Changeset 5243 for trunk


Ignore:
Timestamp:
Mar 22, 2022 10:35:21 AM (3 years ago)
Author:
vondreele
Message:

fix crash in GetTruePosition? if getSelection() = 0
add missing delete option for chiral center restraint
updates to help/gsasII-phase.html

Location:
trunk
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • TabularUnified trunk/GSASIIplot.py

    r5233 r5243  
    91269126        if Add:
    91279127            Indx = GetSelectedAtoms()
     9128        if not getSelection():  #wrong place for doing this
     9129            return
    91289130        if G2frame.phaseDisplay.GetPageText(getSelection()) == 'Map peaks':
    91299131            peakList = data['Map Peaks']
     
    91429144                        SetSelectedAtoms(i,Add)
    91439145                        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)
    91469147            return
    91479148        elif G2frame.phaseDisplay.GetPageText(getSelection()) == 'Draw Atoms':
  • TabularUnified trunk/GSASIIrestrGUI.py

    r5239 r5243  
    14621462                else:
    14631463                    Volumes.Bind(wg.EVT_GRID_CELL_CHANGE, OnCellChange)
    1464                 for i in (G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD):
     1464                for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD):
    14651465                    G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=True)
    14661466                G2frame.Bind(wx.EVT_MENU, OnChangeValue, id=G2G.wxID_RESRCHANGEVAL)
    14671467                G2frame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2G.wxID_RESTCHANGEESD)
     1468                G2frame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2G.wxID_RESTDELETE)
    14681469                mainSizer.Add(wx.StaticText(ChiralRestr,-1,
    14691470                    'Chiral volume restraints: sum(wt*(delt/sig)^2) =    %.2f, mean(wt*(delt/sig)^2) =    %.2f'    \
  • TabularUnified trunk/help/gsasII-phase.html

    r5159 r5243  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele, Robert B.</o:LastAuthor>
    27   <o:Revision>31</o:Revision>
    28   <o:TotalTime>5325</o:TotalTime>
     27  <o:Revision>34</o:Revision>
     28  <o:TotalTime>6559</o:TotalTime>
    2929  <o:Created>2021-06-20T02:30:00Z</o:Created>
    30   <o:LastSaved>2021-06-22T22:15:00Z</o:LastSaved>
     30  <o:LastSaved>2022-03-22T15:32:00Z</o:LastSaved>
    3131  <o:Pages>1</o:Pages>
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    33   <o:Characters>47880</o:Characters>
     32  <o:Words>9185</o:Words>
     33  <o:Characters>52357</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
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    36   <o:Paragraphs>112</o:Paragraphs>
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     36  <o:Paragraphs>122</o:Paragraphs>
     37  <o:CharactersWithSpaces>61420</o:CharactersWithSpaces>
    3838  <o:Version>16.00</o:Version>
    3939 </o:DocumentProperties>
     
    4242 </o:OfficeDocumentSettings>
    4343</xml><![endif]-->
    44 <link rel=dataStoreItem href="gsasII-phase_files/item0058.xml"
    45 target="gsasII-phase_files/props059.xml">
     44<link rel=dataStoreItem href="gsasII-phase_files/item0054.xml"
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    5452  <w:TrackFormatting/>
     
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    19531833
    19541834<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 displayed
    1956 for this page has multiple tabs. The help information is broken down by tab
    1957 section. <o:p></o:p></span></p>
     1835is where to find help on the Phase Tree items in GSAS-II. Note that the window
     1836displayed for this page has multiple tabs. The help information is broken down
     1837by tab section. <o:p></o:p></span></p>
    19581838
    19591839<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
     
    19781858the unit cell parameters and overall parameters for the atom present in the
    19791859phase. 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>
     1860computing Fourier maps for this phase. It can also has the controls for Monte
     1861Carlo/Simulated Annealing for solving structures with flexible rigid molecular bodies..
     1862<span class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
     1863text-underline:none'><o:p></o:p></span></span></span></p>
    19831864
    19841865<h5 style='margin-left:.5in'>What can I do here?</h5>
     
    20081889map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this
    20091890procedure; 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 <span
    2011 class=GramE>shown</span> and the peaks will be shown on the structure drawing
    2012 for this phase as white 3-D crosses.<b><o:p></o:p></b></span></p>
     1891href="#Phase-Map_peaks">Map peaks</a>’ page. This page will immediately be
     1892shown, and the peaks will be shown on the structure drawing for this phase as
     1893white 3-D crosses.<b><o:p></o:p></b></span></p>
    20131894
    20141895<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     
    20191900style='mso-fareast-font-family:"Times New Roman"'>This performs a charge
    20201901flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution
    2021 using the method of <span class=SpellE>Oszlanyi</span> &amp; <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
     1902using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You
     1903will need to select a source for the reflection set and perhaps select an
     1904element for normalization by its form factor, a resolution limit (usually 0.5</span><span
     1905style='font-family:"Calibri",sans-serif;mso-fareast-font-family:"Times New Roman"'>Å</span><span
     1906style='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:
     1908normal'>General</b> window. There are also Test HKLs to show the progress in
     1909phasing with charge flipping cycles. They show the generally chaotic phase
     1910behavior before a solution is found; after that the phases are essentially
     1911fixed. No use is made of this information; it is just for your edification. A
    20271912progress bar showing the charge flip residual is shown while the charge flip is
    20281913in operation. When the residual is no longer decreasing (be patient – it
    20291914doesn’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 will
    2031 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>
     1915normal'>Cancel</b> button to stop the charge flipping, otherwise it will stop
     1916at 10000 cycles. The resulting map will be positioned to properly place
     1917symmetry operators (NB: depends on the quality of the resulting phases; the map
     1918could be still offset by a few steps), searched for peaks and the display
     1919shifts to <b style='mso-bidi-font-weight:normal'>Map peaks</b> to show them.<b><o:p></o:p></b></span></p>
    20351920
    20361921<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     
    20391924style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b><span
    20401925style='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 a
    2042 modulated structure.<o:p></o:p></span></p>
     1926style='mso-fareast-font-family:"Times New Roman"'>4-Dimensional<b> </b>charge
     1927flipping is done for a modulated structure.<o:p></o:p></span></p>
    20431928
    20441929<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     
    20571942style='mso-fareast-font-family:"Times New Roman"'> – Perform Monte
    20581943Carlo/Simulated Annealing structure solution using the model as set up in the
    2059 MC/SA tab.<o:p></o:p></span></p>
     1944MC/SA tab and the controls at the bottom of this tab.<o:p></o:p></span></p>
    20601945
    20611946<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     
    20841969</span></span></span><![endif]><b><span style='mso-fareast-font-family:"Times New Roman"'>Compare
    20851970– </span></b><span style='mso-fareast-font-family:"Times New Roman"'>Compares
    2086 idealized <span class=SpellE>polyhedra</span> (tetrahedron &amp; octahedron) to
    2087 those obtained from a Reverse Monte Carlo run.<b><o:p></o:p></b></span></p>
     1971idealized polyhedra (tetrahedron &amp; octahedron) to those obtained from a
     1972Reverse Monte Carlo run in RMCProfile.<b><o:p></o:p></b></span></p>
    20881973
    20891974<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     
    21051990style='mso-fareast-font-family:"Times New Roman"'>Protein quality</span></b><span
    21061991style='mso-fareast-font-family:"Times New Roman"'> – evaluate protein quality
    2107 by python versions of <span class=SpellE>errat</span> &amp; errat2 codes by <span
    2108 class=SpellE>Colovos</span>, C. &amp; <span class=SpellE>Yeates</span>, T.O. Protein
    2109 Science 2, 1511-1519 (1991).<b><o:p></o:p></b></span></p>
     1992by python versions of errat &amp; errat2 codes by Colovos, C. &amp; Yeates,
     1993T.O. Protein Science 2, 1511-1519 (1991).<b><o:p></o:p></b></span></p>
    21101994
    21111995<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
     
