareast-font-family:"Times New Roman"'> – This is the minimum 2331 d-spacing to be used in a Pawley refinement. <b style='mso-bidi-font-weight: 2332 normal'>NB:</b> be sure to set this to match the minimum d-spacing indicated by 2333 the powder pattern limits (see <b style='mso-bidi-font-weight:normal'>Limits</b> 2334 for the powder data set).<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p> 2208 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 2209 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 2210 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Pawley 2211 dmin</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – This 2212 is the minimum d-spacing to be used in a Pawley refinement. <b 2213 style='mso-bidi-font-weight:normal'>NB:</b> be sure to set this to match the 2214 minimum d-spacing indicated by the powder pattern limits (see <b 2215 style='mso-bidi-font-weight:normal'>Limits</b> for the powder data set).<u><o:p></o:p></u></span></p> 2335 2216 2336 2217 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: … … 2339 2220 color:windowtext;text-decoration:none;text-underline:none'><span 2340 2221 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 2222 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 2223 style='mso-fareast-font-family:"Times New Roman"'>Pawley dmax</span></b><span 2224 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'> – 2225 This is the maximum d-spacing for reflections in a Pawley refinement. It is 2226 usually defined by the beginning of the data collection scan and will thus 2227 remove reflections that have too large d-spacing to be seen in the scan.</span><span 2228 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 2229 color:windowtext'><o:p></o:p></span></span></p> 2230 2231 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: 2232 auto;text-indent:-.25in;mso-list:l0 level2 lfo2;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 2233 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 2234 color:windowtext;text-decoration:none;text-underline:none'><span 2235 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 2341 2236 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 2342 2237 style='mso-fareast-font-family:"Times New Roman"'>Pawley neg. wt.</span></b><span … … 2377 2272 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 2378 2273 style='mso-fareast-font-family:"Times New Roman"'>Reflection sets </span></b><span 2379 style='mso-fareast-font-family:"Times New Roman"'>– This is the source of 2380 structure factors to be used in a charge flip calculation. These may be either 2381 a single crystal data set, or structure factors extracted from a powder pattern 2382 via a Pawleyrefinement or a Rietveld refinement.<span class=MsoHyperlink><span2274 style='mso-fareast-font-family:"Times New Roman"'>– This is the source of structure 2275 factors to be used in a charge flip calculation. These may be either a single 2276 crystal data set, or structure factors extracted from a powder pattern via a 2277 Pawley or LeBail refinement or a Rietveld refinement.<span class=MsoHyperlink><span 2383 2278 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 2384 2279 … … 2390 2285 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 2391 2286 style='mso-fareast-font-family:"Times New Roman"'>Normalizing element </span></b><span 2392 style='mso-fareast-font-family:"Times New Roman"'>– This is an element form 2393 factorchosen to normalize the structure factors before charge flipping. <b2287 style='mso-fareast-font-family:"Times New Roman"'>– This is an element form factor 2288 chosen to normalize the structure factors before charge flipping. <b 2394 2289 style='mso-bidi-font-weight:normal'>None</b> (the default) can be selected from 2395 2290 the lower right of the Periodic Table display shown when this is selected.<span … … 2404 2299 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 2405 2300 style='mso-fareast-font-family:"Times New Roman"'>Map grid step </span></b><span 2406 style='mso-fareast-font-family:"Times New Roman"'>– This is the step size of the 2407 charge flip map; default is 0.25A. The set of reflections is expanded to a full 2408 sphere and zero filled to this 2X this value; this suite of reflections is then 2409 used for charge flipping.<span class=MsoHyperlink><span style='color:windowtext; 2410 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 2301 style='mso-fareast-font-family:"Times New Roman"'>– This is the step size of 2302 the charge flip map; default is 0.25</span><span style='font-family:"Calibri",sans-serif; 2303 mso-fareast-font-family:"Times New Roman"'>Å</span><span style='mso-fareast-font-family: 2304 "Times New Roman"'>. The set of reflections is expanded to a full sphere and 2305 zero filled to 2X this value; this suite of reflections is then used for charge 2306 flipping.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 2307 none;text-underline:none'><o:p></o:p></span></span></span></p> 2411 2308 2412 2309 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: … … 2426 2323 on the density map; all densities above this are charge flipped. In this way 2427 2324 the “uranium solution” problem is avoided. Use k-Max = 10-12 for equal atom 2428 problems and larger for heavy atom ones ( 2X largest atom number).<o:p></o:p></span></p>2325 problems and larger for heavy atom ones (typically 2X largest atom number).<o:p></o:p></span></p> 2429 2326 2430 2327 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: … … 2435 2332 style='mso-fareast-font-family:"Times New Roman"'>Test HKLs</span></b><span 2436 2333 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'> – 2437 plot of phases for selected <span class=SpellE>hkls</span> are shown at end of2438 charge flipping run.</span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>2334 plot of phases for selected hkls are shown at end of charge flipping run. Just 2335 for you to look at.</span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> 2439 2336 2440 2337 <p class=MsoListParagraphCxSpMiddle style='margin-left:73.2pt;mso-add-space: … … 2453 2350 This is the source of structure factors to be used in a charge flip 2454 2351 calculation. These may be either a single crystal data set, or structure 2455 factors extracted from a powder pattern via a Pawley refinement or a Rietveld2456 refinement.<o:p></o:p></span></p>2352 factors extracted from a powder pattern via a Pawley or Lebail refinement or a 2353 Rietveld refinement.<o:p></o:p></span></p> 2457 2354 2458 2355 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: … … 2462 2359 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>d-min 2463 2360 </span></b><span style='mso-fareast-font-family:"Times New Roman"'>- This 2464 restricts the set of reflections to be used in the MC/SA run. Suggest no lower2465 than 2.0.</span></p>2361 restricts the set of reflections to be used in the MC/SA run. Suggest using no 2362 lower than 2.0.</span></p> 2466 2363 2467 2364 <p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space: … … 2518 2415 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 2519 2416 style='mso-fareast-font-family:"Times New Roman"'>An important transformation 2520 may be needed in certain cases when space groups thattwo alternate origin2417 may be needed in certain cases for space groups that have two alternate origin 2521 2418 settings (<a 2522 2419 href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#GSASIIspc.spg2origins">listed … … 2526 2423 a center of symmetry (creating a -x,-y,-z symmetry operator, which means that 2527 2424 reflection phases can only be 0 or π.) GSAS-II requires use of the Origin 2 2528 settings because computations are much faster and simpler without complex 2529 structure factors. Alas, the literature contains a number of structures 2530 reported in Origin 1, where the origin choice may not be clearly communicated. 2531 (The CIF standard does not require that origin choice be indicated.) When a 2532 structure is imported that uses any of the space groups where an origin choice 2533 is possible, a message is shown in GSAS-II notifying the user that they must 2534 confirm that the origin choice is correct. <o:p></o:p></span></p> 2425 settings because computations are much faster and simpler without complex structure 2426 factors. Alas, the literature contains a number of structures reported in 2427 Origin 1, where the origin choice may not be clearly communicated. (The CIF 2428 standard does not require that origin choice be indicated.) When a structure is 2429 imported that uses any of the space groups where an origin choice is possible, 2430 a message is shown in GSAS-II notifying the user that they must confirm that 2431 the origin choice is correct and then provides the opportunity to change 2432 origins. <o:p></o:p></span></p> 2535 2433 2536 2434 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span 2537 2435 style='mso-fareast-font-family:"Times New Roman"'>Example:</span></b><span 2538 style='mso-fareast-font-family:"Times New Roman"'> An example of what can go wrong2539 is illustrated with the structure of anatase. The space group is <i>I</i> 4<sub>1</sub>/<i>a 2540 m d</i>. In Origin 1 the coordinates are: <o:p></o:p></span></p>2436 style='mso-fareast-font-family:"Times New Roman"'> An example of what can go 2437 wrong is illustrated with the structure of anatase. The space group is <i>I</i> 2438 4<sub>1</sub>/<i>a m d</i>. In Origin 1 the coordinates are: <o:p></o:p></span></p> 2541 2439 2542 2440 <table class=MsoNormalTable border=0 cellpadding=0 style='mso-cellspacing:1.5pt; … … 2560 2458 <tr style='mso-yfti-irow:2'> 2561 2459 <td style='padding:.75pt .75pt .75pt .75pt'> 2562 <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family: 2563 "Times New Roman"'>Ti</span></span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> 2460 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Ti<o:p></o:p></span></p> 2564 2461 </td> 2565 2462 <td style='padding:.75pt .75pt .75pt .75pt'> … … 2614 2511 <tr style='mso-yfti-irow:2'> 2615 2512 <td style='padding:.75pt .75pt .75pt .75pt'> 2616 <p class=MsoNormal><span class=SpellE><span style='mso-fareast-font-family: 2617 "Times New Roman"'>Ti</span></span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> 2513 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Ti<o:p></o:p></span></p> 2618 2514 </td> 2619 2515 <td style='padding:.75pt .75pt .75pt .75pt'> … … 2645 2541 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 2646 2542 style='mso-fareast-font-family:"Times New Roman";color:white;mso-color-alt: 2647 windowtext'>where the origin is shifted by (0,0.</span><span class=GramE><span 2648 style='mso-fareast-font-family:"Times New Roman"'>25,-</span></span><span 2649 style='mso-fareast-font-family:"Times New Roman"'>0.125). <o:p></o:p></span></p> 2543 windowtext'>where the origin is shifted by (0,</span><span style='mso-fareast-font-family: 2544 "Times New Roman"'>1/4,-1/8). <o:p></o:p></span></p> 2650 2545 2651 2546 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><!--[if gte vml 1]><v:shape … … 2663 2558 </v:shape><![endif]--><![if !vml]><img width=322 height=190 2664 2559 src="gsasII_files/wrong.png" align=right v:shapes="Picture_x0020_3"><![endif]><span 2665 style='mso-fareast-font-family:"Times New Roman"'> Since GSAS-II always the symmetry2666 operators for Origin 2, if structure is input incorrectly with the coordinates 2667 set for Origin 1, there are several fairly obvious signs of problems: (1) the 2668 site symmetries and multiplicities are wrong, often giving an incorrect 2669 chemical formula, (2) the interatomic distances are incorrect, and (3) a plot 2670 of the structure is improbable. In this case incorrect multiplicities gives 2671 rise to a density of 7.9 g/cc, double the correct value. Impossible interatomic 2672 distances of 1.88Å for <span class=SpellE>Ti-Ti</span>, and 1.39Å for <span 2673 class=SpellE>Ti</span>-O are seen. The unit cell contents with the wrong space 2674 group operators is shown tothe right. <o:p></o:p></span></p>2560 style='mso-fareast-font-family:"Times New Roman"'>GSAS-II always uses the 2561 symmetry operators for Origin 2; if the structure is input incorrectly with the 2562 coordinates set for Origin 1, there are several fairly obvious signs of 2563 problems: (1) the site symmetries and multiplicities are wrong, often giving an 2564 incorrect chemical formula, (2) the interatomic distances are incorrect, and 2565 (3) a plot of the structure is improbable. In this case incorrect 2566 multiplicities gives rise to a density of 7.9 g/cc, double the correct value. 2567 Impossible interatomic distances of 1.88Å for Ti-Ti, and 1.39Å for Ti-O are 2568 seen. The unit cell contents with the wrong space group operators is shown to 2569 the right. <o:p></o:p></span></p> 2675 2570 2676 2571 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 2677 2572 style='mso-fareast-font-family:"Times New Roman"'>With coordinates that match 2678 the space group operations, the correct <span class=SpellE>Ti</span>-O 2679 distances are 1.92Å and 1.97Å and the shortest <span class=SpellE>Ti-Ti</span> 2680 distance is 3.0Å. (Note that interatomic distances can be computed in GSAS-II 2681 using the Phase Atoms tab and the Compute/"Show Distances & 2682 Angles" menu item.) <o:p></o:p></span></p> 2573 the space group operations, the correct Ti-O distances are 1.92Å and 1.97Å and 2574 the shortest Ti-Ti distance is 3.0Å. (Note that interatomic distances can be 2575 computed in GSAS-II using the Phase Atoms tab and the Compute/"Show 2576 Distances & Angles" menu item.) <o:p></o:p></span></p> 2683 2577 2684 2578 <p class=MsoNormal style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><!--[if gte vml 1]><v:shape … … 2697 2591 src="gsasII_files/xform.png" align=right v:shapes="Picture_x0020_4"><![endif]><b><span 2698 2592 style='mso-fareast-font-family:"Times New Roman"'>Transform Origin:</span></b><span 2699 style='mso-fareast-font-family:"Times New Roman"'> To transform a space group 2700 setting from Origin setting 1 to 2, use the Transform option in the Compute menu 2701 and then select the last option in the "Common transformations" 2702 pulldown menu, which will be setting 1->2 for space groups where both 2703 origins are available, as shown to the right. The transformation matrix will be2704 set to the identity and the "V" vector will have the required origin 2705 shiftloaded. Press OK. The changes can be seen by selecting the Atoms tab. </span></p>2593 style='mso-fareast-font-family:"Times New Roman"'> To transform a space group setting 2594 from Origin setting 1 to 2, use the Transform option in the Compute menu and 2595 then select the last option in the "Common transformations" pulldown 2596 menu, which will be setting 1->2 for space groups where both origins are 2597 available, as shown to the right. The transformation matrix will be set to the 2598 identity and the "V" vector will have the required origin shift 2599 loaded. Press OK. The changes can be seen by selecting the Atoms tab. </span></p> 2706 2600 2707 2601 <p class=MsoNormal style='tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span … … 2714 2608 2715 2609 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>This 2716 tab serves several purposes. It is used to link histograms to the selected <span2717 class=GramE>phase</span> and it allows the values and refinement flags to be2718 set for the parameters that are defined for each histogram-phase pair, labeled 2719 as HAP parameters. [Note that some GSAS-II parameters are defined for each 2720 phase(atomic positions, for example), other parameters are defined for each2610 tab serves several purposes. It is used to link histograms to the selected 2611 phase, and it allows the values and refinement flags to be set for the 2612 parameters that are defined for each histogram-phase pair, labeled as HAP 2613 parameters. [Note that some GSAS-II parameters are defined for each phase 2614 (atomic positions, for example), other parameters are defined for each 2721 2615 histogram (scale factors and instrumental constants, for example) but the HAP 2722 2616 parameters have values for each histogram in each phase.] It can also be used … … 2724 2618 2725 2619 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The 2726 HAP parameters include: the phase fraction; the sample contribution to peak2727 broadening: <span class=SpellE>microstrain</span> and crystallite size; a2728 LeBail intensity extraction flag; hydrostatic/elastic strain shifts to lattice 2729 p arameters; corrections to peak intensities due to experimental effects2730 (preferred orientation, extinctionand disordered solvents).</p>2620 HAP parameters include: the phase fraction; the sample contributions to peak 2621 broadening: microstrain and crystallite size; a LeBail intensity extraction 2622 flag; hydrostatic/elastic strain shifts to lattice parameters; corrections to 2623 peak intensities due to experimental effects (preferred orientation, extinction 2624 and disordered solvents).</p> 2731 2625 2732 2626 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>For … … 2746 2640 2747 2641 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span 2748 style='mso-fareast-font-family:"Times New Roman"'> LeBail extraction </span></b><span2642 style='mso-fareast-font-family:"Times New Roman"'>Start LeBail extraction </span></b><span 2749 2643 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> 2750 2644 2751 2645 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 2752 2646 style='mso-fareast-font-family:"Times New Roman"'>When this is selected, 2753 intensities are set to values that are <span class=GramE>best-fit</span> using2754 the LeBail intensity determination method rather than are computed from the 2755 atomic information for the phase. Cycling this setting will reset LeBail 2756 extracted intensities totheir default (F<sup>2</sup> = 100).<o:p></o:p></span></p>2647 intensities are set to values that are best fit using the LeBail intensity 2648 determination method rather than are computed from the atomic information for 2649 the phase. Cycling this setting will reset LeBail extracted intensities to 2650 their default (F<sup>2</sup> = 100).<o:p></o:p></span></p> 2757 2651 2758 2652 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span … … 2761 2655 2762 2656 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 2763 style='mso-fareast-font-family:"Times New Roman"'> used in powder histograms: a2657 style='mso-fareast-font-family:"Times New Roman"'>Used in powder histograms: a 2764 2658 multiplier that determines the relative amount of the selected phase to a 2765 histogram. Note that when the histogram scale factor is varied, these values 2766 are on a relative scale. Conventional practice is to vary the scale factor and 2767 to not vary the phase fraction for one phase in a histogram. Do not refine the 2659 histogram. It is proportional the number of unit cells of the phase in the 2660 sample. Note that when the histogram scale factor is varied, these values are 2661 on a relative scale. Conventional practice is to vary the scale factor and to 2662 not vary the phase fraction for one phase in a histogram. Do not refine the 2768 2663 scale factor and all phase fractions unless a constraint is defined so the 2769 2664 phase fractions add to 1. <o:p></o:p></span></p> … … 2773 2668 2774 2669 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 2775 style='mso-fareast-font-family:"Times New Roman"'> used for single crystal <span2776 class=GramE>data:</span>relates F<sup>2</sup><sub>obs</sub> to F<sup>2</sup><sub>calc</sub>.<o:p></o:p></span></p>2670 style='mso-fareast-font-family:"Times New Roman"'>Used for single crystal data: 2671 relates F<sup>2</sup><sub>obs</sub> to F<sup>2</sup><sub>calc</sub>.<o:p></o:p></span></p> 2777 2672 2778 2673 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span … … 2782 2677 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 2783 2678 style='mso-fareast-font-family:"Times New Roman"'>is computed from size 2784 factor(s) in microns ( 10<sup>-6</sup> m), with the Scherrer constant assumed as2785 unity. Sizes can be computed in three ways: isotropic, uniaxial and2679 factor(s) in microns (μm = 10<sup>-6</sup> m), with the Scherrer constant 2680 assumed as unity. Sizes can be computed in three ways: isotropic, uniaxial and 2786 2681 ellipsoidal. In isotropic broadening, crystallites are assumed to average as 2787 2682 uniform in all directions and a single size value is supplied; with uniaxial … … 2791 2686 perpendicular plane; with ellipsoidal, six terms are used to define a 2792 2687 broadening tensor that has arbitrary orientation -- this model may require 2793 constraints and is seldom lyneeded. Note that size broadening is usually2794 Lorentzian, which corresponds to a <span class=SpellE>LGmix</span> value of2795 1.0; if this value is between 0. and 1., both Gaussian and Lorentz size 2796 broadening is modeled and a value of 0.0 is pure Gaussian. Values less than 0. 