    21532037</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    21542038style='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>
     2039style='mso-fareast-font-family:"Times New Roman"'> – this should be set when the
     2040phase is initialized; it can be changed later. Be careful about the impact on
     2041Atom site symmetry and multiplicity if you do. GSAS-II will recognize any legal
     2042space group symbol using the short Hermann-Mauguin forms; put a space between
     2043the 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
     2045always uses the 2<sup>nd</sup> setting where the center of inversion is located
     2046at the origin. The choice of space group will set the available unit cell
     2047parameters.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    21652048
    21662049<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     
    22902173style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    22912174</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 then the Elements table is shown next on the General page; you may select the
    2294 isotope (only relevant for neutron diffraction experiments). The density (just
    2295 above the Elements) is computed depending on this choice, the unit cell volume
    2296 and the atom fractions/site multiplicities in the entries on the Atoms page.<span
     2175"Times New Roman"'>If there are entries in the Atoms tab, then the Elements
     2176table is shown next on the General page; you may select the isotope (only
     2177relevant for neutron diffraction experiments). The density (just above the
     2178Elements) is computed depending on this choice, the unit cell volume and the
     2179atom fractions/site multiplicities in the entries on the Atoms page.<span
    22972180class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    22982181
     
    23232206<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
    23242207auto;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"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    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>
     2208style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
     2209style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     2210style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Pawley
     2211dmin</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – This
     2212is the minimum d-spacing to be used in a Pawley refinement. <b
     2213style='mso-bidi-font-weight:normal'>NB:</b> be sure to set this to match the
     2214minimum d-spacing indicated by the powder pattern limits (see <b
     2215style='mso-bidi-font-weight:normal'>Limits</b> for the powder data set).<u><o:p></o:p></u></span></p>
    23352216
    23362217<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     
    23392220color:windowtext;text-decoration:none;text-underline:none'><span
    23402221style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     2222</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
     2223style='mso-fareast-font-family:"Times New Roman"'>Pawley dmax</span></b><span
     2224style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'> –
     2225This is the maximum d-spacing for reflections in a Pawley refinement. It is
     2226usually defined by the beginning of the data collection scan and will thus
     2227remove reflections that have too large d-spacing to be seen in the scan.</span><span
     2228class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
     2229color:windowtext'><o:p></o:p></span></span></p>
     2230
     2231<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     2232auto;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
     2233class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
     2234color:windowtext;text-decoration:none;text-underline:none'><span
     2235style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    23412236</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    23422237style='mso-fareast-font-family:"Times New Roman"'>Pawley neg. wt.</span></b><span
     
    23772272</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    23782273style='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 Pawley refinement or a Rietveld refinement.<span class=MsoHyperlink><span
     2274style='mso-fareast-font-family:"Times New Roman"'>– This is the source of structure
     2275factors to be used in a charge flip calculation. These may be either a single
     2276crystal data set, or structure factors extracted from a powder pattern via a
     2277Pawley or LeBail refinement or a Rietveld refinement.<span class=MsoHyperlink><span
    23832278style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    23842279
     
    23902285</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    23912286style='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 factor chosen to normalize the structure factors before charge flipping. <b
     2287style='mso-fareast-font-family:"Times New Roman"'>– This is an element form factor
     2288chosen to normalize the structure factors before charge flipping. <b
    23942289style='mso-bidi-font-weight:normal'>None</b> (the default) can be selected from
    23952290the lower right of the Periodic Table display shown when this is selected.<span
     
    24042299</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    24052300style='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>
     2301style='mso-fareast-font-family:"Times New Roman"'>– This is the step size of
     2302the charge flip map; default is 0.25</span><span style='font-family:"Calibri",sans-serif;
     2303mso-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
     2305zero filled to 2X this value; this suite of reflections is then used for charge
     2306flipping.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
     2307none;text-underline:none'><o:p></o:p></span></span></span></p>
    24112308
    24122309<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     
    24262323on the density map; all densities above this are charge flipped. In this way
    24272324the “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>
     2325problems and larger for heavy atom ones (typically 2X largest atom number).<o:p></o:p></span></p>
    24292326
    24302327<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     
    24352332style='mso-fareast-font-family:"Times New Roman"'>Test HKLs</span></b><span
    24362333style='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 of
    2438 charge flipping run.</span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     2334plot of phases for selected hkls are shown at end of charge flipping run. Just
     2335for you to look at.</span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    24392336
    24402337<p class=MsoListParagraphCxSpMiddle style='margin-left:73.2pt;mso-add-space:
     
    24532350This is the source of structure factors to be used in a charge flip
    24542351calculation. These may be either a single crystal data set, or structure
    2455 factors extracted from a powder pattern via a Pawley refinement or a Rietveld
    2456 refinement.<o:p></o:p></span></p>
     2352factors extracted from a powder pattern via a Pawley or Lebail refinement or a
     2353Rietveld refinement.<o:p></o:p></span></p>
    24572354
    24582355<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     
    24622359style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>d-min
    24632360</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 lower
    2465 than 2.0.</span></p>
     2361restricts the set of reflections to be used in the MC/SA run. Suggest using no
     2362lower than 2.0.</span></p>
    24662363
    24672364<p class=MsoListParagraphCxSpMiddle style='margin-left:121.5pt;mso-add-space:
     
    25182415<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
    25192416style='mso-fareast-font-family:"Times New Roman"'>An important transformation
    2520 may be needed in certain cases when space groups that two alternate origin
     2417may be needed in certain cases for space groups that have two alternate origin
    25212418settings (<a
    25222419href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#GSASIIspc.spg2origins">listed
     
    25262423a center of symmetry (creating a -x,-y,-z symmetry operator, which means that
    25272424reflection 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>
     2425settings because computations are much faster and simpler without complex structure
     2426factors. Alas, the literature contains a number of structures reported in
     2427Origin 1, where the origin choice may not be clearly communicated. (The CIF
     2428standard does not require that origin choice be indicated.) When a structure is
     2429imported that uses any of the space groups where an origin choice is possible,
     2430a message is shown in GSAS-II notifying the user that they must confirm that
     2431the origin choice is correct and then provides the opportunity to change
     2432origins. <o:p></o:p></span></p>
    25352433
    25362434<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
    25372435style='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 wrong
    2539 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>
     2436style='mso-fareast-font-family:"Times New Roman"'> An example of what can go
     2437wrong is illustrated with the structure of anatase. The space group is <i>I</i>
     24384<sub>1</sub>/<i>a m d</i>. In Origin 1 the coordinates are: <o:p></o:p></span></p>
    25412439
    25422440<table class=MsoNormalTable border=0 cellpadding=0 style='mso-cellspacing:1.5pt;
     
    25602458 <tr style='mso-yfti-irow:2'>
    25612459  <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>
    25642461  </td>
    25652462  <td style='padding:.75pt .75pt .75pt .75pt'>
     
    26142511 <tr style='mso-yfti-irow:2'>
    26152512  <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>
    26182514  </td>
    26192515  <td style='padding:.75pt .75pt .75pt .75pt'>
     
    26452541<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
    26462542style='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>
     2543windowtext'>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>
    26502545
    26512546<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
     
    26632558</v:shape><![endif]--><![if !vml]><img width=322 height=190
    26642559src="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 symmetry
    2666 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 to the right. <o:p></o:p></span></p>
     2560style='mso-fareast-font-family:"Times New Roman"'>GSAS-II always uses the
     2561symmetry operators for Origin 2; if the structure is input incorrectly with the
     2562coordinates set for Origin 1, there are several fairly obvious signs of
     2563problems: (1) the site symmetries and multiplicities are wrong, often giving an
     2564incorrect chemical formula, (2) the interatomic distances are incorrect, and
     2565(3) a plot of the structure is improbable. In this case incorrect
     2566multiplicities gives rise to a density of 7.9 g/cc, double the correct value.
     2567Impossible interatomic distances of 1.88Å for Ti-Ti, and 1.39Å for Ti-O are
     2568seen. The unit cell contents with the wrong space group operators is shown to
     2569the right. <o:p></o:p></span></p>
    26752570
    26762571<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
    26772572style='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/&quot;Show Distances &amp;
    2682 Angles&quot; menu item.) <o:p></o:p></span></p>
     2573the space group operations, the correct Ti-O distances are 1.92Å and 1.97Å and
     2574the shortest Ti-Ti distance is 3.0Å. (Note that interatomic distances can be
     2575computed in GSAS-II using the Phase Atoms tab and the Compute/&quot;Show
     2576Distances &amp; Angles&quot; menu item.) <o:p></o:p></span></p>
    26832577
    26842578<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
     
    26972591src="gsasII_files/xform.png" align=right v:shapes="Picture_x0020_4"><![endif]><b><span
    26982592style='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 &quot;Common transformations&quot;
    2702 pulldown menu, which will be setting 1-&gt;2 for space groups where both
    2703 origins are available, as shown to the right. The transformation matrix will be
    2704 set to the identity and the &quot;V&quot; vector will have the required origin
    2705 shift loaded. Press OK. The changes can be seen by selecting the Atoms tab. </span></p>
     2593style='mso-fareast-font-family:"Times New Roman"'> To transform a space group setting
     2594from Origin setting 1 to 2, use the Transform option in the Compute menu and
     2595then select the last option in the &quot;Common transformations&quot; pulldown
     2596menu, which will be setting 1-&gt;2 for space groups where both origins are
     2597available, as shown to the right. The transformation matrix will be set to the
     2598identity and the &quot;V&quot; vector will have the required origin shift
     2599loaded. Press OK. The changes can be seen by selecting the Atoms tab. </span></p>
    27062600
    27072601<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
     
    27142608
    27152609<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 <span
    2717 class=GramE>phase</span> and it allows the values and refinement flags to be
    2718 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 each
     2610tab serves several purposes. It is used to link histograms to the selected
     2611phase, and it allows the values and refinement flags to be set for the
     2612parameters that are defined for each histogram-phase pair, labeled as HAP
     2613parameters. [Note that some GSAS-II parameters are defined for each phase
     2614(atomic positions, for example), other parameters are defined for each
    27212615histogram (scale factors and instrumental constants, for example) but the HAP
    27222616parameters have values for each histogram in each phase.] It can also be used
     
    27242618
    27252619<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 peak
    2727 broadening: <span class=SpellE>microstrain</span> and crystallite size; a
    2728 LeBail intensity extraction flag; hydrostatic/elastic strain shifts to lattice
    2729 parameters; corrections to peak intensities due to experimental effects
    2730 (preferred orientation, extinction and disordered solvents).</p>
     2620HAP parameters include: the phase fraction; the sample contributions to peak
     2621broadening: microstrain and crystallite size; a LeBail intensity extraction
     2622flag; hydrostatic/elastic strain shifts to lattice parameters; corrections to
     2623peak intensities due to experimental effects (preferred orientation, extinction
     2624and disordered solvents).</p>
    27312625
    27322626<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
     
    27462640
    27472641<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><span
     2642style='mso-fareast-font-family:"Times New Roman"'>Start LeBail extraction </span></b><span
    27492643style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    27502644
    27512645<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
    27522646style='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> using
    2754 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 to their default (F<sup>2</sup> = 100).<o:p></o:p></span></p>
     2647intensities are set to values that are best fit using the LeBail intensity
     2648determination method rather than are computed from the atomic information for
     2649the phase. Cycling this setting will reset LeBail extracted intensities to
     2650their default (F<sup>2</sup> = 100).<o:p></o:p></span></p>
    27572651
    27582652<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
     
    27612655
    27622656<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: a
     2657style='mso-fareast-font-family:"Times New Roman"'>Used in powder histograms: a
    27642658multiplier 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
     2659histogram. It is proportional the number of unit cells of the phase in the
     2660sample. Note that when the histogram scale factor is varied, these values are
     2661on a relative scale. Conventional practice is to vary the scale factor and to
     2662not vary the phase fraction for one phase in a histogram. Do not refine the
    27682663scale factor and all phase fractions unless a constraint is defined so the
    27692664phase fractions add to 1. <o:p></o:p></span></p>
     
    27732668
    27742669<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 <span
    2776 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>
     2670style='mso-fareast-font-family:"Times New Roman"'>Used for single crystal data:
     2671relates F<sup>2</sup><sub>obs</sub> to F<sup>2</sup><sub>calc</sub>.<o:p></o:p></span></p>
    27772672
    27782673<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
     
    27822677<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
    27832678style='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 as
    2785 unity. Sizes can be computed in three ways: isotropic, uniaxial and
     2679factor(s) in microns (μm = 10<sup>-6</sup> m), with the Scherrer constant
     2680assumed as unity. Sizes can be computed in three ways: isotropic, uniaxial and
    27862681ellipsoidal. In isotropic broadening, crystallites are assumed to average as
    27872682uniform in all directions and a single size value is supplied; with uniaxial
     
    27912686perpendicular plane; with ellipsoidal, six terms are used to define a
    27922687broadening tensor that has arbitrary orientation -- this model may require
    2793 constraints and is seldomly needed. Note that size broadening is usually
    2794 Lorentzian, which corresponds to a <span class=SpellE>LGmix</span> value of
    2795 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><span
    2801 style='mso-fareast-font-family:"Times New Roman"'> peak broadening </span></b><span
     2688constraints and is seldom needed. Note that size broadening is usually
     2689Lorentzian, which corresponds to a LGmix value of 1.0; if this value is between
     26900. and 1., both Gaussian and Lorentz size broadening is modeled and a value of
     26910.0 is pure Gaussian. Values less than 0. or greater than 1. make no physical
     2692sense. Typical sensitivity is to no more than 4 μm; beyond that the particles
     2693are 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
     2696style='mso-fareast-font-family:"Times New Roman"'>Microstrain peak broadening </span></b><span
    28022697style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    28032698
    28042699<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
    28052700style='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>
     2701fraction of Δd/d (or equivalently ΔQ/Q) times 10<sup>6</sup>. Microstrain can
     2702be represented in three ways: isotropic, uniaxial and generalized. In isotropic
     2703broadening, microstrain broadening assumed to be the same in all
     2704crystallographic directions and a single value is supplied; with uniaxial
     2705broadening, a preferred direction (as a crystallographic axis, such as 0,0,1)
     2706is supplied -- note that for most crystal systems only one axis makes sense --
     2707and two microstrain parameters are defined, one for along the axis and one for
     2708in the perpendicular plane; with generalized, the Nicole Popa/Peter Stephens
     2709second-order expansion model is used and the number of terms will depend on the
     2710crystal system. It is typically possible to refine all terms when significant
     2711anisotropic strain broadening is present. Note that microstrain broadening is
     2712usually Lorentzian, which corresponds to a LGmix value of 1.0; if this value is
     2713between 0. and 1., both Gaussian and Lorentz broadening is modeled and a value
     2714of 0.0 is pure Gaussian. Values less than 0. or greater than 1. make no
     2715physical sense. Typical microstrain is ~1000.<o:p></o:p></span></p>
    28222716
    28232717<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
     