2797 or greater than 1. make no physical sense. <o:p></o:p></span></p> 2798 2799 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 2800 class=SpellE><b><span style='mso-fareast-font-family:"Times New Roman"'>Microstrain</span></b></span><b><span2801 style='mso-fareast-font-family:"Times New Roman"'> peak broadening </span></b><span2688 constraints and is seldom needed. Note that size broadening is usually 2689 Lorentzian, which corresponds to a LGmix value of 1.0; if this value is between 2690 0. and 1., both Gaussian and Lorentz size broadening is modeled and a value of 2691 0.0 is pure Gaussian. Values less than 0. or greater than 1. make no physical 2692 sense. Typical sensitivity is to no more than 4 μm; beyond that the particles 2693 are effectively infinite for a diffraction experiment.<o:p></o:p></span></p> 2694 2695 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span 2696 style='mso-fareast-font-family:"Times New Roman"'>Microstrain peak broadening </span></b><span 2802 2697 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> 2803 2698 2804 2699 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 2805 2700 style='mso-fareast-font-family:"Times New Roman"'>is computed as unitless 2806 fraction of <span class=SpellE>Δd</span>/d (or equivalently ΔQ/Q) times 10<sup>6</sup>. 2807 <span class=SpellE>Microstrain</span> can be computed in three ways: isotropic, 2808 uniaxial and generalized. In isotropic broadening, <span class=SpellE>microstrain</span> 2809 broadening assumed to be the same in all crystallographic directions and a 2810 single value is supplied; with uniaxial broadening, a preferred direction (as a 2811 crystallographic axis, such as 0,0,1) is supplied -- note that for most crystal 2812 systems only one axis makes sense -- and two <span class=SpellE>microstrain</span> 2813 parameters are defined, one for along the axis and one for in the perpendicular 2814 plane; with generalized, the Nicole Popa/Peter Stephens second-order expansion 2815 model is used and the number of terms will depend on the crystal system. It is 2816 typically possible to refine all terms when significant anisotropic strain 2817 broadening is present. Note that <span class=SpellE>microstrain</span> 2818 broadening is usually Lorentzian, which corresponds to a <span class=SpellE>LGmix</span> 2819 value of 1.0; if this value is between 0. and 1., both Gaussian and Lorentz 2820 broadening is modeled and a value of 0.0 is pure Gaussian. Values less than 0. 2821 or greater than 1. make no physical sense. <o:p></o:p></span></p> 2701 fraction of Δd/d (or equivalently ΔQ/Q) times 10<sup>6</sup>. Microstrain can 2702 be represented in three ways: isotropic, uniaxial and generalized. In isotropic 2703 broadening, microstrain broadening assumed to be the same in all 2704 crystallographic directions and a single value is supplied; with uniaxial 2705 broadening, a preferred direction (as a crystallographic axis, such as 0,0,1) 2706 is supplied -- note that for most crystal systems only one axis makes sense -- 2707 and two microstrain parameters are defined, one for along the axis and one for 2708 in the perpendicular plane; with generalized, the Nicole Popa/Peter Stephens 2709 second-order expansion model is used and the number of terms will depend on the 2710 crystal system. It is typically possible to refine all terms when significant 2711 anisotropic strain broadening is present. Note that microstrain broadening is 2712 usually Lorentzian, which corresponds to a LGmix value of 1.0; if this value is 2713 between 0. and 1., both Gaussian and Lorentz broadening is modeled and a value 2714 of 0.0 is pure Gaussian. Values less than 0. or greater than 1. make no 2715 physical sense. Typical microstrain is ~1000.<o:p></o:p></span></p> 2822 2716 2823 2717 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span … … 2844 2738 ways. Intensity corrections can be added to the model here or a full texture 2845 2739 model is possible with the "<u><span style='color:blue'><a href="#Texture">Texture</a></span></u>" 2846 tab (which usually requires multiple histograms at different sample or detector 2847 settings). The approaches available here are March-<span class=SpellE>Dollase</span>, 2848 which requires a definition of a unique axis (in crystallographic coordinates) 2849 and the relative amount of excess or depletion of crystallites in that 2850 direction; or Spherical Harmonics, where the selection of an order determines 2851 the shape of the probability surface (which is always constrained to match the 2852 symmetry of the crystal system). <o:p></o:p></span></p> 2740 tab (which usually requires multiple histograms at different sample orientations 2741 or detector settings). The approaches available here are March-Dollase, which 2742 requires a definition of a unique axis (in crystallographic coordinates) and 2743 the relative amount of excess or depletion of crystallites in that direction; 2744 or Spherical Harmonics, where the selection of an order determines the shape of 2745 the probability surface (which is always constrained to match the symmetry of 2746 the crystal system and the symmetry of the sample; here sample symmetry is 2747 assumed to be cylindrical). <o:p></o:p></span></p> 2853 2748 2854 2749 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span … … 2860 2755 crystals/crystallites have minimal mosaic character, which results in lowering 2861 2756 of diffraction intensities for the most intense reflections. This is not 2862 commonly seen in CW powder <span class=GramE>diffraction, but</span> can be2863 more apparent in neutron TOF data. For single crystal data the extinction model 2864 is more complex allowing forprimary and two types of secondary extinction.<o:p></o:p></span></p>2757 commonly seen in CW powder diffraction but can be more apparent in neutron TOF 2758 data. For single crystal data the extinction model is more complex allowing for 2759 primary and two types of secondary extinction.<o:p></o:p></span></p> 2865 2760 2866 2761 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span 2867 style='mso-fareast-font-family:"Times New Roman"'>Disordered solvent – <span 2868 class=SpellE>Babinet</span> A & B</span></b><span style='mso-fareast-font-family: 2869 "Times New Roman"'><o:p></o:p></span></p> 2762 style='mso-fareast-font-family:"Times New Roman"'>Disordered solvent – Babinet 2763 A & B</span></b><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p> 2870 2764 2871 2765 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 2872 style='mso-fareast-font-family:"Times New Roman"'>This correction, using the <span2873 class=SpellE>Babinet</span> model, is typically used to treat scattering from 2874 solvent that is not well-ordered in protein structures. It probably makes no 2875 sense in most anyother application. <o:p></o:p></span></p>2766 style='mso-fareast-font-family:"Times New Roman"'>This correction, using the 2767 Babinet model, is typically used to treat scattering from solvent that is not 2768 well-ordered in protein structures. It probably makes no sense in most any 2769 other application. <o:p></o:p></span></p> 2876 2770 2877 2771 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><b><span … … 2887 2781 <h5 style='margin-left:.5in'>What can I do here?</h5> 2888 2782 2889 <OL style='margin-left:0.75in'> 2890 <LI>In this tab, menu items allow 2783 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; 2784 margin-left:1.25in;text-indent:-.25in;mso-list:l4 level1 lfo3;tab-stops:list .5in'><![if !supportLists]><span 2785 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 2786 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2787 style='mso-fareast-font-family:"Times New Roman"'>In this tab, menu items allow 2891 2788 copying values or refinement flags to histograms/phases and selection of which 2892 histograms are used in the current phase. </LI> 2893 2894 <LI>The plot selection items 2895 allow for three dimensional representations of the <span class=SpellE>microstrain</span> 2896 or crystallite size distributions (which are spheres for isotropic treatments); 2897 preferred orientation can be plotted as a Psi scan (a plot of relative 2898 crystallite abundance for a particular reflection as a function of azimuthal 2899 angle) or as an inverse pole figure (which shows in a stereographic projection 2900 the probability distribution for different reciprocal lattice directions for a 2901 particular sample orientation). <o:p></o:p></span></LI> 2902 </OL> 2789 histograms are used in the current phase. <o:p></o:p></span></p> 2790 2791 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; 2792 margin-left:1.25in;text-indent:-.25in;mso-list:l4 level1 lfo3;tab-stops:list .5in'><![if !supportLists]><span 2793 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 2794 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span 2795 style='mso-fareast-font-family:"Times New Roman"'>The plot selection items 2796 allow for three dimensional representations of the microstrain or crystallite 2797 size distributions (which are spheres for isotropic treatments); preferred 2798 orientation can be plotted as a Psi scan (a plot of relative crystallite 2799 abundance for a particular reflection as a function of azimuthal angle) or as 2800 an inverse pole figure (which shows a stereographic projection of the 2801 probability distribution for different reciprocal lattice directions as viewed 2802 down the sample cylinder axis). For no texture/preferred orientation this 2803 figure would be flat = 1.0.<o:p></o:p></span></p> 2903 2804 2904 2805 <h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a … … 2916 2817 2917 2818 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto; 2918 text-indent:-.25in;mso-list:l2 level1 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2819 text-indent:-.25in;mso-list:l2 level1 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 2919 2820 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 2920 2821 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b>Atom 2921 selection from table </b>- These are controlled by the mouse and the Shift/Ctrl/Alt2922 keys. Note that for most purposes (one exception is atom reordering which 2923 re quires an Alt-Left-click on the rows), selection of any cell for an atom will2924 work equivalently with selection of the entire row. Upon selection the atoms 2925 will turn green in the structure drawing:</p>2926 2927 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 2928 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2822 selection from table </b>- These are controlled by the mouse and the 2823 Shift/Ctrl/Alt keys. Note that for most purposes (one exception is atom 2824 reordering which requires an Alt-Left-click on the rows), selection of any cell 2825 for an atom will work equivalently with selection of the entire row. Upon 2826 selection the atoms will turn green in the structure drawing:</p> 2827 2828 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 2829 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 2929 2830 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 2930 2831 color:windowtext;text-decoration:none;text-underline:none'><span … … 2937 2838 2938 2839 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 2939 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2840 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 2940 2841 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 2941 2842 color:windowtext;text-decoration:none;text-underline:none'><span … … 2949 2850 2950 2851 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 2951 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2852 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 2952 2853 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 2953 2854 color:windowtext;text-decoration:none;text-underline:none'><span … … 2960 2861 2961 2862 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 2962 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2863 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 2963 2864 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 2964 2865 color:windowtext;text-decoration:none;text-underline:none'><span … … 2970 2871 atom selected. Use <b style='mso-bidi-font-weight:normal'>Alt LMB</b> again to 2971 2872 select a target row for this atom; insertion will be before this row and the 2972 table will be updated to show the change. NB: <span class=GramE>the</span> <b2973 style='mso-bidi-font-weight:normal'>Draw Atoms</b> list is not updated by this 2974 c hange.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:2975 none;text-underline:none'><o:p></o:p></span></span></span></p>2873 table will be updated to show the change. NB: the <b style='mso-bidi-font-weight: 2874 normal'>Draw Atoms</b> list is not updated by this change.<span 2875 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 2876 text-underline:none'><o:p></o:p></span></span></span></p> 2976 2877 2977 2878 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2978 auto;text-indent:-.25in;mso-list:l2 level1 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2879 auto;text-indent:-.25in;mso-list:l2 level1 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 2979 2880 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 2980 2881 color:windowtext;text-decoration:none;text-underline:none'><span 2981 2882 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 2982 2883 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Double 2983 left <span class=GramE>click</span> a Type column heading</b>: a dialog box is2984 s hown that allows you to select all atoms with that type.<span2985 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 2986 color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></p>2884 left click a Type column heading</b>: a dialog box is shown that allows you to 2885 select all atoms with that type. <span class=MsoHyperlink><span 2886 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 2887 none;text-underline:none'><o:p></o:p></span></span></p> 2987 2888 2988 2889 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 2989 auto;text-indent:-.25in;mso-list:l2 level1 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2890 auto;text-indent:-.25in;mso-list:l2 level1 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 2990 2891 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 2991 2892 color:windowtext;text-decoration:none;text-underline:none'><span … … 2998 2899 2999 2900 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3000 auto;text-indent:-.25in;mso-list:l2 level1 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2901 auto;text-indent:-.25in;mso-list:l2 level1 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3001 2902 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3002 2903 color:windowtext;text-decoration:none;text-underline:none'><span … … 3007 2908 the mouse (<b style='mso-bidi-font-weight:normal'>Alt</b> ignored, <b 3008 2909 style='mso-bidi-font-weight:normal'>Shift</b> & <b style='mso-bidi-font-weight: 3009 normal'>Ctrl</b> allow selection of multiple <span class=GramE>cells</span> but3010 no use is made of them). An individual data item can be cut/pasted anywhere 3011 including from/to another document. Bad entries are rejected. If any entry is2910 normal'>Ctrl</b> allow selection of multiple cells but no use is made of them). 2911 An individual data item can be cut/pasted anywhere including from/to another 2912 document. Bad entries are rejected (yellow background). If any entry is 3012 2913 changed, press <b style='mso-bidi-font-weight:normal'>Enter</b> key or select 3013 2914 another atom entry to apply the change.<span class=MsoHyperlink><span … … 3015 2916 3016 2917 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3017 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2918 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3018 2919 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3019 2920 color:windowtext;text-decoration:none;text-underline:none'><span … … 3026 2927 3027 2928 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3028 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2929 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3029 2930 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3030 2931 color:windowtext;text-decoration:none;text-underline:none'><span … … 3038 2939 3039 2940 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3040 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2941 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3041 2942 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3042 2943 color:windowtext;text-decoration:none;text-underline:none'><span … … 3050 2951 3051 2952 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3052 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2953 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3053 2954 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3054 2955 color:windowtext;text-decoration:none;text-underline:none'><span 3055 2956 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 3056 </span></span></span></span><![endif]><span class=SpellE><span class=GramE><b 3057 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>x,y</span></b></span><b 3058 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>,z</span></b></span><span 2957 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 2958 style='mso-fareast-font-family:"Times New Roman"'>x,y,z</span></b><span 3059 2959 style='mso-fareast-font-family:"Times New Roman"'> – change atom coordinate. 3060 2960 Fractions (e.g. 1/3, 1/4) are allowed.<span class=MsoHyperlink><span … … 3062 2962 3063 2963 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3064 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2964 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3065 2965 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3066 2966 color:windowtext;text-decoration:none;text-underline:none'><span 3067 2967 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 3068 </span></span></span></span><![endif]><span class=SpellE><span class=GramE><b 3069 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>frac,Uiso</span></b></span><b 3070 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>,Uij</span></b></span><span 2968 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 2969 style='mso-fareast-font-family:"Times New Roman"'>frac,Uiso,Uij</span></b><span 3071 2970 style='mso-fareast-font-family:"Times New Roman"'> – change these values; 3072 2971 fractions (e.g. 1/3, 1/4) are allowed.