    28442738ways. Intensity corrections can be added to the model here or a full texture
    28452739model is possible with the &quot;<u><span style='color:blue'><a href="#Texture">Texture</a></span></u>&quot;
    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>
     2740tab (which usually requires multiple histograms at different sample orientations
     2741or detector settings). The approaches available here are March-Dollase, which
     2742requires a definition of a unique axis (in crystallographic coordinates) and
     2743the relative amount of excess or depletion of crystallites in that direction;
     2744or Spherical Harmonics, where the selection of an order determines the shape of
     2745the probability surface (which is always constrained to match the symmetry of
     2746the crystal system and the symmetry of the sample; here sample symmetry is
     2747assumed to be cylindrical). <o:p></o:p></span></p>
    28532748
    28542749<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
     
    28602755crystals/crystallites have minimal mosaic character, which results in lowering
    28612756of diffraction intensities for the most intense reflections. This is not
    2862 commonly seen in CW powder <span class=GramE>diffraction, but</span> can be
    2863 more apparent in neutron TOF data. For single crystal data the extinction model
    2864 is more complex allowing for primary and two types of secondary extinction.<o:p></o:p></span></p>
     2757commonly seen in CW powder diffraction but can be more apparent in neutron TOF
     2758data. For single crystal data the extinction model is more complex allowing for
     2759primary and two types of secondary extinction.<o:p></o:p></span></p>
    28652760
    28662761<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 &amp; B</span></b><span style='mso-fareast-font-family:
    2869 "Times New Roman"'><o:p></o:p></span></p>
     2762style='mso-fareast-font-family:"Times New Roman"'>Disordered solvent – Babinet
     2763A &amp; B</span></b><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    28702764
    28712765<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 <span
    2873 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 any other application. <o:p></o:p></span></p>
     2766style='mso-fareast-font-family:"Times New Roman"'>This correction, using the
     2767Babinet model, is typically used to treat scattering from solvent that is not
     2768well-ordered in protein structures. It probably makes no sense in most any
     2769other application. <o:p></o:p></span></p>
    28762770
    28772771<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
     
    28872781<h5 style='margin-left:.5in'>What can I do here?</h5>
    28882782
    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;
     2784margin-left:1.25in;text-indent:-.25in;mso-list:l4 level1 lfo3;tab-stops:list .5in'><![if !supportLists]><span
     2785style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     2786style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     2787style='mso-fareast-font-family:"Times New Roman"'>In this tab, menu items allow
    28912788copying 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>
     2789histograms 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;
     2792margin-left:1.25in;text-indent:-.25in;mso-list:l4 level1 lfo3;tab-stops:list .5in'><![if !supportLists]><span
     2793style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     2794style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     2795style='mso-fareast-font-family:"Times New Roman"'>The plot selection items
     2796allow for three dimensional representations of the microstrain or crystallite
     2797size distributions (which are spheres for isotropic treatments); preferred
     2798orientation can be plotted as a Psi scan (a plot of relative crystallite
     2799abundance for a particular reflection as a function of azimuthal angle) or as
     2800an inverse pole figure (which shows a stereographic projection of the
     2801probability distribution for different reciprocal lattice directions as viewed
     2802down the sample cylinder axis). For no texture/preferred orientation this
     2803figure would be flat = 1.0.<o:p></o:p></span></p>
    29032804
    29042805<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
     
    29162817
    29172818<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    2918 text-indent:-.25in;mso-list:l2 level1 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
     2819text-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
    29192820style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    29202821style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b>Atom
    2921 selection from table </b>- These are controlled by the mouse and the Shift/Ctrl/Alt
    2922 keys. Note that for most purposes (one exception is atom reordering which
    2923 requires an Alt-Left-click on the rows), selection of any cell for an atom will
    2924 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 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
     2822selection from table </b>- These are controlled by the mouse and the
     2823Shift/Ctrl/Alt keys. Note that for most purposes (one exception is atom
     2824reordering which requires an Alt-Left-click on the rows), selection of any cell
     2825for an atom will work equivalently with selection of the entire row. Upon
     2826selection the atoms will turn green in the structure drawing:</p>
     2827
     2828<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     2829auto;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
    29292830class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    29302831color:windowtext;text-decoration:none;text-underline:none'><span
     
    29372838
    29382839<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    2939 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
     2840auto;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
    29402841class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    29412842color:windowtext;text-decoration:none;text-underline:none'><span
     
    29492850
    29502851<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    2951 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
     2852auto;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
    29522853class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    29532854color:windowtext;text-decoration:none;text-underline:none'><span
     
    29602861
    29612862<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    2962 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
     2863auto;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
    29632864class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    29642865color:windowtext;text-decoration:none;text-underline:none'><span
     
    29702871atom selected. Use <b style='mso-bidi-font-weight:normal'>Alt LMB</b> again to
    29712872select 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> <b
    2973 style='mso-bidi-font-weight:normal'>Draw Atoms</b> list is not updated by this
    2974 change.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    2975 none;text-underline:none'><o:p></o:p></span></span></span></p>
     2873table will be updated to show the change. NB: the <b style='mso-bidi-font-weight:
     2874normal'>Draw Atoms</b> list is not updated by this change.<span
     2875class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
     2876text-underline:none'><o:p></o:p></span></span></span></p>
    29762877
    29772878<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    2978 auto;text-indent:-.25in;mso-list:l2 level1 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
     2879auto;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
    29792880class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    29802881color:windowtext;text-decoration:none;text-underline:none'><span
    29812882style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    29822883</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 is
    2984 shown that allows you to select all atoms with that type. <span
    2985 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>
     2884left click a Type column heading</b>: a dialog box is shown that allows you to
     2885select all atoms with that type. <span class=MsoHyperlink><span
     2886style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
     2887none;text-underline:none'><o:p></o:p></span></span></p>
    29872888
    29882889<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    2989 auto;text-indent:-.25in;mso-list:l2 level1 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
     2890auto;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
    29902891class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    29912892color:windowtext;text-decoration:none;text-underline:none'><span
     
    29982899
    29992900<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    3000 auto;text-indent:-.25in;mso-list:l2 level1 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
     2901auto;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
    30012902class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    30022903color:windowtext;text-decoration:none;text-underline:none'><span
     
    30072908the mouse (<b style='mso-bidi-font-weight:normal'>Alt</b> ignored, <b
    30082909style='mso-bidi-font-weight:normal'>Shift</b> &amp; <b style='mso-bidi-font-weight:
    3009 normal'>Ctrl</b> allow selection of multiple <span class=GramE>cells</span> but
    3010 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 is
     2910normal'>Ctrl</b> allow selection of multiple cells but no use is made of them).
     2911An individual data item can be cut/pasted anywhere including from/to another
     2912document. Bad entries are rejected (yellow background). If any entry is
    30122913changed, press <b style='mso-bidi-font-weight:normal'>Enter</b> key or select
    30132914another atom entry to apply the change.<span class=MsoHyperlink><span
     
    30152916
    30162917<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3017 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
     2918auto;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
    30182919class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    30192920color:windowtext;text-decoration:none;text-underline:none'><span
     