<span class=MsoHyperlink><span … … 3074 2973 3075 2974 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3076 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2975 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3077 2976 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 3078 2977 color:windowtext;text-decoration:none;text-underline:none'><span … … 3081 2980 style='mso-fareast-font-family:"Times New Roman"'>I/A</span></b><span 3082 2981 style='mso-fareast-font-family:"Times New Roman"'> – select one of <b 3083 style='mso-bidi-font-weight:normal'>I</b>(<span class=SpellE>sotropic</span>) 3084 or <b style='mso-bidi-font-weight:normal'>A</b>(<span class=SpellE>nisotropic</span>); 3085 the <span class=SpellE><b style='mso-bidi-font-weight:normal'>Uiso</b></span><b 3086 style='mso-bidi-font-weight:normal'>/<span class=SpellE>Uij</span></b> entries 3087 will change appropriately. <span class=MsoHyperlink><span style='color:windowtext; 3088 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 2982 style='mso-bidi-font-weight:normal'>I</b>(sotropic) or <b style='mso-bidi-font-weight: 2983 normal'>A</b>(nisotropic); the <b style='mso-bidi-font-weight:normal'>Uiso/Uij</b> 2984 entries will change appropriately. <span class=MsoHyperlink><span 2985 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 3089 2986 3090 2987 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3091 auto;text-indent:-.25in;mso-list:l2 level1 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2988 auto;text-indent:-.25in;mso-list:l2 level1 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3092 2989 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span 3093 2990 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu … … 3097 2994 3098 2995 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3099 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span2996 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3100 2997 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 3101 2998 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b>On … … 3103 3000 3104 3001 <p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space: 3105 auto;text-indent:-.25in;mso-list:l2 level4 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3002 auto;text-indent:-.25in;mso-list:l2 level4 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3106 3003 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 3107 3004 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3110 3007 3111 3008 <p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space: 3112 auto;text-indent:-.25in;mso-list:l2 level4 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3009 auto;text-indent:-.25in;mso-list:l2 level4 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3113 3010 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 3114 3011 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3115 3012 style='mso-bidi-font-weight:normal'>Modify parameters</b> – A popup dialog box 3116 3013 appears with a list of atom parameter names; select one to apply to all 3117 selected atoms. <b style='mso-bidi-font-weight:normal'>Name</b> will rename selected 3118 atoms according to position in table (e.g. <span class=GramE>Na(</span>1) for 3119 Na atom as 1<sup>st</sup> atom in list in row ‘0’). <b style='mso-bidi-font-weight: 3120 normal'>Type</b> will give periodic table popup; selected element valence will 3121 be used for all selected atoms and atoms names will be changed. <b 3122 style='mso-bidi-font-weight:normal'>I/A</b> will give popup with choices to be 3123 used for all selected atoms. <span class=SpellE><span class=GramE><b 3124 style='mso-bidi-font-weight:normal'>x,y</b></span><b style='mso-bidi-font-weight: 3125 normal'>,z</b></span> will give popup for shift to be applied to the parameter 3126 for all selected atoms. <span class=SpellE><b style='mso-bidi-font-weight:normal'>Uiso</b></span> 3127 and <b style='mso-bidi-font-weight:normal'>frac</b> will give popup for new 3128 value to be used for all selected atoms. </p> 3014 selected atoms. <b style='mso-bidi-font-weight:normal'>Name</b> will rename 3015 selected atoms according to position in table (e.g. Na(1) for Na atom as 1<sup>st</sup> 3016 atom in list in row ‘0’). <b style='mso-bidi-font-weight:normal'>Type</b> will 3017 give periodic table popup; selected element valence will be used for all 3018 selected atoms and atoms names will be changed. <b style='mso-bidi-font-weight: 3019 normal'>I/A</b> will give popup with choices to be used for all selected atoms. 3020 <b style='mso-bidi-font-weight:normal'>x,y,z</b> will give popup for shift to 3021 be applied to the parameter for all selected atoms. <b style='mso-bidi-font-weight: 3022 normal'>Uiso</b> and <b style='mso-bidi-font-weight:normal'>frac</b> will give 3023 popup for new value to be used for all selected atoms. </p> 3129 3024 3130 3025 <p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space: 3131 auto;text-indent:-.25in;mso-list:l2 level4 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3026 auto;text-indent:-.25in;mso-list:l2 level4 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3132 3027 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 3133 3028 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b>Set … … 3135 3030 3136 3031 <p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space: 3137 auto;text-indent:-.25in;mso-list:l2 level4 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3032 auto;text-indent:-.25in;mso-list:l2 level4 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3138 3033 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 3139 3034 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3142 3037 3143 3038 <p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space: 3144 auto;text-indent:-.25in;mso-list:l2 level4 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3039 auto;text-indent:-.25in;mso-list:l2 level4 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3145 3040 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span 3146 3041 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3147 style='mso-bidi-font-weight:normal'>Insert atom</b> – insert an H atom (name= <span3148 class=SpellE>Unk</span>) at 0,0,0 before the selected atom, it is also drawn as 3149 an H atom in the structure plot.</p>3042 style='mso-bidi-font-weight:normal'>Insert atom</b> – insert an H atom (name= 3043 Unk) at 0,0,0 before the selected atom, it is also drawn as an H atom in the 3044 structure plot (small white ball).</p> 3150 3045 3151 3046 <p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space: 3152 auto;text-indent:-.25in;mso-list:l2 level4 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3047 auto;text-indent:-.25in;mso-list:l2 level4 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3153 3048 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span 3154 3049 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3155 3050 style='mso-bidi-font-weight:normal'>Insert viewpoint</b> – insert an H atom 3156 (name= <span class=SpellE>Unk</span>) before the selected atom with coordinates 3157 matching the location of the viewpoint, it is also drawn as an H atom in the 3158 structure plot.</p> 3051 (name= Unk) before the selected atom with coordinates matching the location of 3052 the viewpoint, it is also drawn as an H atom in the structure plot.</p> 3159 3053 3160 3054 <p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space: 3161 auto;text-indent:-.25in;mso-list:l2 level4 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3055 auto;text-indent:-.25in;mso-list:l2 level4 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3162 3056 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>7.<span 3163 3057 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3166 3060 3167 3061 <p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space: 3168 auto;text-indent:-.25in;mso-list:l2 level4 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3062 auto;text-indent:-.25in;mso-list:l2 level4 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3169 3063 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>8.<span 3170 3064 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3173 3067 3174 3068 <p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space: 3175 auto;text-indent:-.25in;mso-list:l2 level4 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3069 auto;text-indent:-.25in;mso-list:l2 level4 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3176 3070 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>9.<span 3177 3071 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3179 3073 appears; select space group operator/unit cell translation to apply to the 3180 3074 selected atoms. You can optionally force the result to be within the unit cell 3181 and optionally generate a new set of atom positions. You may also invert a <span3182 class=SpellE>noncentrosymmetric</span> structure. NB: many of these operations 3183 only make sense ifall atoms are selected.</p>3075 and optionally generate a new set of atom positions. You may also invert a 3076 noncentrosymmetric structure. NB: many of these operations only make sense if 3077 all atoms are selected.</p> 3184 3078 3185 3079 <p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space: 3186 auto;text-indent:-.25in;mso-list:l2 level4 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3080 auto;text-indent:-.25in;mso-list:l2 level4 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3187 3081 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>10.<span 3188 3082 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3191 3085 3192 3086 <p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space: 3193 auto;text-indent:-.25in;mso-list:l2 level4 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3087 auto;text-indent:-.25in;mso-list:l2 level4 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3194 3088 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>11.<span 3195 3089 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3196 style='mso-bidi-font-weight:normal'>Select from list </b>– A popup appears 3197 allowing selection of atoms for further changes. Selected atoms will turn 3198 green.</p> 3199 3200 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3201 auto;text-indent:-.25in;mso-list:l2 level2 lfo6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3090 style='mso-bidi-font-weight:normal'>Select from list </b>– A popup appears allowing 3091 selection of atoms for further changes. Selected atoms will turn green.</p> 3092 3093 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3094 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3202 3095 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 3203 3096 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3204 style='mso-bidi-font-weight:normal'>Append atom</b> – add an H atom (name= <span3205 class=SpellE>Unk</span>) at 0,0,0 to the end of the atom table, it is also 3206 drawn as an H atom in thestructure plot.</p>3207 3208 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3209 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3097 style='mso-bidi-font-weight:normal'>Append atom</b> – add an H atom (name= Unk) 3098 at 0,0,0 to the end of the atom table, it is also drawn as an H atom in the 3099 structure plot.</p> 3100 3101 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3102 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3210 3103 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 3211 3104 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3212 3105 style='mso-bidi-font-weight:normal'>Append viewpoint</b> – add an H atom (name= 3213 <span class=SpellE>Unk</span>) to the end of the atom table with coordinates 3214 matching the location of the viewpoint, it is drawn as an H atom in the 3215 structure plot.</p> 3216 3217 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3218 auto;text-indent:-.25in;mso-list:l2 level2 lfo6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3106 Unk) to the end of the atom table with coordinates matching the location of the 3107 viewpoint, it is drawn as an H atom in the structure plot.</p> 3108 3109 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3110 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3219 3111 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 3220 3112 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3221 style='mso-bidi-font-weight:normal'>Update H atoms </b>– </p> 3222 3223 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3224 auto;text-indent:-.25in;mso-list:l2 level2 lfo6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3113 style='mso-bidi-font-weight:normal'>Update H atoms </b>– Reset H-atoms 3114 according to bonding geometry; only applies to H-atoms initially placed via 3115 Calc H-atoms. Usually used after running a structure refinement.</p> 3116 3117 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3118 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3225 3119 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span 3226 3120 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b>Assemble 3227 molecule</b> – move atoms to create single <span class=GramE>molecule;</span>3228 not appropriate forextended structures.</p>3229 3230 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3231 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3121 molecule</b> – move atoms to create single molecule, not appropriate for 3122 extended structures.</p> 3123 3124 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3125 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3232 3126 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span 3233 3127 style='font:7.0pt "Times New Roman"'> … … 3236 3130 3237 3131 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3238 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3132 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3239 3133 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span 3240 3134 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3241 3135 style='mso-bidi-font-weight:normal'>Reload draw atoms</b> – reload drawing 3242 atoms from current atom list.</p> 3136 atoms from current atom list. Generally needed after a refinement.</p> 3137 3138 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3139 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3140 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span 3141 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3142 style='mso-bidi-font-weight:normal'>Reimport atoms </b>– from any importable phase 3143 file (e.g. cif, gpx)</p> 3243 3144 3244 3145 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3245 auto;text-indent:-.25in;mso-list:l2 level1 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3146 auto;text-indent:-.25in;mso-list:l2 level1 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3246 3147 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span 3247 3148 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu<b … … 3249 3150 3250 3151 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3251 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3152 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3252 3153 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 3253 3154 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3254 3155 style='mso-bidi-font-weight:normal'>Show Distances & Angles – </b>compute 3255 distances and angles with <span class=SpellE>esds</span> (if possible) for 3256 selected atoms. A popup dialog box will appear with distance angle controls. 3257 NB: if atoms have been added or their type changed, you may need to do a <b 3258 style='mso-bidi-font-weight:normal'>Reset</b> of this dialog box before 3259 proceeding.</p> 3260 3261 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3262 auto;text-indent:-.25in;mso-list:l2 level2 lfo6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3156 distances and angles with esds (if possible) for selected atoms. A popup dialog 3157 box will appear with distance angle controls. NB: if atoms have been added or 3158 their type changed, you may need to do a <b style='mso-bidi-font-weight:normal'>Reset</b> 3159 of this dialog box before proceeding.</p> 3160 3161 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3162 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3263 3163 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 3264 3164 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3265 3165 style='mso-bidi-font-weight:normal'>Save Distances & Angles –</b> same as 3266 a. but reports result to a file with extension <span class=GramE>“.<span 3267 class=SpellE>disagl</span></span>”.</p> 3268 3269 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3270 auto;text-indent:-.25in;mso-list:l2 level2 lfo6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3166 a. but reports result to a file with extension “.disagl”.</p> 3167 3168 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3169 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3271 3170 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 3272 3171 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b>Histogram … … 3275 3174 3276 3175 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3277 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3176 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3278 3177 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 3279 3178 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b>Apportion … … 3283 3182 3284 3183 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3285 auto;text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3184 auto;text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3286 3185 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span 3287 3186 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b>Density … … 3289 3188 3290 3189 <p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto; 3291 text-indent:-.25in;mso-list:l2 level2 lfo 6;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3190 text-indent:-.25in;mso-list:l2 level2 lfo5;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3292 3191 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span 3293 3192 style='font:7.0pt "Times New Roman"'> 3294 </span></span></span><![endif]><b>ISODISTORT mode values</b> - </p> 3295 3296 <h5 style='margin-left:.5in'>What can I do with the plot?</span></h5> 3297 3298 <p style='margin-left:1.0in'>A 3299 plot will be displayed only if the Draw Options or Draw Atoms tabs are visited 3300 before use of the Atoms tab. In that case the crystal structure is shown. Use 3301 of the mouse buttons changes the view of the structure and can be used to 3302 select atoms.<o:p></o:p></p> 3303 3304 <DL style='margin-left:1.25in'> 3305 <DT><b>Left drag</b>: 3306 <DD>Holding down left button rotates axes around screen x & y 3307 <DT><b>Right drag</b>: 3308 <DD>Holding down right button 3309 translates the fractional coordinates assigned to the viewpoint (which is kept 3310 at the center of the plot). The structure will appear to translate. The 3311 viewpoint can also be entered directly in the Draw Options. 3312 <DT><b>Middle drag</b>: 3313 <DD>Holding down center button rotates axes around screen z (direction perpendicular to screen). 3314 <DT><b>Mouse Wheel</b>: 3315 <DD>Rotating the scroll wheel changes “camera distance” (zoom 3316 in/out) 3317 <DT><b>Shift+Left Click</b>: 3318 <DD>Holding down the shift key 3319 while clicking on an atom with the left mouse button causes that atom to be 3320 selected (Shift + a Right click does the same). Any previously selected atoms 3321 will be reset. If two atoms are overlapped in the current view, then the 3193 </span></span></span><![endif]><b>ISODISTORT mode values</b> – there must be 3194 available the ISODISTORT mode displacement constraints available. This will 3195 compute the mode displacements for the current atom positions and display them 3196 in a popup window.</p> 3197 3198 <h5 style='margin-left:.5in'>What can I do with the drawing?</h5> 3199 3200 <p style='margin-left:1.0in'>A drawing of the crystal structure will be 3201 displayed only if the Draw Options or Draw Atoms tabs are visited first. When back 3202 at the Atoms tab, the following are applicable and use of the mouse buttons 3203 changes the view of the structure and can be used to select atoms.</p> 3204 3205 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3206 "Times New Roman"'>Left drag</span></b><span style='mso-fareast-font-family: 3207 "Times New Roman"'>: <o:p></o:p></span></p> 3208 3209 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3210 "Times New Roman"'>Holding down left button rotates axes around screen x & 3211 y <o:p></o:p></span></p> 3212 3213 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3214 "Times New Roman"'>Right drag</span></b><span style='mso-fareast-font-family: 3215 "Times New Roman"'>: <o:p></o:p></span></p> 3216 3217 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3218 "Times New Roman"'>Holding down right button translates the fractional coordinates 3219 assigned to the viewpoint (which is kept at the center of the drawing). The 3220 structure will appear to translate. The viewpoint can also be entered directly 3221 in the Draw Options. <o:p></o:p></span></p> 3222 3223 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3224 "Times New Roman"'>Middle drag</span></b><span style='mso-fareast-font-family: 3225 "Times New Roman"'>: <o:p></o:p></span></p> 3226 3227 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3228 "Times New Roman"'>Holding down center button rotates axes around screen z (direction 3229 perpendicular to screen). <o:p></o:p></span></p> 3230 3231 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3232 "Times New Roman"'>Mouse Wheel</span></b><span style='mso-fareast-font-family: 3233 "Times New Roman"'>: <o:p></o:p></span></p> 3234 3235 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3236 "Times New Roman"'>Rotating the scroll wheel changes “camera distance” (zoom 3237 in/out) <o:p></o:p></span></p> 3238 3239 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3240 "Times New Roman"'>Shift+Left Click</span></b><span style='mso-fareast-font-family: 3241 "Times New Roman"'>: <o:p></o:p></span></p> 3242 3243 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3244 "Times New Roman"'>Holding down the shift key while clicking on an atom with 3245 the left mouse button causes that atom to be selected (Shift + a Right click 3246 does the same). Any previously selected atoms will be reset. If two atoms are 3247 overlapped in the current view, then the top-most atom will usually be 3248 selected. Only atoms in the asymmetric unit can be selected from the plot in 3249 this way. <o:p></o:p></span></p> 3250 3251 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3252 "Times New Roman"'>Shift+Right click</span></b><span style='mso-fareast-font-family: 3253 "Times New Roman"'>: <o:p></o:p></span></p> 3254 3255 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3256 "Times New Roman"'>Holding down the shift key while clicking on an atom with 3257 the right mouse button causes the atom to be selected if previously unselected 3258 and unselected if previously selected. Any previously selected atoms will be 3259 continue to be selected so shift-right click can be used to add atoms to the 3260 selection list. If two atoms are overlapped in the current view, then the 3322 3261 top-most atom will usually be selected. Only atoms in the asymmetric unit can 3323 be selected from the plot in this way. 3324 <DT><b>Shift+Right click</b>: 3325 <DD>Holding down the shift key 3326 while clicking on an atom with the right mouse button causes the atom to be 3327 selected if previously unselected and unselected if previously selected. Any 3328 previously selected atoms will be continue to be 3329 selected so shift-right click can be used to add atoms to the selection list. 3330 If two atoms are overlapped in the current view, then the top-most atom will 3331 usually be selected. Only atoms in the asymmetric unit can be selected from the 3332 plot in this way. 3333 (On a Mac, <span class=SpellE>control+mouse</span> click is an 3334 alternate way to do this.) 3335 <DT><B>Key n</b>: 3336 <DD>Pressing the "n" key selects the next atom in the displayed atom list. 3337 <DT><B>Key p</b>: 3338 <DD>Pressing the "p" key selects the previous atom in the displayed atom list. 3339 <DT><B>Key c</b>: 3340 <DD>Pressing the "c" key sets the plot viewpoint at unit cell 3341 center. Also resets n/p selection item to the 1<sup>st</sup> 3342 atom. 3343 </DL> 3344 3345 <h4 style='margin-left:.25in'><a name="Phase-Draw_Options"> 3346 <u>Draw Options</u></a></h4> 3262 be selected from the plot in this way. (On a Mac, control+mouse click is an 3263 alternate way to do this.) <o:p></o:p></span></p> 3264 3265 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3266 "Times New Roman"'>Key n</span></b><span style='mso-fareast-font-family:"Times New Roman"'>: 3267 <o:p></o:p></span></p> 3268 3269 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3270 "Times New Roman"'>Pressing the "n" key selects the next atom in the 3271 displayed atom list. <o:p></o:p></span></p> 3272 3273 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3274 "Times New Roman"'>Key p</span></b><span style='mso-fareast-font-family:"Times New Roman"'>: 3275 <o:p></o:p></span></p> 3276 3277 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3278 "Times New Roman"'>Pressing the "p" key selects the previous atom in 3279 the displayed atom list. <o:p></o:p></span></p> 3280 3281 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3282 "Times New Roman"'>Key c</span></b><span style='mso-fareast-font-family:"Times New Roman"'>: 3283 <o:p></o:p></span></p> 3284 3285 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3286 "Times New Roman"'>Pressing the "c" key sets the plot viewpoint at 3287 unit cell center. Also resets n/p selection item to the 1<sup>st</sup> atom.<o:p></o:p></span></p> 3288 3289 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3290 "Times New Roman"'>Key s:<o:p></o:p></span></b></p> 3291 3292 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3293 "Times New Roman"'>Pressing the “s” key brings up a (large) selection of color 3294 schemes for the slice contours. Default – “Paired” (Green – positive, red – 3295 negative & yellow – zero).<o:p></o:p></span></p> 3296 3297 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3298 "Times New Roman"'>Key k:<o:p></o:p></span></b></p> 3299 3300 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3301 "Times New Roman"'>Pressing the “k” key cycles through the possible slice 3302 contouring options (none, lines, colors, lines+colors)<o:p></o:p></span></p> 3303 3304 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3305 "Times New Roman"'>Key +:<o:p></o:p></span></b></p> 3306 3307 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3308 "Times New Roman"'>Pressing the “+” (or “=”) key steps the viewpoint in 3309 positive drawing z-direction (away from viewer). If structure is incommensurate, 3310 “+” steps the structure and map through the 4<sup>th</sup> dimension (+tau).<o:p></o:p></span></p> 3311 3312 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3313 "Times New Roman"'>Key -:<o:p></o:p></span></b></p> 3314 3315 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3316 "Times New Roman"'>Pressing the “-“ key steps the viewpoint in negative drawing 3317 z-direction (toward from viewer). If structure is incommensurate, “-” steps the 3318 structure and map through the 4<sup>th</sup> dimension (-tau).<o:p></o:p></span></p> 3319 3320 <h4 style='margin-left:.25in'><a name="Phase-Draw_Options"><u>Draw Options</u></a></h4> 3321 3347 3322 <h5 style='margin-left:.5in'>What can I do here?</h5> 3348 3323 3349 <p class=MsoNormal style='margin-left:.75in'>The 3350 Draw Options window provides access to a number of items that control how the 3351 structure is displayed. </p> 3352 3353 <h5 style='margin-left:.5in'>What is plotted here?</h5> 3354 3355 <p style='margin-left:.75in'>A 3356 plot that shows the atoms of the crystal structure is generated. The 3357 way that the structure is displayed is determined according to the 3358 controls in this page as well as the options on the <a 3359 href="#Phase-Draw_Atoms">Draw Atoms</a> page.</p> 3360 3361 <h5 style='margin-left:.5in'>What can I do with the plot?</span></h5> 3362 3363 <p style='margin-left:.75in'>Use 3364 of the mouse buttons when viewing a crystal structure changes the view of the 3365 structure:<o:p></o:p></p> 3366 3367 <DL style='margin-left:1.25in'> 3368 <DT><b>Left drag</b>: 3369 <DD>Holding down left button rotates axes around screen x & y 3370 3371 <DT><b>Right drag</b>: 3372 <DD>Holding down right button 3373 translates the fractional coordinates assigned to the viewpoint (which is kept 3374 at the center of the plot). The structure will appear to translate. The 3375 viewpoint can also be entered directly in the Draw Options. 3376 3377 <DT><b>Middle drag</b>: 3378 <DD>Holding down center button rotates axes around screen z (direction perpendicular to screen). 3379 <DT><b>Mouse Wheel</b>: 3380 <DD>Rotating the scroll wheel changes “camera distance” (zoom 3381 in/out) 3382 </DL> 3383 3384 <h4 style='margin-left:.25in'> 3385 <a name="Phase-Draw_Atoms"></a><a name="_Draw_Atoms"></a> 3386 <u>Draw Atoms</u></h4> 3324 <p class=MsoNormal style='margin-left:.75in'>The Draw Options window provides 3325 access to a number of items that control how the structure is displayed. If a 3326 map is available (Fourier of charge flipping), one can display a 10<span 3327 style='font-family:"Calibri",sans-serif'>Å</span>x10<span style='font-family: 3328 "Calibri",sans-serif'>Å</span> contoured slice centered at the viewpoint. 3329 Contouring done as lines, colors or lines & colors combined. 3-D contouring 3330 is also available as green (red for negative density) map grid points. One can 3331 also draw individual or stack of hkl planes across unit cell.</p> 3332 3333 <h5 style='margin-left:.5in'>What is drawn here?</h5> 3334 3335 <p style='margin-left:.75in'>A drawing that shows the atoms of the crystal 3336 structure is generated. The way that the structure is displayed is determined 3337 according to the controls in this page as well as the options on the <a 3338 href="#Phase-Draw_Atoms">Draw Atoms</a> page.</p> 3339 3340 <h5 style='margin-left:.5in'>What can I do with the drawing?</h5> 3341 3342 <p style='margin-left:.75in'>Use of the mouse buttons and key presses when 3343 viewing a crystal structure changes the view of the structure; see Atoms or 3344 Draw Atoms for details</p> 3345 3346 <h4 style='margin-left:.25in'><a name="Phase-Draw_Atoms"></a><a 3347 name="_Draw_Atoms"></a><u>Draw Atoms</u></h4> 3387 3348 3388 3349 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>This 3389 3350 gives a list of the atoms and bonds that are to be rendered as lines, van der 3390 Waals radii balls, sticks, balls & sticks, ellipsoids & sticks or <span 3391 class=SpellE>polyhedra</span>. There are two menus for this tab; Edit allows 3392 modification of the list of atoms to be rendered and Compute gives some options 3393 for geometric characterization of selected atoms.</p> 3351 Waals radii balls, sticks, balls & sticks, ellipsoids & sticks or 3352 polyhedra. There are four menus for this tab; Edit allows modification of the 3353 list of atoms to be rendered, Compute gives some options for geometric 3354 characterization of selected atoms, Restraints allows definition of 4 different 3355 types of restraints on the structure and Rigid body allows selection of atoms 3356 that form a previously defined rigid body.</p> 3394 3357 3395 3358 <h5 style='margin-left:.5in'>What can I do here?</h5> 3396 3359 3397 3360 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto; 3398 text-indent:-.25in;mso-list:l5 level1 lfo 10;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3361 text-indent:-.25in;mso-list:l5 level1 lfo7;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3399 3362 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 3400 3363 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3409 3372 3410 3373 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3411 auto;text-indent:-.25in;mso-list:l5 level1 lfo 10;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3374 auto;text-indent:-.25in;mso-list:l5 level1 lfo7;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3412 3375 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 3413 3376 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3414 style='mso-bidi-font-weight:normal'>Atom Selection from plot</b>: select an3415 atom by a left click of the mouse while holding down the Shift key and pointed 3416 atthe center of the displayed atom, it will turn green if successful and the3377 style='mso-bidi-font-weight:normal'>Atom Selection from drawing</b>: select an 3378 atom by a left click of the mouse while holding down the Shift key and pointed at 3379 the center of the displayed atom, it will turn green if successful and the 3417 3380 corresponding entry in the table will be highlighted (in grey); any previous 3418 selections will be cleared. To add <span class=GramE>to .your</span> selection3419 use the right mouse button (Shift down); if a previously selection is 3420 reselected it is removed from the selection list. <b style='mso-bidi-font-weight: 3421 normal'>NB</b>: beware of atoms that are hiding behind the one you are trying 3422 to <span class=GramE>select,</span> they may be selected inadvertently. You can 3423 rotate the structure anytime during theselection process.</p>3381 selections will be cleared. To add to your selection, use the right mouse 3382 button (Shift down); if a previously selection is reselected it is removed from 3383 the selection list. <b style='mso-bidi-font-weight:normal'>NB</b>: beware of 3384 atoms that are hiding behind the one you are trying to select they may be 3385 selected inadvertently. You can rotate the structure anytime during the 3386 selection process.</p> 3424 3387 3425 3388 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3426 auto;text-indent:-.25in;mso-list:l5 level1 lfo 10;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3389 auto;text-indent:-.25in;mso-list:l5 level1 lfo7;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3427 3390 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 3428 3391 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3429 style='mso-bidi-font-weight:normal'>Double left <span class=GramE>click</span> 3430 a Name, Type and <span class=SpellE>Sym</span> Op column heading</b>: a dialog 3431 box is shown that allows you to select all atoms with that characteristic. For 3432 example, selecting the Type column will show all the atom types; your choice 3433 will then cause all those atoms to be selected.</p> 3392 style='mso-bidi-font-weight:normal'>Double left click a Name, Type and Sym Op 3393 column heading</b>: a dialog box is shown that allows you to select all atoms 3394 with that characteristic. For example, selecting the Type column will show all 3395 the atom types; your choice will then cause all those atoms to be selected.</p> 3434 3396 3435 3397 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3436 auto;text-indent:-.25in;mso-list:l5 level1 lfo 10;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3398 auto;text-indent:-.25in;mso-list:l5 level1 lfo7;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3437 3399 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 3438 3400 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3439 style='mso-bidi-font-weight:normal'>Double left <span class=GramE>click</span> 3440 a Style, Label or Color column</b>: a dialog box is shown that allows you to 3441 select a rendering option for all the atoms. For Color a color choice dialog is 3442 displayed that covers the entire color spectrum. Choose a color by any of the 3443 means available, press the “Add to Custom Colors”, select that color in the 3444 Custom colors display and then press OK. <b style='mso-bidi-font-weight:normal'>NB</b>: 3445 selecting Color will make all atoms have the same color and for Style “blank” 3446 means the atoms aren’t rendered and thus the plot will not show any atoms or 3447 bonds!</p> 3401 style='mso-bidi-font-weight:normal'>Double left click a Style, Label or Color 3402 column</b>: a dialog box is shown that allows you to select a rendering option 3403 for all the atoms. For Color a color choice dialog is displayed that covers the 3404 entire color spectrum. Choose a color by any of the means available, press the 3405 “Add to Custom Colors”, select that color in the Custom colors display and then 3406 press OK. <b style='mso-bidi-font-weight:normal'>NB</b>: selecting Color will 3407 make all atoms have the same color and for Style “blank” means the atoms aren’t 3408 rendered and thus the drawing will not show any atoms or bonds!</p> 3448 3409 3449 3410 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3450 auto;text-indent:-.25in;mso-list:l5 level1 lfo 10;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3411 auto;text-indent:-.25in;mso-list:l5 level1 lfo7;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3451 3412 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span 3452 3413 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu … … 3454 3415 operations that can be performed on your selected atoms. You must select one or 3455 3416 more atoms before using any of the menu items. Most of these items can also be 3456 accessed by selecting one or more atoms and <span class=GramE>right-clicking</span> 3457 the mouse.</p> 3458 3459 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3460 auto;text-indent:-.25in;mso-list:l8 level1 lfo12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3417 accessed by selecting one or more atoms and right-clicking the mouse.</p> 3418 3419 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3420 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3461 3421 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 3462 3422 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3465 3425 3466 3426 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3467 auto;text-indent:-.25in;mso-list:l8 level1 lfo 12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3427 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3468 3428 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 3469 3429 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3470 style='mso-bidi-font-weight:normal'>Atom label</b> – select the item to be shown3471 as a label for each atom in selection. The choices <span class=GramE>are:</span> 3472 none, type, name or number.</p>3473 3474 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3475 auto;text-indent:-.25in;mso-list:l8 level1 lfo 12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3430 style='mso-bidi-font-weight:normal'>Atom label</b> – select the item to be 3431 shown as a label for each atom in selection. The choices are: none, type, name 3432 or number. (NB: atom labelling slows drawing response time).</p> 3433 3434 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3435 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3476 3436 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 3477 3437 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3482 3442 3483 3443 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3484 auto;text-indent:-.25in;mso-list:l8 level1 lfo 12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3444 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3485 3445 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span 3486 3446 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3489 3449 3490 3450 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3491 auto;text-indent:-.25in;mso-list:l8 level1 lfo 12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3451 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3492 3452 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span 3493 3453 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3494 style='mso-bidi-font-weight:normal'>Edit atom radii </b>- </p> 3495 3496 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3497 auto;text-indent:-.25in;mso-list:l8 level1 lfo12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3454 style='mso-bidi-font-weight:normal'>Edit atom radii </b>– modify atom radii 3455 used in the bond assignment algorithm.</p> 3456 3457 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3458 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3498 3459 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span 3499 3460 style='font:7.0pt "Times New Roman"'> 3500 </span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight: 3501 normal'>View point</b></span> – position the plot view point to the first atom 3502 in the selection.</p> 3503 3504 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3505 auto;text-indent:-.25in;mso-list:l8 level1 lfo12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3461 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>View 3462 point</b> – position the plot view point to the first atom in the selection.</p> 3463 3464 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3465 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3506 3466 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span 3507 3467 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3508 style='mso-bidi-font-weight:normal'>Select from list </b>- </p> 3509 3510 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3511 auto;text-indent:-.25in;mso-list:l8 level1 lfo12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3468 style='mso-bidi-font-weight:normal'>Select from list </b>– select atoms from a 3469 popup list of names.</p> 3470 3471 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3472 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3512 3473 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span 3513 3474 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3516 3477 symmetry operator and unit cell translation selected via a dialog display. 3517 3478 Duplicate atom positions are not retained. Any anisotropic thermal displacement 3518 parameters ( <span class=SpellE>Uij</span>) will be transformed as appropriate.</p>3519 3520 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3521 auto;text-indent:-.25in;mso-list:l8 level1 lfo 12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3479 parameters (Uij) will be transformed as appropriate.