    30262927
    30272928<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3028 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
     2929auto;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
    30292930class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    30302931color:windowtext;text-decoration:none;text-underline:none'><span
     
    30382939
    30392940<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3040 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
     2941auto;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
    30412942class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    30422943color:windowtext;text-decoration:none;text-underline:none'><span
     
    30502951
    30512952<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3052 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
     2953auto;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
    30532954class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    30542955color:windowtext;text-decoration:none;text-underline:none'><span
    30552956style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    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
     2958style='mso-fareast-font-family:"Times New Roman"'>x,y,z</span></b><span
    30592959style='mso-fareast-font-family:"Times New Roman"'> – change atom coordinate.
    30602960Fractions (e.g. 1/3, 1/4) are allowed.<span class=MsoHyperlink><span
     
    30622962
    30632963<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3064 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
     2964auto;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
    30652965class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    30662966color:windowtext;text-decoration:none;text-underline:none'><span
    30672967style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    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
     2969style='mso-fareast-font-family:"Times New Roman"'>frac,Uiso,Uij</span></b><span
    30712970style='mso-fareast-font-family:"Times New Roman"'> – change these values;
    30722971fractions (e.g. 1/3, 1/4) are allowed.<span class=MsoHyperlink><span
     
    30742973
    30752974<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3076 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
     2975auto;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
    30772976class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    30782977color:windowtext;text-decoration:none;text-underline:none'><span
     
    30812980style='mso-fareast-font-family:"Times New Roman"'>I/A</span></b><span
    30822981style='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>
     2982style='mso-bidi-font-weight:normal'>I</b>(sotropic) or <b style='mso-bidi-font-weight:
     2983normal'>A</b>(nisotropic); the <b style='mso-bidi-font-weight:normal'>Uiso/Uij</b>
     2984entries will change appropriately. <span class=MsoHyperlink><span
     2985style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    30892986
    30902987<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    3091 auto;text-indent:-.25in;mso-list:l2 level1 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
     2988auto;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
    30922989style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    30932990style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     
    30972994
    30982995<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3099 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
     2996auto;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
    31002997style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    31012998style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b>On
     
    31033000
    31043001<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    3105 auto;text-indent:-.25in;mso-list:l2 level4 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
     3002auto;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
    31063003style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    31073004style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b
     
    31103007
    31113008<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    3112 auto;text-indent:-.25in;mso-list:l2 level4 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
     3009auto;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
    31133010style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    31143011style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b
    31153012style='mso-bidi-font-weight:normal'>Modify parameters</b> – A popup dialog box
    31163013appears 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>
     3014selected atoms. <b style='mso-bidi-font-weight:normal'>Name</b> will rename
     3015selected atoms according to position in table (e.g. Na(1) for Na atom as 1<sup>st</sup>
     3016atom in list in row ‘0’). <b style='mso-bidi-font-weight:normal'>Type</b> will
     3017give periodic table popup; selected element valence will be used for all
     3018selected atoms and atoms names will be changed. <b style='mso-bidi-font-weight:
     3019normal'>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
     3021be applied to the parameter for all selected atoms. <b style='mso-bidi-font-weight:
     3022normal'>Uiso</b> and <b style='mso-bidi-font-weight:normal'>frac</b> will give
     3023popup for new value to be used for all selected atoms. </p>
    31293024
    31303025<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    3131 auto;text-indent:-.25in;mso-list:l2 level4 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
     3026auto;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
    31323027style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    31333028style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b>Set
     
    31353030
    31363031<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    3137 auto;text-indent:-.25in;mso-list:l2 level4 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
     3032auto;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
    31383033style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    31393034style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b
     
    31423037
    31433038<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    3144 auto;text-indent:-.25in;mso-list:l2 level4 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
     3039auto;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
    31453040style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    31463041style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b
    3147 style='mso-bidi-font-weight:normal'>Insert atom</b> – insert an H atom (name= <span
    3148 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>
     3042style='mso-bidi-font-weight:normal'>Insert atom</b> – insert an H atom (name=
     3043Unk) at 0,0,0 before the selected atom, it is also drawn as an H atom in the
     3044structure plot (small white ball).</p>
    31503045
    31513046<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    3152 auto;text-indent:-.25in;mso-list:l2 level4 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
     3047auto;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
    31533048style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span
    31543049style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b
    31553050style='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
     3052the viewpoint, it is also drawn as an H atom in the structure plot.</p>
    31593053
    31603054<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    3161 auto;text-indent:-.25in;mso-list:l2 level4 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
     3055auto;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
    31623056style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>7.<span
    31633057style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b
     
    31663060
    31673061<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    3168 auto;text-indent:-.25in;mso-list:l2 level4 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
     3062auto;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
    31693063style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>8.<span
    31703064style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b
     
    31733067
    31743068<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    3175 auto;text-indent:-.25in;mso-list:l2 level4 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
     3069auto;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
    31763070style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>9.<span
    31773071style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b
     
    31793073appears; select space group operator/unit cell translation to apply to the
    31803074selected 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 <span
    3182 class=SpellE>noncentrosymmetric</span> structure. NB: many of these operations
    3183 only make sense if all atoms are selected.</p>
     3075and optionally generate a new set of atom positions. You may also invert a
     3076noncentrosymmetric structure. NB: many of these operations only make sense if
     3077all atoms are selected.</p>
    31843078
    31853079<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    3186 auto;text-indent:-.25in;mso-list:l2 level4 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
     3080auto;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
    31873081style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>10.<span
    31883082style='font:7.0pt "Times New Roman"'>&nbsp; </span></span></span><![endif]><b
     
    31913085
    31923086<p class=MsoListParagraphCxSpMiddle style='margin-left:2.0in;mso-add-space:
    3193 auto;text-indent:-.25in;mso-list:l2 level4 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
     3087auto;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
    31943088style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>11.<span
    31953089style='font:7.0pt "Times New Roman"'>&nbsp; </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
     3090style='mso-bidi-font-weight:normal'>Select from list </b>– A popup appears allowing
     3091selection of atoms for further changes. Selected atoms will turn green.</p>
     3092
     3093<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3094auto;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
    32023095style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    32033096style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3204 style='mso-bidi-font-weight:normal'>Append atom</b> – add an H atom (name= <span
    3205 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 the structure plot.</p>
    3207 
    3208 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3209 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
     3097style='mso-bidi-font-weight:normal'>Append atom</b> – add an H atom (name= Unk)
     3098at 0,0,0 to the end of the atom table, it is also drawn as an H atom in the
     3099structure plot.</p>
     3100
     3101<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3102auto;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
    32103103style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    32113104style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    32123105style='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
     3106Unk) to the end of the atom table with coordinates matching the location of the
     3107viewpoint, 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:
     3110auto;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
    32193111style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    32203112style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </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
     3113style='mso-bidi-font-weight:normal'>Update H atoms </b>– Reset H-atoms
     3114according to bonding geometry; only applies to H-atoms initially placed via
     3115Calc H-atoms. Usually used after running a structure refinement.</p>
     3116
     3117<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3118auto;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
    32253119style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    32263120style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b>Assemble
    3227 molecule</b> – move atoms to create single <span class=GramE>molecule;</span>
    3228 not appropriate for extended structures.</p>
    3229 
    3230 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3231 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
     3121molecule</b> – move atoms to create single molecule, not appropriate for
     3122extended structures.</p>
     3123
     3124<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3125auto;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
    32323126style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    32333127style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    32363130
    32373131<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3238 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
     3132auto;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
    32393133style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
    32403134style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    32413135style='mso-bidi-font-weight:normal'>Reload draw atoms</b> – reload drawing
    3242 atoms from current atom list.</p>
     3136atoms from current atom list. Generally needed after a refinement.</p>
     3137
     3138<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3139auto;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
     3140style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span
     3141style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     3142style='mso-bidi-font-weight:normal'>Reimport atoms </b>– from any importable phase
     3143file (e.g. cif, gpx)</p>
    32433144
    32443145<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    3245 auto;text-indent:-.25in;mso-list:l2 level1 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
     3146auto;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
    32463147style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span
    32473148style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu<b
     
    32493150
    32503151<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3251 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
     3152auto;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
    32523153style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    32533154style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    32543155style='mso-bidi-font-weight:normal'>Show Distances &amp; 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
     3156distances and angles with esds (if possible) for selected atoms. A popup dialog
     3157box will appear with distance angle controls. NB: if atoms have been added or
     3158their type changed, you may need to do a <b style='mso-bidi-font-weight:normal'>Reset</b>
     3159of this dialog box before proceeding.</p>
     3160
     3161<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3162auto;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
    32633163style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    32643164style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    32653165style='mso-bidi-font-weight:normal'>Save Distances &amp; 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
     3166a. but reports result to a file with extension “.disagl”.</p>
     3167
     3168<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3169auto;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
    32713170style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    32723171style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b>Histogram
     
    32753174
    32763175<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3277 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
     3176auto;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
    32783177style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    32793178style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b>Apportion
     
    32833182
    32843183<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3285 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
     3184auto;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
    32863185style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    32873186style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b>Density
     
    32893188
    32903189<p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto;
    3291 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
     3190text-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
    32923191style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    32933192style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    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 &amp; 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
     3194available the ISODISTORT mode displacement constraints available. This will
     3195compute the mode displacements for the current atom positions and display them
     3196in 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
     3201displayed only if the Draw Options or Draw Atoms tabs are visited first. When back
     3202at the Atoms tab, the following are applicable and use of the mouse buttons
     3203changes 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 &amp;
     3211y <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
     3219assigned to the viewpoint (which is kept at the center of the drawing). The
     3220structure will appear to translate. The viewpoint can also be entered directly
     3221in 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
     3229perpendicular 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
     3237in/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
     3245the left mouse button causes that atom to be selected (Shift + a Right click
     3246does the same). Any previously selected atoms will be reset. If two atoms are
     3247overlapped in the current view, then the top-most atom will usually be
     3248selected. Only atoms in the asymmetric unit can be selected from the plot in
     3249this 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
     3257the right mouse button causes the atom to be selected if previously unselected
     3258and unselected if previously selected. Any previously selected atoms will be
     3259continue to be selected so shift-right click can be used to add atoms to the
     3260selection list. If two atoms are overlapped in the current view, then the
    33223261top-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>
     3262be selected from the plot in this way. (On a Mac, control+mouse click is an
     3263alternate 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 &quot;n&quot; key selects the next atom in the
     3271displayed 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 &quot;p&quot; key selects the previous atom in
     3279the 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 &quot;c&quot; key sets the plot viewpoint at
     3287unit 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
     3294schemes for the slice contours. Default – “Paired” (Green – positive, red –
     3295negative &amp; 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
     3302contouring 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
     3309positive 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
     3317z-direction (toward from viewer). If structure is incommensurate, “-” steps the
     3318structure 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
    33473322<h5 style='margin-left:.5in'>What can I do here?</h5>
    33483323
    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 &amp; 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
     3325access to a number of items that control how the structure is displayed. If a
     3326map is available (Fourier of charge flipping), one can display a 10<span
     3327style='font-family:"Calibri",sans-serif'>Å</span>x10<span style='font-family:
     3328"Calibri",sans-serif'>Å</span> contoured slice centered at the viewpoint.
     3329Contouring done as lines, colors or lines &amp; colors combined. 3-D contouring
     3330is also available as green (red for negative density) map grid points. One can
     3331also 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
     3336structure is generated. The way that the structure is displayed is determined
     3337according to the controls in this page as well as the options on the <a
     3338href="#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
     3343viewing a crystal structure changes the view of the structure; see Atoms or
     3344Draw Atoms for details</p>
     3345
     3346<h4 style='margin-left:.25in'><a name="Phase-Draw_Atoms"></a><a
     3347name="_Draw_Atoms"></a><u>Draw Atoms</u></h4>
    33873348
    33883349<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
    33893350gives a list of the atoms and bonds that are to be rendered as lines, van der
    3390 Waals radii balls, sticks, balls &amp; sticks, ellipsoids &amp; 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>
     3351Waals radii balls, sticks, balls &amp; sticks, ellipsoids &amp; sticks or
     3352polyhedra. There are four menus for this tab; Edit allows modification of the
     3353list of atoms to be rendered, Compute gives some options for geometric
     3354characterization of selected atoms, Restraints allows definition of 4 different
     3355types of restraints on the structure and Rigid body allows selection of atoms
     3356that form a previously defined rigid body.</p>
    33943357
    33953358<h5 style='margin-left:.5in'>What can I do here?</h5>
    33963359
    33973360<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    3398 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
     3361text-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
    33993362style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    34003363style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    34093372
    34103373<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    3411 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
     3374auto;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
    34123375style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    34133376style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3414 style='mso-bidi-font-weight:normal'>Atom Selection from plot</b>: select an
    3415 atom by a left click of the mouse while holding down the Shift key and pointed
    3416 at the center of the displayed atom, it will turn green if successful and the
     3377style='mso-bidi-font-weight:normal'>Atom Selection from drawing</b>: select an
     3378atom by a left click of the mouse while holding down the Shift key and pointed at
     3379the center of the displayed atom, it will turn green if successful and the
    34173380corresponding entry in the table will be highlighted (in grey); any previous
    3418 selections will be cleared. To add <span class=GramE>to .your</span> selection
    3419 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 the selection process.</p>
     3381selections will be cleared. To add to your selection, use the right mouse
     3382button (Shift down); if a previously selection is reselected it is removed from
     3383the selection list. <b style='mso-bidi-font-weight:normal'>NB</b>: beware of
     3384atoms that are hiding behind the one you are trying to select they may be
     3385selected inadvertently. You can rotate the structure anytime during the
     3386selection process.</p>
    34243387
    34253388<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    3426 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
     3389auto;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
    34273390style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    34283391style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </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>
     3392style='mso-bidi-font-weight:normal'>Double left click a Name, Type and Sym Op
     3393column heading</b>: a dialog box is shown that allows you to select all atoms
     3394with that characteristic. For example, selecting the Type column will show all
     3395the atom types; your choice will then cause all those atoms to be selected.</p>
    34343396
    34353397<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    3436 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
     3398auto;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
    34373399style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    34383400style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </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>
     3401style='mso-bidi-font-weight:normal'>Double left click a Style, Label or Color
     3402column</b>: a dialog box is shown that allows you to select a rendering option
     3403for all the atoms. For Color a color choice dialog is displayed that covers the
     3404entire 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
     3406press OK. <b style='mso-bidi-font-weight:normal'>NB</b>: selecting Color will
     3407make all atoms have the same color and for Style “blank” means the atoms aren’t
     3408rendered and thus the drawing will not show any atoms or bonds!</p>
    34483409
    34493410<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    3450 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
     3411auto;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
    34513412style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    34523413style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     
    34543415operations that can be performed on your selected atoms. You must select one or
    34553416more 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
     3417accessed 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:
     3420auto;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
    34613421style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    34623422style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    34653425
    34663426<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3467 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
     3427auto;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
    34683428style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    34693429style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3470 style='mso-bidi-font-weight:normal'>Atom label</b> – select the item to be shown
    3471 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 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
     3430style='mso-bidi-font-weight:normal'>Atom label</b> – select the item to be
     3431shown as a label for each atom in selection. The choices are: none, type, name
     3432or number. (NB: atom labelling slows drawing response time).</p>
     3433
     3434<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3435auto;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
    34763436style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    34773437style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    34823442
    34833443<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3484 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
     3444auto;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
    34853445style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    34863446style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    34893449
    34903450<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3491 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
     3451auto;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
    34923452style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    34933453style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </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
     3454style='mso-bidi-font-weight:normal'>Edit atom radii </b>– modify atom radii
     3455used in the bond assignment algorithm.</p>
     3456
     3457<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3458auto;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
    34983459style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    34993460style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    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
     3462point</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:
     3465auto;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
    35063466style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
    35073467style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </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
     3468style='mso-bidi-font-weight:normal'>Select from list </b>– select atoms from a
     3469popup list of names.</p>
     3470
     3471<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3472auto;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
    35123473style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span