</p> 3480 3481 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3482 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3522 3483 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span 3523 3484 style='font:7.0pt "Times New Roman"'> 3524 3485 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Add 3525 sphere of atoms </b>- </p> 3526 3527 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3528 auto;text-indent:-.25in;mso-list:l8 level1 lfo12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3486 sphere of atoms </b>– fill in all equivalent atoms that fall within a sphere of 3487 selected radius about selected atoms.</p> 3488 3489 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3490 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3529 3491 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span 3530 3492 style='font:7.0pt "Times New Roman"'> … … 3532 3494 draw atoms</b> – apply a symmetry operator and unit cell translation to the set 3533 3495 of selected atoms; they will be changed in place. Any anisotropic thermal 3534 displacement parameters (<span class=SpellE>Uij</span>) will be transformed as 3535 appropriate.</p> 3536 3537 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3538 auto;text-indent:-.25in;mso-list:l8 level1 lfo12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3496 displacement parameters (Uij) will be transformed as appropriate.</p> 3497 3498 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3499 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3539 3500 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>k.<span 3540 3501 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3542 3503 currently in the draw atom table, find all atoms that belong in the 3543 3504 coordination sphere around the selected atoms via unit cell translations. NB: 3544 symmetry operations are not used in this search .</p>3545 3546 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3547 auto;text-indent:-.25in;mso-list:l8 level1 lfo 12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3505 symmetry operations are not used in this search; do Fill unit cell first.</p> 3506 3507 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3508 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3548 3509 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>l.<span 3549 3510 style='font:7.0pt "Times New Roman"'> … … 3554 3515 3555 3516 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3556 auto;text-indent:-.25in;mso-list:l8 level1 lfo 12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3517 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3557 3518 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>m.<span 3558 3519 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3559 style='mso-bidi-font-weight:normal'>Complete molecule </b>– </p> 3560 3561 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3562 auto;text-indent:-.25in;mso-list:l8 level1 lfo12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3520 style='mso-bidi-font-weight:normal'>Complete molecule </b>– beginning with a 3521 selected atom, transform other atoms to equivalent positions that form a 3522 contiguous molecule. Not appropriate for continuous structures (a warning will 3523 appear)</p> 3524 3525 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3526 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3563 3527 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>n.<span 3564 3528 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3565 style='mso-bidi-font-weight:normal'>Create void map </b>- </p> 3566 3567 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3568 auto;text-indent:-.25in;mso-list:l8 level1 lfo12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3529 style='mso-bidi-font-weight:normal'>Create void map </b>– by using a grid of 3530 probe positions, locate points outside of normal contact distances within a 3531 structure. Result is a mesh of small blue points in structural voids (e.g. possible 3532 locations of missing water molecules).</p> 3533 3534 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3535 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3569 3536 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>o.<span 3570 3537 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3574 3541 3575 3542 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3576 auto;text-indent:-.25in;mso-list:l8 level1 lfo 12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span3543 auto;text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3577 3544 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>p.<span 3578 3545 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3579 style='mso-bidi-font-weight:normal'>Update draw atoms </b>– </p> 3580 3581 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3582 auto;text-indent:-.25in;mso-list:l8 level1 lfo12;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3546 style='mso-bidi-font-weight:normal'>Update draw atoms </b>– refresh the drawn 3547 atom positions from the Atoms list.</p> 3548 3549 <p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto; 3550 text-indent:-.25in;mso-list:l8 level1 lfo9;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3583 3551 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>q.<span 3584 3552 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3585 style='mso-bidi-font-weight:normal'>Load selected atoms </b>- </p> 3586 3587 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 3588 auto;text-indent:-.25in;mso-list:l5 level1 lfo10;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3553 style='mso-bidi-font-weight:normal'>Load selected atoms </b>- refresh the selected 3554 drawn atom positions from the Atoms list.<o:p></o:p></p> 3555 3556 <p class=MsoNormal style='margin-left:1.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><o:p> </o:p></p> 3557 3558 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto; 3559 text-indent:-.25in;mso-list:l5 level1 lfo7;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 3589 3560 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span 3590 3561 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu 3591 3562 ‘<b style='mso-bidi-font-weight:normal'>Compute’</b> - The compute menu gives a 3592 choice of geometric calculations to be performed with the selected atoms. You must3593 select the appropriate number of atoms for these to work and the computation is 3594 done for the atoms in selection order.</p>3595 3596 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3597 auto;text-indent:-.25in;mso-list:l5 level2 lfo 10;tab-stops:list 1.0in'><![if !supportLists]><span3563 choice of geometric calculations to be performed with the selected atoms. You 3564 must select the appropriate number of atoms for these to work and the 3565 computation is done for the atoms in selection order.</p> 3566 3567 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3568 auto;text-indent:-.25in;mso-list:l5 level2 lfo7;tab-stops:list 1.0in'><![if !supportLists]><span 3598 3569 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 3599 3570 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 3600 3571 style='mso-bidi-font-weight:normal'>View pt. dist.</b> - this calculates 3601 distance from <span class=GramE>view point</span> to all selected draw atoms;3602 result is given on theconsole window.</p>3603 3604 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3605 auto;text-indent:-.25in;mso-list:l5 level2 lfo 10;tab-stops:list 1.0in'><![if !supportLists]><span3572 distance from view-point to all selected draw atoms; result is given on the 3573 console window.</p> 3574 3575 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 3576 auto;text-indent:-.25in;mso-list:l5 level2 lfo7;tab-stops:list 1.0in'><![if !supportLists]><span 3606 3577 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 3607 3578 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3609 3580 normal'>Tors. </b>– when 2-4 atoms are selected, a distance, angle or torsion 3610 3581 angle will be found for them. The angles are computed for the atoms in their 3611 selection order. The torsion angle is a <span class=GramE>right hand</span> 3612 angle about the A2-A3 vector for the sequence of atoms A1-A2-A3-A4. An 3613 estimated standard deviation is given for the calculated value if a current 3614 variance-covariance matrix is available. The result is shown on the console 3615 window; it may be cut & pasted to another application (e.g. Microsoft 3616 Word).</p> 3582 selection order. The torsion angle is a right-hand angle about the A2-A3 vector 3583 for the sequence of atoms A1-A2-A3-A4. An estimated standard deviation is given 3584 for the calculated value if a current variance-covariance matrix is available. 3585 The result is shown on the console window; it may be cut & pasted to 3586 another application (e.g. Microsoft Word).</p> 3617 3587 3618 3588 <p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto; 3619 text-indent:-.25in;mso-list:l5 level2 lfo 10;tab-stops:list 1.0in'><![if !supportLists]><span3589 text-indent:-.25in;mso-list:l5 level2 lfo7;tab-stops:list 1.0in'><![if !supportLists]><span 3620 3590 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span 3621 3591 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 3634 3604 unweighted center of the selected atoms.</p> 3635 3605 3636 <h5 style='margin-left:.5in'>What is plotted here?</h5> 3606 <p class=MsoNormal style='margin-left:58.5pt'>7. Menu ‘<b>Restraints’</b> – Individual 3607 restraints may be generated by selecting atoms and the corresponding restraint 3608 type from the menu</p> 3609 3610 <p class=MsoNormal style='margin-left:1.5in;text-indent:-.25in'>a. <b>Add bond 3611 restraint</b> – for selected atom pair (A-B).</p> 3612 3613 <p class=MsoNormal style='margin-left:1.5in;text-indent:-.25in'>b. <b>Add angle 3614 restraint</b> – for selected atom triple (A-B-C)</p> 3615 3616 <p class=MsoNormal style='margin-left:1.5in;text-indent:-.25in'>c. <b>Add plane 3617 restraint</b> – for selected 4 or more atoms</p> 3618 3619 <p class=MsoNormal style='margin-left:1.5in;text-indent:-.25in'>d. <b>Add 3620 chiral restrain</b>t – for selected 4 atoms; chiral atom first followed by 3 3621 other atoms; if selected in righthand sequence, chiral volume will be > 0.</p> 3622 3623 <p class=MsoNormal><span style='mso-tab-count:1'> </span>8. Menu ‘<b>Rigid 3624 body</b>’/’<b>Define rigid body</b>’ – assign a previously defined rigid body 3625 to selected atoms.</p> 3626 3627 <h5 style='margin-left:.5in'>What is drawn here?</h5> 3637 3628 3638 3629 <p style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>A 3639 plot that shows the atoms of the crystal structure is generated. The atoms are 3640 displayed according to the controls in the in this page as well as options on 3641 the <a href="#Phase-Draw_Options">Draw Options</a> page. </p> 3642 3643 <h5 style='margin-left:.5in'>What can I do with the plot?</h5> 3644 3645 <p style='margin-left:1.0in'> 3646 Use of the mouse buttons when viewing a crystal structure changes the 3647 view of the structure:<o:p></o:p></p> 3648 3649 <DL style='margin-left:1.25in'> 3650 <DT><b>Left drag</b>: 3651 <DD>Holding down left button rotates axes around screen x & y 3652 <DT><b>Right drag</b>: 3653 <DD>Holding down right button 3630 drawing that shows the atoms of the crystal structure is generated. The atoms 3631 are displayed according to the controls in the in this page as well as options 3632 on the <a href="#Phase-Draw_Options">Draw Options</a> page. </p> 3633 3634 <h5 style='margin-left:.5in'>What can I do with the drawing?</h5> 3635 3636 <p style='margin-left:1.0in'>Use of the mouse buttons and key presses when 3637 viewing a crystal structure changes the view of the structure:</p> 3638 3639 <p class=MsoNormal style='margin-left:1.25in'><a name="Phase-RB_Models"><b><span 3640 style='mso-fareast-font-family:"Times New Roman"'>Left drag</span></b></a><span 3641 style='mso-bookmark:Phase-RB_Models'><span style='mso-fareast-font-family:"Times New Roman"'>: 3642 <o:p></o:p></span></span></p> 3643 3644 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3645 style='mso-fareast-font-family:"Times New Roman"'>Holding down left button 3646 rotates axes around screen x & y <o:p></o:p></span></span></p> 3647 3648 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3649 style='mso-fareast-font-family:"Times New Roman"'>Right drag</span></b></span><span 3650 style='mso-bookmark:Phase-RB_Models'><span style='mso-fareast-font-family:"Times New Roman"'>: 3651 <o:p></o:p></span></span></p> 3652 3653 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3654 style='mso-fareast-font-family:"Times New Roman"'>Holding down right button 3654 3655 translates the fractional coordinates assigned to the viewpoint (which is kept 3655 at the center of the plot). The structure will appear to translate. The 3656 viewpoint can also be entered directly in the Draw Options. 3657 <DT><b>Middle drag</b>: 3658 <DD>Holding down center button rotates axes around screen z (direction perpendicular to screen). 3659 <DT><b>Mouse Wheel</b>: 3660 <DD>Rotating the scroll wheel changes “camera distance” (zoom 3661 in/out) 3662 <DT><b>Shift+Left Click</b>: 3663 <DD>Holding down the shift key 3656 at the center of the drawing). The structure will appear to translate. The 3657 viewpoint can also be entered directly in the Draw Options. <o:p></o:p></span></span></p> 3658 3659 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3660 style='mso-fareast-font-family:"Times New Roman"'>Middle drag</span></b></span><span 3661 style='mso-bookmark:Phase-RB_Models'><span style='mso-fareast-font-family:"Times New Roman"'>: 3662 <o:p></o:p></span></span></p> 3663 3664 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3665 style='mso-fareast-font-family:"Times New Roman"'>Holding down center button 3666 rotates axes around screen z (direction perpendicular to screen). <o:p></o:p></span></span></p> 3667 3668 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3669 style='mso-fareast-font-family:"Times New Roman"'>Mouse Wheel</span></b></span><span 3670 style='mso-bookmark:Phase-RB_Models'><span style='mso-fareast-font-family:"Times New Roman"'>: 3671 <o:p></o:p></span></span></p> 3672 3673 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3674 style='mso-fareast-font-family:"Times New Roman"'>Rotating the scroll wheel 3675 changes “camera distance” (zoom in/out) <o:p></o:p></span></span></p> 3676 3677 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3678 style='mso-fareast-font-family:"Times New Roman"'>Shift+Left Click</span></b></span><span 3679 style='mso-bookmark:Phase-RB_Models'><span style='mso-fareast-font-family:"Times New Roman"'>: 3680 <o:p></o:p></span></span></p> 3681 3682 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3683 style='mso-fareast-font-family:"Times New Roman"'>Holding down the shift key 3664 3684 while clicking on an atom with the left mouse button causes that atom to be 3665 3685 selected (Shift + a Right click does the same). Any previously selected atoms 3666 3686 will be reset. If two atoms are overlapped in the current view, then the 3667 top-most atom will usually be selected. Atom selection requires that 3668 either the "Atoms" or "Draw Atoms" phase be displayed. 3669 <DT><b>Shift+Right click</b>: 3670 <DD>Holding down the shift key 3687 top-most atom will usually be selected. Only atoms in the asymmetric unit can 3688 be selected from the plot in this way. <o:p></o:p></span></span></p> 3689 3690 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3691 style='mso-fareast-font-family:"Times New Roman"'>Shift+Right click</span></b></span><span 3692 style='mso-bookmark:Phase-RB_Models'><span style='mso-fareast-font-family:"Times New Roman"'>: 3693 <o:p></o:p></span></span></p> 3694 3695 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3696 style='mso-fareast-font-family:"Times New Roman"'>Holding down the shift key 3671 3697 while clicking on an atom with the right mouse button causes the atom to be 3672 selected, if previously unselected, or unselected, if previously selected. Any 3673 previously selected atoms will be continue to be 3674 selected so shift-right click can be used to add atoms to the selection list. 3675 If two atoms are overlapped in the current view, then the top-most atom will 3676 usually be selected. 3677 Atom selection requires that either the "Atoms" 3678 or "Draw Atoms" phase be displayed. 3679 (On a Mac, <span class=SpellE>control+mouse</span> click is an 3680 alternate way to do this.) 3681 </DL> 3682 3683 <h4 style='margin-left:.25in'> 3684 <a name="Phase-RB_Models">RB Models</a></h4> 3698 selected if previously unselected and unselected if previously selected. Any 3699 previously selected atoms will be continue to be selected so shift-right click 3700 can be used to add atoms to the selection list. If two atoms are overlapped in 3701 the current view, then the top-most atom will usually be selected. Only atoms 3702 in the asymmetric unit can be selected from the plot in this way. (On a Mac, control+mouse 3703 click is an alternate way to do this.) <o:p></o:p></span></span></p> 3704 3705 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3706 style='mso-fareast-font-family:"Times New Roman"'>Key n</span></b></span><span 3707 style='mso-bookmark:Phase-RB_Models'><span style='mso-fareast-font-family:"Times New Roman"'>: 3708 <o:p></o:p></span></span></p> 3709 3710 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3711 style='mso-fareast-font-family:"Times New Roman"'>Pressing the "n" 3712 key selects the next atom in the displayed atom list. <o:p></o:p></span></span></p> 3713 3714 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3715 style='mso-fareast-font-family:"Times New Roman"'>Key p</span></b></span><span 3716 style='mso-bookmark:Phase-RB_Models'><span style='mso-fareast-font-family:"Times New Roman"'>: 3717 <o:p></o:p></span></span></p> 3718 3719 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3720 style='mso-fareast-font-family:"Times New Roman"'>Pressing the "p" 3721 key selects the previous atom in the displayed atom list. <o:p></o:p></span></span></p> 3722 3723 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3724 style='mso-fareast-font-family:"Times New Roman"'>Key c</span></b></span><span 3725 style='mso-bookmark:Phase-RB_Models'><span style='mso-fareast-font-family:"Times New Roman"'>: 3726 <o:p></o:p></span></span></p> 3727 3728 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3729 style='mso-fareast-font-family:"Times New Roman"'>Pressing the "c" 3730 key sets the plot viewpoint at unit cell center. Also resets n/p selection item 3731 to the 1<sup>st</sup> atom.<o:p></o:p></span></span></p> 3732 3733 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3734 style='mso-fareast-font-family:"Times New Roman"'>Key s:<o:p></o:p></span></b></span></p> 3735 3736 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3737 style='mso-fareast-font-family:"Times New Roman"'>Pressing the “s” key brings 3738 up a (large) selection of color schemes for the slice contours. Default – “Paired” 3739 (Green – positive, red – negative & yellow – zero).<o:p></o:p></span></span></p> 3740 3741 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3742 style='mso-fareast-font-family:"Times New Roman"'>Key k:<o:p></o:p></span></b></span></p> 3743 3744 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3745 style='mso-fareast-font-family:"Times New Roman"'>Pressing the “k” key cycles 3746 through the possible slice contouring options (none, lines, colors, 3747 lines+colors)<o:p></o:p></span></span></p> 3748 3749 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3750 style='mso-fareast-font-family:"Times New Roman"'>Key +:<o:p></o:p></span></b></span></p> 3751 3752 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3753 style='mso-fareast-font-family:"Times New Roman"'>Pressing the “+” (or “=”) key 3754 steps the viewpoint in positive drawing z-direction (away from viewer). If 3755 structure is incommensurate, “+” steps the structure and map through the 4<sup>th</sup> 3756 dimension (+tau).<o:p></o:p></span></span></p> 3757 3758 <p class=MsoNormal style='margin-left:1.25in'><span style='mso-bookmark:Phase-RB_Models'><b><span 3759 style='mso-fareast-font-family:"Times New Roman"'>Key -:<o:p></o:p></span></b></span></p> 3760 3761 <p class=MsoNormal style='margin-left:.5in'><span style='mso-bookmark:Phase-RB_Models'><span 3762 style='mso-fareast-font-family:"Times New Roman"'>Pressing the “-“ key steps 3763 the viewpoint in negative drawing z-direction (toward from viewer). If 3764 structure is incommensurate, “-” steps the structure and map through the 4<sup>th</sup> 3765 dimension (-tau).