    35133474style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    35163477symmetry operator and unit cell translation selected via a dialog display.
    35173478Duplicate 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 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
     3479parameters (Uij) will be transformed as appropriate.</p>
     3480
     3481<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3482auto;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
    35223483style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span
    35233484style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    35243485</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
     3486sphere of atoms </b>– fill in all equivalent atoms that fall within a sphere of
     3487selected radius about selected atoms.</p>
     3488
     3489<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3490auto;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
    35293491style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span
    35303492style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    35323494draw atoms</b> – apply a symmetry operator and unit cell translation to the set
    35333495of 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
     3496displacement parameters (Uij) will be transformed as appropriate.</p>
     3497
     3498<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3499auto;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
    35393500style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>k.<span
    35403501style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    35423503currently in the draw atom table, find all atoms that belong in the
    35433504coordination 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 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
     3505symmetry 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:
     3508auto;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
    35483509style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>l.<span
    35493510style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    35543515
    35553516<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3556 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
     3517auto;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
    35573518style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>m.<span
    35583519style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp; </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
     3520style='mso-bidi-font-weight:normal'>Complete molecule </b>– beginning with a
     3521selected atom, transform other atoms to equivalent positions that form a
     3522contiguous molecule. Not appropriate for continuous structures (a warning will
     3523appear)</p>
     3524
     3525<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3526auto;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
    35633527style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>n.<span
    35643528style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </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
     3529style='mso-bidi-font-weight:normal'>Create void map </b>– by using a grid of
     3530probe positions, locate points outside of normal contact distances within a
     3531structure. Result is a mesh of small blue points in structural voids (e.g. possible
     3532locations of missing water molecules).</p>
     3533
     3534<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3535auto;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
    35693536style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>o.<span
    35703537style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    35743541
    35753542<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3576 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
     3543auto;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
    35773544style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>p.<span
    35783545style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </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
     3546style='mso-bidi-font-weight:normal'>Update draw atoms </b>– refresh the drawn
     3547atom positions from the Atoms list.</p>
     3548
     3549<p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto;
     3550text-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
    35833551style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>q.<span
    35843552style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </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
     3553style='mso-bidi-font-weight:normal'>Load selected atoms </b>- refresh the selected
     3554drawn 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>&nbsp;</o:p></p>
     3557
     3558<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
     3559text-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
    35893560style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>6.<span
    35903561style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
    35913562‘<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 must
    3593 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 lfo10;tab-stops:list 1.0in'><![if !supportLists]><span
     3563choice of geometric calculations to be performed with the selected atoms. You
     3564must select the appropriate number of atoms for these to work and the
     3565computation is done for the atoms in selection order.</p>
     3566
     3567<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3568auto;text-indent:-.25in;mso-list:l5 level2 lfo7;tab-stops:list 1.0in'><![if !supportLists]><span
    35983569style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    35993570style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    36003571style='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 the console window.</p>
    3603 
    3604 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    3605 auto;text-indent:-.25in;mso-list:l5 level2 lfo10;tab-stops:list 1.0in'><![if !supportLists]><span
     3572distance from view-point to all selected draw atoms; result is given on the
     3573console window.</p>
     3574
     3575<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     3576auto;text-indent:-.25in;mso-list:l5 level2 lfo7;tab-stops:list 1.0in'><![if !supportLists]><span
    36063577style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    36073578style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    36093580normal'>Tors. </b>– when 2-4 atoms are selected, a distance, angle or torsion
    36103581angle 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 &amp; pasted to another application (e.g. Microsoft
    3616 Word).</p>
     3582selection order. The torsion angle is a right-hand angle about the A2-A3 vector
     3583for the sequence of atoms A1-A2-A3-A4. An estimated standard deviation is given
     3584for the calculated value if a current variance-covariance matrix is available.
     3585The result is shown on the console window; it may be cut &amp; pasted to
     3586another application (e.g. Microsoft Word).</p>
    36173587
    36183588<p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto;
    3619 text-indent:-.25in;mso-list:l5 level2 lfo10;tab-stops:list 1.0in'><![if !supportLists]><span
     3589text-indent:-.25in;mso-list:l5 level2 lfo7;tab-stops:list 1.0in'><![if !supportLists]><span
    36203590style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    36213591style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    36343604unweighted center of the selected atoms.</p>
    36353605
    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
     3607restraints may be generated by selecting atoms and the corresponding restraint
     3608type from the menu</p>
     3609
     3610<p class=MsoNormal style='margin-left:1.5in;text-indent:-.25in'>a. <b>Add bond
     3611restraint</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
     3614restraint</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
     3617restraint</b> – for selected 4 or more atoms</p>
     3618
     3619<p class=MsoNormal style='margin-left:1.5in;text-indent:-.25in'>d. <b>Add
     3620chiral restrain</b>t – for selected 4 atoms; chiral atom first followed by 3
     3621other atoms; if selected in righthand sequence, chiral volume will be &gt; 0.</p>
     3622
     3623<p class=MsoNormal><span style='mso-tab-count:1'>            </span>8. Menu ‘<b>Rigid
     3624body</b>’/’<b>Define rigid body</b>’ – assign a previously defined rigid body
     3625to selected atoms.</p>
     3626
     3627<h5 style='margin-left:.5in'>What is drawn here?</h5>
    36373628
    36383629<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 &amp; y
    3652 <DT><b>Right drag</b>:
    3653 <DD>Holding down right button
     3630drawing that shows the atoms of the crystal structure is generated. The atoms
     3631are displayed according to the controls in the in this page as well as options
     3632on 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
     3637viewing 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
     3640style='mso-fareast-font-family:"Times New Roman"'>Left drag</span></b></a><span
     3641style='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
     3645style='mso-fareast-font-family:"Times New Roman"'>Holding down left button
     3646rotates axes around screen x &amp; 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
     3649style='mso-fareast-font-family:"Times New Roman"'>Right drag</span></b></span><span
     3650style='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
     3654style='mso-fareast-font-family:"Times New Roman"'>Holding down right button
    36543655translates 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
     3656at the center of the drawing). The structure will appear to translate. The
     3657viewpoint 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
     3660style='mso-fareast-font-family:"Times New Roman"'>Middle drag</span></b></span><span
     3661style='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
     3665style='mso-fareast-font-family:"Times New Roman"'>Holding down center button
     3666rotates 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
     3669style='mso-fareast-font-family:"Times New Roman"'>Mouse Wheel</span></b></span><span
     3670style='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
     3674style='mso-fareast-font-family:"Times New Roman"'>Rotating the scroll wheel
     3675changes “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
     3678style='mso-fareast-font-family:"Times New Roman"'>Shift+Left Click</span></b></span><span
     3679style='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
     3683style='mso-fareast-font-family:"Times New Roman"'>Holding down the shift key
    36643684while clicking on an atom with the left mouse button causes that atom to be
    36653685selected (Shift + a Right click does the same). Any previously selected atoms
    36663686will 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 &quot;Atoms&quot; or &quot;Draw Atoms&quot; phase be displayed.
    3669 <DT><b>Shift+Right click</b>:
    3670 <DD>Holding down the shift key
     3687top-most atom will usually be selected. Only atoms in the asymmetric unit can
     3688be 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
     3691style='mso-fareast-font-family:"Times New Roman"'>Shift+Right click</span></b></span><span
     3692style='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
     3696style='mso-fareast-font-family:"Times New Roman"'>Holding down the shift key
    36713697while 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 &quot;Atoms&quot;
    3678   or &quot;Draw Atoms&quot; 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>
     3698selected if previously unselected and unselected if previously selected. Any
     3699previously selected atoms will be continue to be selected so shift-right click
     3700can be used to add atoms to the selection list. If two atoms are overlapped in
     3701the current view, then the top-most atom will usually be selected. Only atoms
     3702in the asymmetric unit can be selected from the plot in this way. (On a Mac, control+mouse
     3703click 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
     3706style='mso-fareast-font-family:"Times New Roman"'>Key n</span></b></span><span
     3707style='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
     3711style='mso-fareast-font-family:"Times New Roman"'>Pressing the &quot;n&quot;
     3712key 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
     3715style='mso-fareast-font-family:"Times New Roman"'>Key p</span></b></span><span
     3716style='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
     3720style='mso-fareast-font-family:"Times New Roman"'>Pressing the &quot;p&quot;
     3721key 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
     3724style='mso-fareast-font-family:"Times New Roman"'>Key c</span></b></span><span
     3725style='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
     3729style='mso-fareast-font-family:"Times New Roman"'>Pressing the &quot;c&quot;
     3730key sets the plot viewpoint at unit cell center. Also resets n/p selection item
     3731to 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
     3734style='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
     3737style='mso-fareast-font-family:"Times New Roman"'>Pressing the “s” key brings
     3738up a (large) selection of color schemes for the slice contours. Default – “Paired”
     3739(Green – positive, red – negative &amp; 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
     3742style='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
     3745style='mso-fareast-font-family:"Times New Roman"'>Pressing the “k” key cycles
     3746through the possible slice contouring options (none, lines, colors,
     3747lines+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
     3750style='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
     3753style='mso-fareast-font-family:"Times New Roman"'>Pressing the “+” (or “=”) key
     3754steps the viewpoint in positive drawing z-direction (away from viewer). If
     3755structure is incommensurate, “+” steps the structure and map through the 4<sup>th</sup>
     3756dimension (+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
     3759style='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
     3762style='mso-fareast-font-family:"Times New Roman"'>Pressing the “-“ key steps
     3763the viewpoint in negative drawing z-direction (toward from viewer). If
     3764structure is incommensurate, “-” steps the structure and map through the 4<sup>th</sup>
     3765dimension (-tau).<o:p></o:p></span></span></p>
     3766
     3767<h4 style='margin-left:.25in'><span style='mso-bookmark:Phase-RB_Models'>RB
     3768Models</span></h4>
    36853769
    36863770<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
     