<o:p></o:p></span></span></p> 3766 3767 <h4 style='margin-left:.25in'><span style='mso-bookmark:Phase-RB_Models'>RB 3768 Models</span></h4> 3685 3769 3686 3770 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>This … … 3689 3773 It also allows control of the location of the rigid body and in this phase</p> 3690 3774 3691 <h5 style='margin-left:.5in'>What can I do with the plot?</span></h5>3775 <h5 style='margin-left:.5in'>What can I do with the drawing?</h5> 3692 3776 3693 3777 <p style='margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>Use 3694 3778 of the mouse buttons when viewing a crystal structure changes the view of the 3695 structure:<o:p></o:p></p> 3696 3697 <DL style='margin-left:1.25in'> 3698 <DT><b>Left drag</b>: 3699 <DD>Holding down left button rotates axes around screen x & y 3700 <DT><b>Right drag</b>: 3701 <DD>Holding down right button 3702 translates the fractional coordinates assigned to the viewpoint (which is kept 3703 at the center of the plot). The structure will appear to translate. The 3704 viewpoint can also be entered directly in the Draw Options. 3705 <DT><b>Middle drag</b>: 3706 <DD>Holding down center button rotates axes around screen z (direction perpendicular to screen). 3707 <DT><b>Mouse Wheel</b>: 3708 <DD>Rotating the scroll wheel changes “camera distance” (zoom 3709 in/out) 3710 </DL> 3711 3712 <p style='margin-left:1.0in'>When 3713 a rigid body is being inserted into a structure, both the rigid body and the 3714 crystal structure are displayed. It is useful to plan for this by preselecting 3715 the atoms in the Draw Atoms list and to have atoms displayed as 3716 "Sticks" or "Ball-and-Sticks." The rigid body will be 3717 displayed as "Ball-and-Sticks" but bonds will be in green. Use of the 3718 Alt key causes the above mouse movements to reposition the rigid body rather 3719 than change the view of the crystal structure:<o:p></o:p></p> 3720 3721 <DL style='margin-left:1.25in'> 3722 <DT><b>Alt+Left drag</b>: 3723 <DD>Holding Alt while dragging 3724 the mouse with the left button down rotates the rigid body around screen x 3725 & y axes 3726 3727 <DT><b>Alt+Middle drag</b>: 3728 <DD>Holding Alt while dragging 3729 the mouse with the middle button down rotates the rigid body around screen z 3730 axis (out of screen) 3731 3732 <DT><b>Alt+Right drag</b>: 3733 <DD>Holding Alt while dragging 3734 the mouse with the right button down translates the rigid body in the screen x 3735 & y directions (rotate the plot to see and move in the rigid body in the 3736 third direction.) Pressing the "Lock" checkbox next to the origin location 3737 prevents the origin from being changed in this way. 3738 </DL> 3739 3740 <h4 style='margin-left:.25in'><a 3741 name=Texture></a><a name="_Ref74983049"></a><a name=Phase-Texture></a> 3742 Texture</h4> 3779 structure:</p> 3780 3781 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3782 "Times New Roman"'>Left drag</span></b><span style='mso-fareast-font-family: 3783 "Times New Roman"'>: <o:p></o:p></span></p> 3784 3785 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3786 "Times New Roman"'>Holding down left button rotates axes around screen x & 3787 y <o:p></o:p></span></p> 3788 3789 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3790 "Times New Roman"'>Right drag</span></b><span style='mso-fareast-font-family: 3791 "Times New Roman"'>: <o:p></o:p></span></p> 3792 3793 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3794 "Times New Roman"'>Holding down right button translates the fractional 3795 coordinates assigned to the viewpoint (which is kept at the center of the 3796 plot). The structure will appear to translate. The viewpoint can also be 3797 entered directly in the Draw Options. <o:p></o:p></span></p> 3798 3799 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3800 "Times New Roman"'>Middle drag</span></b><span style='mso-fareast-font-family: 3801 "Times New Roman"'>: <o:p></o:p></span></p> 3802 3803 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3804 "Times New Roman"'>Holding down center button rotates axes around screen z 3805 (direction perpendicular to screen). <o:p></o:p></span></p> 3806 3807 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3808 "Times New Roman"'>Mouse Wheel</span></b><span style='mso-fareast-font-family: 3809 "Times New Roman"'>: <o:p></o:p></span></p> 3810 3811 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3812 "Times New Roman"'>Rotating the scroll wheel changes “camera distance” (zoom 3813 in/out) <o:p></o:p></span></p> 3814 3815 <p style='margin-left:1.0in'>When a rigid body is being inserted into a 3816 structure, both the rigid body and the crystal structure are displayed. It is 3817 useful to plan for this by preselecting the atoms in the Draw Atoms list and to 3818 have atoms displayed as "Sticks" or "Ball-and-Sticks." The 3819 rigid body will be displayed as "Ball-and-Sticks" but bonds will be 3820 in green. Use of the Alt key causes the above mouse movements to reposition the 3821 rigid body rather than change the view of the crystal structure:</p> 3822 3823 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3824 "Times New Roman"'>Alt+Left drag</span></b><span style='mso-fareast-font-family: 3825 "Times New Roman"'>: <o:p></o:p></span></p> 3826 3827 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3828 "Times New Roman"'>Holding Alt while dragging the mouse with the left button 3829 down rotates the rigid body around screen x & y axes <o:p></o:p></span></p> 3830 3831 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3832 "Times New Roman"'>Alt+Middle drag</span></b><span style='mso-fareast-font-family: 3833 "Times New Roman"'>: <o:p></o:p></span></p> 3834 3835 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3836 "Times New Roman"'>Holding Alt while dragging the mouse with the middle button 3837 down rotates the rigid body around screen z axis (out of screen) <o:p></o:p></span></p> 3838 3839 <p class=MsoNormal style='margin-left:1.25in'><b><span style='mso-fareast-font-family: 3840 "Times New Roman"'>Alt+Right drag</span></b><span style='mso-fareast-font-family: 3841 "Times New Roman"'>: <o:p></o:p></span></p> 3842 3843 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 3844 "Times New Roman"'>Holding Alt while dragging the mouse with the right button 3845 down translates the rigid body in the screen x & y directions (rotate the 3846 plot to see and move in the rigid body in the third direction.) Pressing the 3847 "Lock" checkbox next to the origin location prevents the origin from 3848 being changed in this way. <o:p></o:p></span></p> 3849 3850 <h4 style='margin-left:.25in'><a name=Texture></a><a name="_Ref74983049"></a><a 3851 name=Phase-Texture></a>Texture</h4> 3743 3852 3744 3853 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><o:p> </o:p></p> … … 3761 3870 analysis using GSAS-II employs spherical harmonics modeling, as described by 3762 3871 Bunge, "Texture Analysis in Materials Science" (1982), and 3763 implemented by Von Dreele, J. Appl. <span class=SpellE>Cryst</span>., <b 3764 style='mso-bidi-font-weight:normal'>30</b>, 517-525 (1997) in GSAS. The even 3765 part of the orientation distribution function (ODF) via the general axis 3766 equation</p> 3872 implemented by Von Dreele, J. Appl. Cryst., <b style='mso-bidi-font-weight: 3873 normal'>30</b>, 517-525 (1997) in GSAS. The even part of the orientation 3874 distribution function (ODF) via the general axis equation</p> 3767 3875 3768 3876 <p class=MsoNormal style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt; … … 3894 4002 of a unit vector coincident with h relative to the reciprocal lattice. For most 3895 4003 crystal symmetries, <span style='font-family:Symbol'>f</span> is the angle 3896 between h and the n- <span class=SpellE>th</span> order major rotation axis of3897 the space group (usually the c-axis) and <span style='font-family:Symbol'>b</span>3898 is the angle between the projections of h and any secondary axis (usuallythe3899 a-axis) onto the normal plane.<span style='mso-spacerun:yes'> </span>In a 3900 s imilar way the sample harmonic factor, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span4004 between h and the n-th order major rotation axis of the space group (usually 4005 the c-axis) and <span style='font-family:Symbol'>b</span> is the angle between 4006 the projections of h and any secondary axis (usually the a-axis) onto the 4007 normal plane.<span style='mso-spacerun:yes'> </span>In a similar way the 4008 sample harmonic factor, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span 3901 4009 style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math"; 3902 4010 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: … … 3995 4103 a diffraction experiment the crystal reflection coordinates (<span 3996 4104 style='font-family:Symbol'>f</span>, <span style='font-family:Symbol'>b</span>) 3997 are determined by the choice of reflection index ( <span class=SpellE>hkl</span>)3998 while the sample coordinates (<span style='font-family:Symbol'>y</span>, <span 3999 style='font-family:Symbol'>g</span>) are determined by the sample orientation 4000 on the diffractometer. To define the sample coordinates (<span 4001 style='font-family:Symbol'>y</span>, <span style='font-family:Symbol'>g</span>), 4002 we have defined an instrument coordinate system (I, J, K) such that K is normal 4003 to thediffraction plane and J is coincident with the direction of the incident4105 are determined by the choice of reflection index (hkl) while the sample 4106 coordinates (<span style='font-family:Symbol'>y</span>, <span style='font-family: 4107 Symbol'>g</span>) are determined by the sample orientation on the 4108 diffractometer. To define the sample coordinates (<span style='font-family: 4109 Symbol'>y</span>, <span style='font-family:Symbol'>g</span>), we have defined 4110 an instrument coordinate system (I, J, K) such that K is normal to the 4111 diffraction plane and J is coincident with the direction of the incident 4004 4112 radiation beam toward the source. We further define a standard set of 4005 4113 right-handed eulerian goniometer angles (<span style='font-family:Symbol'>W</span>, … … 4015 4123 <span style='font-family:Symbol'>C</span><sub>s</sub>, <span style='font-family: 4016 4124 Symbol'>F</span><sub>s</sub>) that describe the rotation from (I<sub>s</sub>, J<sub>s</sub>, 4017 K<sub>s</sub>) to (I, J, K).<span style='mso-spacerun:yes'> </span>The sample rotation4018 angles are defined so that with the goniometer angles at zero <span4125 K<sub>s</sub>) to (I, J, K).<span style='mso-spacerun:yes'> </span>The sample 4126 rotation angles are defined so that with the goniometer angles at zero <span 4019 4127 style='font-family:Symbol'>W</span><sub>s</sub> and <span style='font-family: 4020 4128 Symbol'>F</span><sub>s</sub> are rotations about K and <span style='font-family: … … 4035 4143 normal'><span style='font-family:Symbol'>F</span>+</b><b style='mso-bidi-font-weight: 4036 4144 normal'><span style='font-family:Symbol'>F</span><sub>s</sub>)</b><b 4037 style='mso-bidi-font-weight:normal'><span style='font-family:Symbol'>C</span><s pan4038 class=SpellE><sub>s</sub><span style='font-family:Symbol'>W</span><sub>s</sub></span><o:p></o:p></b></p>4145 style='mso-bidi-font-weight:normal'><span style='font-family:Symbol'>C</span><sub>s</sub></b><b 4146 style='mso-bidi-font-weight:normal'><span style='font-family:Symbol'>W</span><sub>s</sub><o:p></o:p></b></p> 4039 4147 4040 4148 <p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt; … … 4045 4153 4046 4154 <p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt; 4047 margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>< span4048 class=GramE><i>cos</i>(</span><spanstyle='font-family:Symbol'>y</span>) = <!--[if gte msEquation 12]><m:oMath><i4155 margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><i>cos</i>(<span 4156 style='font-family:Symbol'>y</span>) = <!--[if gte msEquation 12]><m:oMath><i 4049 4157 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>M</m:r></span></i><m:d><m:dPr><span 4050 4158 style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math"; … … 4097 4205 top:15.0pt;mso-text-raise:-15.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4098 4206 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4099 type="#_x0000_t75" style='width:80. 25pt;height:50.25pt'>4207 type="#_x0000_t75" style='width:80.1pt;height:50.2pt'> 4100 4208 <v:imagedata src="gsasII-phase_files/image015.png" o:title="" chromakey="white"/> 4101 4209 </v:shape><![endif]--><![if !vml]><img width=107 height=67 … … 4116 4224 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4117 4225 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4118 type="#_x0000_t75" style='width:45. 75pt;height:26.25pt'>4226 type="#_x0000_t75" style='width:45.65pt;height:26.35pt'> 4119 4227 <v:imagedata src="gsasII-phase_files/image017.png" o:title="" chromakey="white"/> 4120 4228 </v:shape><![endif]--><![if !vml]><img width=61 height=35 … … 4132 4240 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4133 4241 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4134 type="#_x0000_t75" style='width:43. 5pt;height:26.25pt'>4242 type="#_x0000_t75" style='width:43.6pt;height:26.35pt'> 4135 4243 <v:imagedata src="gsasII-phase_files/image019.png" o:title="" chromakey="white"/> 4136 4244 </v:shape><![endif]--><![if !vml]><img width=58 height=35 … … 4148 4256 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4149 4257 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4150 type="#_x0000_t75" style='width:45. 6pt;height:26.4pt'>4258 type="#_x0000_t75" style='width:45.75pt;height:26.25pt'> 4151 4259 <v:imagedata src="gsasII-phase_files/image017.png" o:title="" chromakey="white"/> 4152 4260 </v:shape><![endif]--><![if !vml]><img width=61 height=35 … … 4202 4310 "Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US; 4203 4311 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape 4204 id="_x0000_i1025" type="#_x0000_t75" style='width:158. 4pt;height:42pt'>4312 id="_x0000_i1025" type="#_x0000_t75" style='width:158.25pt;height:42pt'> 4205 4313 <v:imagedata src="gsasII-phase_files/image021.png" o:title="" chromakey="white"/> 4206 4314 </v:shape><![endif]--><![if !vml]><img width=211 height=56 … … 4224 4332 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4225 4333 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4226 type="#_x0000_t75" style='width:30. 8pt;height:26.4pt'>4334 type="#_x0000_t75" style='width:30.75pt;height:26.25pt'> 4227 4335 <v:imagedata src="gsasII-phase_files/image023.png" o:title="" chromakey="white"/> 4228 4336 </v:shape><![endif]--><![if !vml]><img width=41 height=35 … … 4274 4382 "Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US; 4275 4383 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape 4276 id="_x0000_i1025" type="#_x0000_t75" style='width:149.2 pt;height:52.4pt'>4384 id="_x0000_i1025" type="#_x0000_t75" style='width:149.25pt;height:52.5pt'> 4277 4385 <v:imagedata src="gsasII-phase_files/image025.png" o:title="" chromakey="white"/> 4278 4386 </v:shape><![endif]--><![if !vml]><img width=199 height=70 … … 4327 4435 "Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US; 4328 4436 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape 4329 id="_x0000_i1025" type="#_x0000_t75" style='width:153. 6pt;height:52.4pt'>4437 id="_x0000_i1025" type="#_x0000_t75" style='width:153.75pt;height:52.5pt'> 4330 4438 <v:imagedata src="gsasII-phase_files/image027.png" o:title="" chromakey="white"/> 4331 4439 </v:shape><![endif]--><![if !vml]><img width=205 height=70 … … 4334 4442 <p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt; 4335 4443 margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>for 4336 <span class=SpellE>n</span> odd.<span style='mso-spacerun:yes'> </span>Each 4337 sum is only over either the even or odd values of s, respectively, because of 4338 the properties of the Fouriercoefficients, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span4444 n odd.<span style='mso-spacerun:yes'> </span>Each sum is only over either the 4445 even or odd values of s, respectively, because of the properties of the Fourier 4446 coefficients, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span 4339 4447 style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math"; 4340 4448 mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style: … … 4348 4456 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4349 4457 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4350 type="#_x0000_t75" style='width:21. 6pt;height:26.4pt'>4458 type="#_x0000_t75" style='width:21.75pt;height:26.25pt'> 4351 4459 <v:imagedata src="gsasII-phase_files/image029.png" o:title="" chromakey="white"/> 4352 4460 </v:shape><![endif]--><![if !vml]><img width=29 height=35 … … 4473 4581 "Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US; 4474 4582 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape 4475 id="_x0000_i1025" type="#_x0000_t75" style='width:408. 8pt;height:55.6pt'>4583 id="_x0000_i1025" type="#_x0000_t75" style='width:408.7pt;height:55.25pt'> 4476 4584 <v:imagedata src="gsasII-phase_files/image031.png" o:title="" chromakey="white"/> 4477 4585 </v:shape><![endif]--><![if !vml]><img width=545 height=74 … … 4509 4617 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4510 4618 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4511 type="#_x0000_t75" style='width:10 2pt;height:26.4pt'>4619 type="#_x0000_t75" style='width:101.9pt;height:26.35pt'> 4512 4620 <v:imagedata src="gsasII-phase_files/image033.png" o:title="" chromakey="white"/> 4513 4621 </v:shape><![endif]--><![if !vml]><img width=136 height=35 … … 4542 4650 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4543 4651 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4544 type="#_x0000_t75" style='width:94. 4pt;height:26.4pt'>4652 type="#_x0000_t75" style='width:94.3pt;height:26.35pt'> 4545 4653 <v:imagedata src="gsasII-phase_files/image035.png" o:title="" chromakey="white"/> 4546 4654 </v:shape><![endif]--><![if !vml]><img width=126 height=35 … … 4561 4669 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4562 4670 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4563 type="#_x0000_t75" style='width:45. 6pt;height:26.4pt'>4671 type="#_x0000_t75" style='width:45.75pt;height:26.25pt'> 4564 4672 <v:imagedata src="gsasII-phase_files/image037.png" o:title="" chromakey="white"/> 4565 4673 </v:shape><![endif]--><![if !vml]><img width=61 height=35 … … 4578 4686 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4579 4687 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4580 type="#_x0000_t75" style='width:47.2 pt;height:26.4pt'>4688 type="#_x0000_t75" style='width:47.25pt;height:26.25pt'> 4581 4689 <v:imagedata src="gsasII-phase_files/image039.png" o:title="" chromakey="white"/> 4582 4690 </v:shape><![endif]--><![if !vml]><img width=63 height=35 … … 4595 4703 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4596 4704 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4597 type="#_x0000_t75" style='width:45. 6pt;height:26.4pt'>4705 type="#_x0000_t75" style='width:45.75pt;height:26.25pt'> 4598 4706 <v:imagedata src="gsasII-phase_files/image037.png" o:title="" chromakey="white"/> 4599 4707 </v:shape><![endif]--><![if !vml]><img width=61 height=35 … … 4672 4780 top:4.0pt;mso-text-raise:-4.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4673 4781 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4674 type="#_x0000_t75" style='width:18. 8pt;height:29.2pt'>4782 type="#_x0000_t75" style='width:18.75pt;height:29.25pt'> 4675 4783 <v:imagedata src="gsasII-phase_files/image043.png" o:title="" chromakey="white"/> 4676 4784 </v:shape><![endif]--><![if !vml]><img width=25 height=39 … … 4692 4800 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4693 4801 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4694 type="#_x0000_t75" style='width:21. 6pt;height:26.4pt'>4802 type="#_x0000_t75" style='width:21.75pt;height:26.25pt'> 4695 4803 <v:imagedata src="gsasII-phase_files/image045.png" o:title="" chromakey="white"/> 4696 4804 </v:shape><![endif]--><![if !vml]><img width=29 height=35 … … 4711 4819 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 4712 4820 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 4713 type="#_x0000_t75" style='width:21. 6pt;height:26.4pt'>4821 type="#_x0000_t75" style='width:21.75pt;height:26.25pt'> 4714 4822 <v:imagedata src="gsasII-phase_files/image045.png" o:title="" chromakey="white"/> 4715 4823 </v:shape><![endif]--><![if !vml]><img width=29 height=35 … … 4767 4875 "Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US; 4768 4876 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape 4769 id="_x0000_i1025" type="#_x0000_t75" style='width:180. 8pt;height:54pt'>4877 id="_x0000_i1025" type="#_x0000_t75" style='width:180.75pt;height:54pt'> 4770 4878 <v:imagedata src="gsasII-phase_files/image047.png" o:title="" chromakey="white"/> 4771 4879 </v:shape><![endif]--><![if !vml]><img width=241 height=72 … … 4782 4890 of this correction. In one, a suite of spherical harmonics coefficients is 4783 4891 defined for the texture of a phase in the sample; this can have any of the 4784 possible sample symmetries and is the usual result desired for texture 4785 analysis. The other is the suite of spherical harmonics terms for cylindrical 4786 s ample symmetry for each phase in each powder pattern (“histogram”) and is4787 us ually used to accommodate preferred orientation effects in a Rietveld4788 refinement. The former description allows refinement of the sample orientation4789 zeros, <span style='font-family:Symbol'>W</span><sub>s</sub>, <span 4790 style='font-family:Symbol'>C</span><sub>s</sub>, <span style='font-family:Symbol'>F</span><sub>s</sub>, 4791 but the latter description does not (they are assumed to be zero and not 4792 refinable). The sample orientation angles, (<span style='font-family:Symbol'>W</span>, 4793 <spanstyle='font-family:Symbol'>C</span>, <span style='font-family:Symbol'>F) </span>are4892 possible sample symmetries and is the usual result desired for texture analysis. 4893 The other is the suite of spherical harmonics terms for cylindrical sample 4894 symmetry for each phase in each powder pattern (“histogram”) and is usually 4895 used to accommodate preferred orientation effects in a Rietveld refinement. The 4896 former description allows refinement of the sample orientation zeros, <span 4897 style='font-family:Symbol'>W</span><sub>s</sub>, <span style='font-family:Symbol'>C</span><sub>s</sub>, 4898 <span style='font-family:Symbol'>F</span><sub>s</sub>, but the latter 4899 description does not (they are assumed to be zero and not refinable). The 4900 sample orientation angles, (<span style='font-family:Symbol'>W</span>, <span 4901 style='font-family:Symbol'>C</span>, <span style='font-family:Symbol'>F) </span>are 4794 4902 specified in the Sample Parameters table in the GSAS-II data tree structure and 4795 4903 are applied for either description.</p> … … 4805 4913 incident and diffracted beams at equal angles (theta) on opposite sides of the 4806 4914 sample. The sample is frequently spun about its normal to improve powder 4807 statistics and impose cylindrical symmetry on any preferred orientation (texture).4808 Thus, the diffraction plane (source, diffraction vector & detector) 4809 contains the K-vector which is parallel to the diffraction vector and <a 4810 name="_Hlk74813217"><span style='font-family:Symbol'>W</span>, </a><span4915 statistics and impose cylindrical symmetry on any preferred orientation 4916 (texture). Thus, the diffraction plane (source, diffraction vector & 4917 detector) contains the K-vector which is parallel to the diffraction vector and 4918 <a name="_Hlk74813217"><span style='font-family:Symbol'>W</span>, </a><span 4811 4919 style='mso-bookmark:_Hlk74813217'><span style='font-family:Symbol'>C</span>, </span><span 4812 4920 style='mso-bookmark:_Hlk74813217'><span style='font-family:Symbol'>F = 0.</span></span><span … … 4829 4937 4830 4938 <p class=MsoNormal style='margin-left:.5in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'>The 4831 area detector is presumed to be directly behind the sample with the incident beam4832 somewhere near the center of the detector. The detector axes are defined (for a 4833 synchrotron) with the X-axis toward the synchrotron ring and the Y-axis4939 area detector is presumed to be directly behind the sample with the incident 4940 beam somewhere near the center of the detector. The detector axes are defined 4941 (for a synchrotron) with the X-axis toward the synchrotron ring and the Y-axis 4834 4942 vertical “up”; one views the detector image as if looking from the x-ray 4835 4943 source. The sample is assumed to be a capillary (which may be spun to impose … … 4846 4954 <p class=MsoNormal style='margin-left:.75in'>1. Menu ‘<b>Texture/Refine 4847 4955 texture’ </b>– refines the spherical harmonics texture model using the 4848 predetermined values of <span class=SpellE>Prfo</span> for all histogram4849 reflection sets as demonstratedin <a4956 predetermined values of Prfo for all histogram reflection sets as demonstrated 4957 in <a 4850 4958 href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DTexture/Texture%20analysis%20of%202D%20data%20in%20GSAS-II.htm">2DTexture</a> 4851 tutorial.<o:p></o:p></span></p> 4852 4853 <p></p> 4959 tutorial.</p> 4854 4960 4855 4961 <p class=MsoNormal style='margin-left:.75in'>2. Texture settings:</p> … … 4871 4977 4872 4978 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; 4873 margin-left:1.25in;text-indent:-.25in;mso-list:l1 level1 lfo1 4;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span4979 margin-left:1.25in;text-indent:-.25in;mso-list:l1 level1 lfo11;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 4874 4980 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; 4875 4981 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span 4876 4982 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> 4877 4983 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>as 4878 an "Axial pole distribution" which simulates the intensity of a 4879 reflectionduring a phi scan.<o:p></o:p></span></p>4984 an "Axial pole distribution" which simulates the intensity of a reflection 4985 during a phi scan.<o:p></o:p></span></p> 4880 4986 4881 4987 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; 4882 margin-left:1.25in;text-indent:-.25in;mso-list:l1 level1 lfo1 4;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span4988 margin-left:1.25in;text-indent:-.25in;mso-list:l1 level1 lfo11;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 4883 4989 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; 4884 4990 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span … … 4886 4992 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>as 4887 4993 a "pole figure," where a projection of the probability of finding a 4888 pole (<span class=SpellE>hkl</span>) is plotted as a function of sample 4889 orientation.<o:p></o:p></span></p> 4994 pole (hkl) is plotted as a function of sample orientation.<o:p></o:p></span></p> 4890 4995 4891 4996 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; 4892 margin-left:1.25in;text-indent:-.25in;mso-list:l1 level1 lfo1 4;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span4997 margin-left:1.25in;text-indent:-.25in;mso-list:l1 level1 lfo11;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 4893 4998 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; 4894 4999 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span 4895 5000 style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> 4896 5001 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>as 4897 <span class=GramE>a</span> "inverse pole figure," where a projection 4898 of the probability of finding all poles (<span class=SpellE>hkls</span>) is 4899 plotted for a selected sample orientation.<o:p></o:p></span></p> 5002 an "inverse pole figure," where a projection of the probability of 5003 finding all poles (hkls) is plotted for a selected sample orientation.<o:p></o:p></span></p> 4900 5004 4901 5005 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; 4902 margin-left:1.25in;text-indent:-.25in;mso-list:l1 level1 lfo1 4;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5006 margin-left:1.25in;text-indent:-.25in;mso-list:l1 level1 lfo11;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 4903 5007 style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol; 4904 5008 mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span … … 4906 5010 </span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>or 4907 5011 as a "3D pole distribution" that shows the probability of finding a 4908 pole (<span class=SpellE>hkl</span>) is plotted as a function of sample 4909 orientation. <o:p></o:p></span></p> 5012 pole (hkl) is plotted as a function of sample orientation. <o:p></o:p></span></p> 4910 5013 4911 5014 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; 4912 5015 margin-left:1.0in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 4913 5016 style='mso-fareast-font-family:"Times New Roman"'>For Axial distribution, pole 4914 figure and 3D pole distribution one must next select the <span class=SpellE>hkl</span>4915 of the desired pole, for Inverse pole figure one must select a sample direction 4916 (typically 0 01).<o:p></o:p></span></p>5017 figure and 3D pole distribution one must next select the hkl of the desired 5018 pole, for Inverse pole figure one must select a sample direction (typically 0 0 5019 1).<o:p></o:p></span></p> 4917 5020 4918 5021 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto; … … 4944 5047 magnitude. The crystal structure plot shows each peak position as a white to 4945 5048 dark gray cross; the shade is determined from the magnitude for the peak 4946 relative to the maximum peak magnitude. Negative peaks shown in orange.</p> 5049 relative to the maximum peak magnitude; some are connected by white sticks as 5050 possible bonds. Negative peaks are shown in orange.</p> 4947 5051 4948 5052 <h5 style='margin-left:.5in'>What can I do here?</h5> 4949 5053 4950 5054 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto; 4951 text-indent:-.25in;mso-list:l 10 level1 lfo16;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5055 text-indent:-.25in;mso-list:l9 level1 lfo13;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 4952 5056 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 4953 5057 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 4962 5066 4963 5067 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 4964 auto;text-indent:-.25in;mso-list:l 10 level1 lfo16;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a5068 auto;text-indent:-.25in;mso-list:l9 level1 lfo13;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a 4965 5069 name=Phase-Pawley><![if !supportLists]><span style='mso-fareast-font-family: 4966 5070 "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> … … 4969 5073 4970 5074 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 4971 auto;text-indent:-.25in;mso-list:l 10 level1 lfo16;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a5075 auto;text-indent:-.25in;mso-list:l9 level1 lfo13;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a 4972 5076 name=Pawley><![if !supportLists]><span style='mso-fareast-font-family:"Times New Roman"'><span 4973 5077 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> 4974 </span></span></span><![endif]>Select the </a><span class=SpellE><span 4975 style='mso-bookmark:Pawley'><b style='mso-bidi-font-weight:normal'>dzero</b></span></span><span 4976 style='mso-bookmark:Pawley'> column – the entries will be sorted with the 4977 smallest (distance from origin) at the top.</span></p> 5078 </span></span></span><![endif]>Select the <b style='mso-bidi-font-weight:normal'>dzero</b> 5079 column – the entries will be sorted with the smallest (distance from origin) at 5080 the top.</a></p> 4978 5081 4979 5082 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 4980 auto;text-indent:-.25in;mso-list:l 10 level1 lfo16;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span5083 auto;text-indent:-.25in;mso-list:l9 level1 lfo13;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 4981 5084 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 4982 5085 "Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> 4983 </span></span></span><![endif]>Select the <span class=SpellE><b>dcent</b></span> 4984 column – the entries will be sorted with the smallest distance from the unit 4985 cell center at the top.</span></p> 5086 </span></span></span><![endif]>Select the <b>dcent</b> column – the entries 5087 will be sorted with the smallest distance from the unit cell center at the top.</span></p> 4986 5088 4987 5089 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 4988 auto;text-indent:-.25in;mso-list:l 10 level1 lfo16;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span5090 auto;text-indent:-.25in;mso-list:l9 level1 lfo13;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 4989 5091 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 4990 5092 "Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> 4991 5093 </span></span></span><![endif]>Menu <b style='mso-bidi-font-weight:normal'>‘Map 4992 peaks<span class=GramE>’ <span style='font-weight:normal'><span 4993 style='mso-spacerun:yes'> </span>–</span></span></b></span></p> 4994 4995 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 4996 auto;text-indent:-.25in;mso-list:l10 level2 lfo16;tab-stops:list 1.0in'><span 5094 peaks’ </b><span style='mso-spacerun:yes'> </span>–</span></p> 5095 5096 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5097 auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 4997 5098 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 4998 5099 "Times New Roman"'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> … … 5011 5112 5012 5113 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5013 auto;text-indent:-.25in;mso-list:l 10 level2 lfo16;tab-stops:list 1.0in'><span5114 auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 5014 5115 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5015 5116 "Times New Roman"'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 5016 </span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight: 5017 normal'>View point</b></span><b style='mso-bidi-font-weight:normal'> </b>– this 5018 positions the view point (large 3D RGB cross) at the 1<sup>st</sup> selected 5019 peak.</span></p> 5020 5021 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5022 auto;text-indent:-.25in;mso-list:l10 level2 lfo16;tab-stops:list 1.0in'><span 5117 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>View 5118 point </b>– this positions the viewpoint (large 3D RGB cross) at the 1<sup>st</sup> 5119 selected peak.</span></p> 5120 5121 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5122 auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 5023 5123 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5024 5124 "Times New Roman"'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 5025 5125 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>View pt</b>. 5026 5126 <b style='mso-bidi-font-weight:normal'>dist</b>. – this calculates distance 5027 from <span class=GramE>view point</span>to all selected map peaks.</span></p>5028 5029 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5030 auto;text-indent:-.25in;mso-list:l 10 level2 lfo16;tab-stops:list 1.0in'><span5127 from viewpoint to all selected map peaks.</span></p> 5128 5129 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5130 auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 5031 5131 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5032 5132 "Times New Roman"'><span style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> … … 5035 5135 5036 5136 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5037 auto;text-indent:-.25in;mso-list:l 10 level2 lfo16;tab-stops:list 1.0in'><span5137 auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 5038 5138 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5039 5139 "Times New Roman"'><span style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> 5040 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Calc <span5041 class=SpellE>dist</span>/ang </b>– if 2 peaks are selected, this calculates the 5042 distance between them. If 3 peaks are selected this calculates the angle 5043 between them; NB: selection order matters. If selection is not 2 or 3 peaks 5044 this is ignored.Output is on the console window.</span></p>5045 5046 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5047 auto;text-indent:-.25in;mso-list:l 10 level2 lfo16;tab-stops:list 1.0in'><span5140 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Calc 5141 dist/ang </b>– if 2 peaks are selected, this calculates the distance between 5142 them. If 3 peaks are selected this calculates the angle between them; NB: 5143 selection order matters. If selection is not 2 or 3 peaks this is ignored. 5144 Output is on the console window.</span></p> 5145 5146 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5147 auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 5048 5148 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5049 5149 "Times New Roman"'><span style='mso-list:Ignore'>f.<span style='font:7.0pt "Times New Roman"'> … … 5053 5153 5054 5154 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5055 auto;text-indent:-.25in;mso-list:l 10 level2 lfo16;tab-stops:list 1.0in'><span5155 auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 5056 5156 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5057 5157 "Times New Roman"'><span style='mso-list:Ignore'>g.<span style='font:7.0pt "Times New Roman"'> … … 5060 5160 5061 5161 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5062 auto;text-indent:-.25in;mso-list:l 10 level2 lfo16;tab-stops:list 1.0in'><span5162 auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 5063 5163 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5064 5164 "Times New Roman"'><span style='mso-list:Ignore'>h.<span style='font:7.0pt "Times New Roman"'> … … 5068 5168 5069 5169 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5070 auto;text-indent:-.25in;mso-list:l 10 level2 lfo16;tab-stops:list 1.0in'><span5170 auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 5071 5171 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5072 5172 "Times New Roman"'><span style='mso-list:Ignore'>i.<span style='font:7.0pt "Times New Roman"'> … … 5077 5177 5078 5178 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5079 auto;text-indent:-.25in;mso-list:l 10 level2 lfo16;tab-stops:list 1.0in'><span5179 auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 5080 5180 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5081 5181 "Times New Roman"'><span style='mso-list:Ignore'>j.<span style='font:7.0pt "Times New Roman"'> … … 5084 5184 5085 5185 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5086 auto;text-indent:-.25in;mso-list:l 10 level2 lfo16;tab-stops:list 1.0in'><span5186 auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 5087 5187 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5088 5188 "Times New Roman"'><span style='mso-list:Ignore'>k.<span style='font:7.0pt "Times New Roman"'> 5089 5189 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Delete 5090 peaks </b>– this deletes selected peaks. The shading on the remaining peaks is changed5091 to reflect any change in the maximum after deletion.</span></p>5190 peaks </b>– this deletes selected peaks. The shading on the remaining peaks is 5191 changed to reflect any change in the maximum after deletion.</span></p> 5092 5192 5093 5193 <p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto; 5094 text-indent:-.25in;mso-list:l 10 level2 lfo16;tab-stops:list 1.0in'><span5194 text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span 5095 5195 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5096 5196 "Times New Roman"'><span style='mso-list:Ignore'>l.<span style='font:7.0pt "Times New Roman"'> … … 5110 5210 style='mso-bookmark:Pawley'>).</span></p> 5111 5211 5112 <h5 style='margin-left:.5in'>What can I do here?</h5> 5212 <h5 style='margin-left:.5in'><span style='mso-bookmark:Pawley'>What can I do 5213 here?</span></h5> 5113 5214 5114 5215 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto; 5115 text-indent:-.25in;mso-list:l3 level1 lfo1 8;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span5216 text-indent:-.25in;mso-list:l3 level1 lfo15;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 5116 5217 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5117 5218 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> … … 5120 5221 5121 5222 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5122 auto;text-indent:-.25in;mso-list:l7 level2 lfo 20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span5223 auto;text-indent:-.25in;mso-list:l7 level2 lfo17;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 5123 5224 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5124 5225 "Times New Roman"'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> … … 5129 5230 5130 5231 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5131 auto;text-indent:-.25in;mso-list:l7 level2 lfo 20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span5232 auto;text-indent:-.25in;mso-list:l7 level2 lfo17;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 5132 5233 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5133 5234 "Times New Roman"'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> 5134 5235 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Pawley 5135 create</b> – this creates a new set of Pawley reflections, over writing any 5136 preexisting Pawley set. They are generated with d-spacings larger than the 5137 limit set as ‘Pawley <span class=SpellE>dmin</span>’ in the General tab for 5138 this phase. By <span class=GramE>default</span> the refine flags are not set 5139 and the <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>) = 100.0.</span></p> 5140 5141 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5142 auto;text-indent:-.25in;mso-list:l7 level2 lfo20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 5236 create</b> – this creates a new set of Pawley reflections, over writing any preexisting 5237 Pawley set. They are generated with d-spacings larger than the limit set as 5238 ‘Pawley dmin’ in the General tab for this phase. By default the refine flags 5239 are not set and the Fsq(hkl) = 100.0.</span></p> 5240 5241 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5242 auto;text-indent:-.25in;mso-list:l7 level2 lfo17;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 5143 5243 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5144 5244 "Times New Roman"'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> 5145 5245 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Pawley 5146 estimate</b> – this attempts an estimate of <span class=SpellE>Fsq</span>(<span 5147 class=SpellE>hkl</span>) from the peak heights of the reflection as seen in the 5148 1<sup>st</sup> powder pattern of those selected in the </span><a href="#_Data"><span 5149 style='mso-bookmark:Pawley'>Data</span><span style='mso-bookmark:Pawley'></span></a><span 5150 style='mso-bookmark:Pawley'> tab.</span></p> 5151 5152 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5153 auto;text-indent:-.25in;mso-list:l7 level2 lfo20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 5246 estimate</b> – this attempts an estimate of Fsq(hkl) from the peak heights of 5247 the reflection as seen in the 1<sup>st</sup> powder pattern of those selected 5248 in the </span><a href="#_Data"><span style='mso-bookmark:Pawley'>Data</span><span 5249 style='mso-bookmark:Pawley'></span></a><span style='mso-bookmark:Pawley'> tab.</span></p> 5250 5251 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5252 auto;text-indent:-.25in;mso-list:l7 level2 lfo17;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 5154 5253 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5155 5254 "Times New Roman"'><span style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> 5156 5255 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Pawley 5157 5256 update </b>– process Pawley reflection set for negative intensities. These are 5158 set to ½ its absolute value for <span class=SpellE>noncentrosymmetric</span>5159 space groups (0.3 otherwise); the refine flag is turned off. One should repeat5160 Pawley refinement and then do </span><span style='mso-bookmark:Pawley'><b><span 5161 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 5162 m so-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Refine all</span></b>5163 a nd an additional refinement. Repeat as needed to remove negative intensities.5164 Set </span><spanstyle='mso-bookmark:Pawley'><b><span style='font-family:"Calibri",sans-serif;5257 set to ½ its absolute value for noncentrosymmetric space groups (0.3 5258 otherwise); the refine flag is turned off. One should repeat Pawley refinement 5259 and then do </span><span style='mso-bookmark:Pawley'><b><span style='font-family: 5260 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 5261 minor-latin;mso-bidi-theme-font:minor-latin'>Refine all</span></b> and an 5262 additional refinement. Repeat as needed to remove negative intensities. Set </span><span 5263 style='mso-bookmark:Pawley'><b><span style='font-family:"Calibri",sans-serif; 5165 5264 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: 5166 5265 minor-latin'>Pawley neg. wt.</span></b> (see </span><span style='mso-bookmark: … … 5170 5269 5171 5270 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5172 auto;text-indent:-.25in;mso-list:l7 level2 lfo 20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span5271 auto;text-indent:-.25in;mso-list:l7 level2 lfo17;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 5173 5272 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5174 5273 "Times New Roman"'><span style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> … … 5177 5276 5178 5277 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5179 auto;text-indent:-.25in;mso-list:l7 level2 lfo 20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span5278 auto;text-indent:-.25in;mso-list:l7 level2 lfo17;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 5180 5279 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5181 5280 "Times New Roman"'><span style='mso-list:Ignore'>f.<span style='font:7.0pt "Times New Roman"'> … … 5184 5283 5185 5284 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 5186 auto;text-indent:-.25in;mso-list:l7 level2 lfo 20;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span5285 auto;text-indent:-.25in;mso-list:l7 level2 lfo17;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 5187 5286 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5188 5287 "Times New Roman"'><span style='mso-list:Ignore'>g.<span style='font:7.0pt "Times New Roman"'> … … 5191 5290 5192 5291 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5193 auto;text-indent:-.25in;mso-list:l3 level1 lfo1 8;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span5292 auto;text-indent:-.25in;mso-list:l3 level1 lfo15;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><span 5194 5293 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family: 5195 5294 "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> 5196 </span></span></span><![endif]>You can change the refine flags either by clicking5197 on the box or by selecting one and then selecting the column (a single click on 5198 the column heading). Then type ‘y’ to set the refine flags or ‘n’ to clear the 5199 flags. You should not refine those reflections that fall below the lower limit 5200 or above the upper limit of the powder pattern otherwise you may have a 5201 singular matrix error in your Pawley refinement.</span></p>5295 </span></span></span><![endif]>You can change the refine flags either by 5296 clicking on the box or by selecting one and then selecting the column (a single 5297 click on the column heading). Then type ‘y’ to set the refine flags or ‘n’ to 5298 clear the flags. You should not refine those reflections that fall below the 5299 lower limit or above the upper limit of the powder pattern otherwise you may 5300 have a singular matrix error in your Pawley refinement.</span></p> 5202 5301 5203 5302 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5204 auto;text-indent:-.25in;mso-list:l3 level1 lfo1 8;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5303 auto;text-indent:-.25in;mso-list:l3 level1 lfo15;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5205 5304 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 5206 5305 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>You 5207 5306 can delete an individual reflection from the Pawley set by selecting its row 5208 5307 (will be highlighted) and then pressing the Delete key (this is not reversable 5209 & only <span class=GramE>deletes</span>the 1<sup>st</sup> one selected).</p>5308 & only deletes the 1<sup>st</sup> one selected).</p> 5210 5309 5211 5310 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; 5212 text-indent:-.25in;mso-list:l3 level1 lfo1 8;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5311 text-indent:-.25in;mso-list:l3 level1 lfo15;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5213 5312 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span 5214 5313 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>You 5215 can change the individual <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>) 5216 values by selecting it, typing in the new value and then pressing enter or 5217 selecting somewhere else in the table.</p> 5314 can change the individual Fsq(hkl) values by selecting it, typing in the new 5315 value and then pressing enter or selecting somewhere else in the table.</p> 5218 5316 5219 5317 <h4 style='margin-left:.25in;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><a 5220 5318 name=Phase-Layers>Layers</a></h4> 5221 5319 5222 <p class=MsoNormal style='margin-left:.5in'>This is 5223 used to set up stacking fault models for simulations of x-ray diffraction 5224 patterns. See for example the<a5320 <p class=MsoNormal style='margin-left:.5in'>This is used to set up stacking 5321 fault models for simulations of x-ray diffraction patterns. See for example the 5322 <a 5225 5323 href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/StackingFaults-I/Stacking%20Faults-I.htm">Stacking 5226 Faults-I</a> tutorial. The computations are done by a modified version of <span 5227 class=SpellE>DIFFaX</span>. See M.M.J. Treacy, J.M. Newsam and M.W. Deem, 5228 Proc. Roy. Soc. <span class=SpellE>Lond</span>. 433A, 499-520 (1991) 5229 for more information on DIFFaX and please cite this if you use this 5230 section of GSAS-II.</p> 5324 Faults-I</a> tutorial. The computations are done by a modified version of 5325 DIFFaX. See M.M.J. Treacy, J.M. Newsam and M.W. Deem, Proc. Roy. Soc. Lond. 5326 433A, 499-520 (1991) for more information on DIFFaX and please cite this if you 5327 use this section of GSAS-II.</p> 5231 5328 5232 5329 <h5 style='margin-left:.5in'>What can I do here?</h5> 5233 5330 5234 5331 <p class=MsoListParagraphCxSpFirst style='margin-left:63.8pt;mso-add-space: 5235 auto;text-indent:-.25in;mso-list:l6 level1 lfo 22;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5332 auto;text-indent:-.25in;mso-list:l6 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5236 5333 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 5237 5334 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Menu … … 5239 5336 5240 5337 <p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space: 5241 auto;text-indent:-.25in;mso-list:l6 level2 lfo 22;tab-stops:45.8pt 91.6pt list 99.8pt left 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5338 auto;text-indent:-.25in;mso-list:l6 level2 lfo19;tab-stops:45.8pt 91.6pt list 99.8pt left 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5242 5339 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span 5243 5340 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5244 style='mso-bidi-font-weight:normal'>Load from <span class=SpellE>DIFFaX</span> 5245 file – </b><span style='mso-bidi-font-weight:bold'>load parameters from a <span 5246 class=SpellE>DIFFaX</span> input file</span></p> 5341 style='mso-bidi-font-weight:normal'>Load from DIFFaX file – </b><span 5342 style='mso-bidi-font-weight:bold'>load parameters from a DIFFaX input file</span></p> 5247 5343 5248 5344 <p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space: 5249 auto;text-indent:-.25in;mso-list:l6 level2 lfo 22;tab-stops:45.8pt 91.6pt list 99.8pt left 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5345 auto;text-indent:-.25in;mso-list:l6 level2 lfo19;tab-stops:45.8pt 91.6pt list 99.8pt left 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5250 5346 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span 5251 5347 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 5255 5351 5256 5352 <p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space: 5257 auto;text-indent:-.25in;mso-list:l6 level2 lfo 22;tab-stops:45.8pt 91.6pt list 99.8pt left 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5353 auto;text-indent:-.25in;mso-list:l6 level2 lfo19;tab-stops:45.8pt 91.6pt list 99.8pt left 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5258 5354 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span 5259 5355 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5260 5356 style='mso-bidi-font-weight:normal'>Simulate pattern – </b><span 5261 style='mso-bidi-font-weight:bold'>run <span class=SpellE>DIFFaX</span> to 5262 simulate selected pattern<o:p></o:p></span></p> 5357 style='mso-bidi-font-weight:bold'>run DIFFaX to simulate selected pattern<o:p></o:p></span></p> 5263 5358 5264 5359 <p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space: 5265 auto;text-indent:-.25in;mso-list:l6 level2 lfo 22;tab-stops:45.8pt 91.6pt list 99.8pt left 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5360 auto;text-indent:-.25in;mso-list:l6 level2 lfo19;tab-stops:45.8pt 91.6pt list 99.8pt left 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5266 5361 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span 5267 5362 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b 5268 5363 style='mso-bidi-font-weight:normal'>Fit pattern – </b><span style='mso-bidi-font-weight: 5269 bold'>refine stacking <span class=SpellE>fult</span> parameters to fit observed5270 pattern (not availableyet)<o:p></o:p></span></p>5364 bold'>refine stacking fult parameters to fit observed pattern (not available 5365 yet)<o:p></o:p></span></p> 5271 5366 5272 5367 <p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space: 5273 auto;text-indent:-.25in;mso-list:l6 level2 lfo 22;tab-stops:45.8pt 91.6pt list 99.8pt left 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5368 auto;text-indent:-.25in;mso-list:l6 level2 lfo19;tab-stops:45.8pt 91.6pt list 99.8pt left 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5274 5369 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span 5275 5370 style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b … … 5279 5374 5280 5375 <p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space: 5281 auto;text-indent:-.25in;mso-list:l6 level1 lfo 22;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5376 auto;text-indent:-.25in;mso-list:l6 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5282 5377 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span 5283 5378 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> … … 5286 5381 5287 5382 <p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space: 5288 auto;text-indent:-.25in;mso-list:l6 level1 lfo 22;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5383 auto;text-indent:-.25in;mso-list:l6 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5289 5384 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span 5290 5385 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> … … 5293 5388 5294 5389 <p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space: 5295 auto;text-indent:-.25in;mso-list:l6 level1 lfo 22;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5390 auto;text-indent:-.25in;mso-list:l6 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5296 5391 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span 5297 5392 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> … … 5301 5396 5302 5397 <p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space: 5303 auto;text-indent:-.25in;mso-list:l6 level1 lfo 22;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5398 auto;text-indent:-.25in;mso-list:l6 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5304 5399 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span 5305 5400 style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> … … 5309 5404 5310 5405 <p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space: 5311 auto;text-indent:-.25in;mso-list:l6 level1 lfo 22;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5406 auto;text-indent:-.25in;mso-list:l6 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5312 5407 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span 5313 5408 style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'> 5314 5409 </span></span></span><![endif]><span style='mso-bidi-font-weight:bold'>Next are 5315 5410 descriptions of the layers to be used in the calculations. They can be created 5316 atom-by-atom or imported from another GSAS-II <span class=SpellE>gpx</span> 5317 file. If a layer is already present, then the new layer can be the same; give 5318 it a different name.<o:p></o:p></span></p> 5411 atom-by-atom or imported from another GSAS-II gpx file. If a layer is already 5412 present, then the new layer can be the same; give it a different name.<o:p></o:p></span></p> 5319 5413 5320 5414 <p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space: 5321 auto;text-indent:-.25in;mso-list:l6 level1 lfo 22;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5415 auto;text-indent:-.25in;mso-list:l6 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5322 5416 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span 5323 5417 style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'> … … 5327 5421 5328 5422 <p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space: 5329 auto;text-indent:-.25in;mso-list:l6 level1 lfo 22;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5423 auto;text-indent:-.25in;mso-list:l6 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5330 5424 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span 5331 5425 style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'> … … 5334 5428 1).<o:p></o:p></span></p> 5335 5429 5336 <p class=MsoListParagraphCxSp Middle style='margin-left:63.8pt;mso-add-space:5337 auto;text-indent:-.25in;mso-list:l6 level1 lfo22;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span5430 <p class=MsoListParagraphCxSpLast style='margin-left:63.8pt;mso-add-space:auto; 5431 text-indent:-.25in;mso-list:l6 level1 lfo19;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt'><![if !supportLists]><span 5338 5432 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span 5339 5433 style='mso-list:Ignore'>9.<span style='font:7.0pt "Times New Roman"'> … … 5342 5436 simulation<o:p></o:p></span></p> 5343 5437 5344 <p style='margin-left:.5in'> 5345 You can draw the layer structures as well as 5346 sequences of layers to check on how they fit together; see the <b>Plot</B> 5438 <p style='margin-left:.5in'>You can draw the layer structures as well as 5439 sequences of layers to check on how they fit together; see the <b>Plot</b> 5347 5440 boxes for this.</p> 5348 5441 5349 <h4 style='margin-left:.25in'> 5350 <a name="Phase-Wave_Data"></a>Wave Data</h4> 5442 <h4 style='margin-left:.25in'><a name="Phase-Wave_Data"></a>Wave Data</h4> 5443 5351 5444 <h5 style='margin-left:.5in'>What can I do here?</h5> 5352 5445 5353 <h4 style='margin-left:.25in'> 5354 <a name="Phase-MC/SA">MC/SA</a></h4> 5446 <h4 style='margin-left:.25in'><a name="Phase-MC/SA">MC/SA</a></h4> 5447 5355 5448 <h5 style='margin-left:.5in'>What can I do here?</h5> 5356 5449 5357 <h4 style='margin-left:.25in'> 5358 <a name="Phase-RMC">RMC</a></h4> 5450 <h4 style='margin-left:.25in'><a name=Phase-RMC>RMC</a></h4> 5451 5359 5452 <h5 style='margin-left:.5in'>What can I do here?</h5> 5360 5453 5361 <h4 style='margin-left:.25in'> 5362 <a name="Phase-ISODISTORT">ISODISTORT</a></h4> 5454 <h4 style='margin-left:.25in'><a name=Phase-ISODISTORT>ISODISTORT</a></h4> 5455 5363 5456 <h5 style='margin-left:.5in'>What can I do here?</h5> 5364 5457 5365 <h4 style='margin-left:.25in'> 5366 <a name="Phase-Pawley_reflections">Pawley_reflections</a></h4> 5367 <h5 style='margin-left:.5in'>What can I do here?</h5> 5368 5369 5458 <div class=MsoNormal align=center style='text-align:center'><span 5459 style='mso-fareast-font-family:"Times New Roman"'> 5370 5460 5371 5461 <hr size=3 width="100%" align=center> 5372 5462 5373 <p class=MsoNormal> 5374 <span style='mso-fareast-font-family:"Times New Roman"'> 5375 <!-- hhmts start -->Last modified: Tue Jan 25 09:29:56 CST 2022 <!-- hhmts end --><o:p></o:p></span></p> 5463 </span></div> 5464 5465 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><!-- hhmts start -->Last 5466 modified: Tue Jan 25 09:29:56 CST 2022 <!-- hhmts end --><o:p></o:p></span></p> 5376 5467 5377 5468 </div>
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