    36893773It also allows control of the location of the rigid body and in this phase</p>
    36903774
    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>
    36923776
    36933777<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
    36943778of 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 &amp; 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 &quot;Sticks&quot; or &quot;Ball-and-Sticks.&quot; The rigid body will be
    3717 displayed as &quot;Ball-and-Sticks&quot; 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 &amp; 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 &amp; y directions (rotate the plot to see and move in the rigid body in the
    3736 third direction.) Pressing the &quot;Lock&quot; 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>
     3779structure:</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 &amp;
     3787y <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
     3795coordinates assigned to the viewpoint (which is kept at the center of the
     3796plot). The structure will appear to translate. The viewpoint can also be
     3797entered 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
     3813in/out) <o:p></o:p></span></p>
     3814
     3815<p style='margin-left:1.0in'>When a rigid body is being inserted into a
     3816structure, both the rigid body and the crystal structure are displayed. It is
     3817useful to plan for this by preselecting the atoms in the Draw Atoms list and to
     3818have atoms displayed as &quot;Sticks&quot; or &quot;Ball-and-Sticks.&quot; The
     3819rigid body will be displayed as &quot;Ball-and-Sticks&quot; but bonds will be
     3820in green. Use of the Alt key causes the above mouse movements to reposition the
     3821rigid 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
     3829down rotates the rigid body around screen x &amp; 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
     3837down 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
     3845down translates the rigid body in the screen x &amp; y directions (rotate the
     3846plot to see and move in the rigid body in the third direction.) Pressing the
     3847&quot;Lock&quot; checkbox next to the origin location prevents the origin from
     3848being 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
     3851name=Phase-Texture></a>Texture</h4>
    37433852
    37443853<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>&nbsp;</o:p></p>
     
    37613870analysis using GSAS-II employs spherical harmonics modeling, as described by
    37623871Bunge, &quot;Texture Analysis in Materials Science&quot; (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>
     3872implemented by Von Dreele, J. Appl. Cryst., <b style='mso-bidi-font-weight:
     3873normal'>30</b>, 517-525 (1997) in GSAS. The even part of the orientation
     3874distribution function (ODF) via the general axis equation</p>
    37673875
    37683876<p class=MsoNormal style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
     
    38944002of a unit vector coincident with h relative to the reciprocal lattice. For most
    38954003crystal 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 of
    3897 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 (usually the
    3899 a-axis) onto the normal plane.<span style='mso-spacerun:yes'>  </span>In a
    3900 similar way the sample harmonic factor, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
     4004between h and the n-th order major rotation axis of the space group (usually
     4005the c-axis) and <span style='font-family:Symbol'>b</span> is the angle between
     4006the projections of h and any secondary axis (usually the a-axis) onto the
     4007normal plane.<span style='mso-spacerun:yes'>  </span>In a similar way the
     4008sample harmonic factor, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
    39014009   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    39024010   mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
     
    39954103a diffraction experiment the crystal reflection coordinates (<span
    39964104style='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 the diffraction plane and J is coincident with the direction of the incident
     4105are determined by the choice of reflection index (hkl) while the sample
     4106coordinates (<span style='font-family:Symbol'>y</span>, <span style='font-family:
     4107Symbol'>g</span>) are determined by the sample orientation on the
     4108diffractometer. To define the sample coordinates (<span style='font-family:
     4109Symbol'>y</span>, <span style='font-family:Symbol'>g</span>), we have defined
     4110an instrument coordinate system (I, J, K) such that K is normal to the
     4111diffraction plane and J is coincident with the direction of the incident
    40044112radiation beam toward the source. We further define a standard set of
    40054113right-handed eulerian goniometer angles (<span style='font-family:Symbol'>W</span>,
     
    40154123<span style='font-family:Symbol'>C</span><sub>s</sub>, <span style='font-family:
    40164124Symbol'>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 rotation
    4018 angles are defined so that with the goniometer angles at zero <span
     4125K<sub>s</sub>) to (I, J, K).<span style='mso-spacerun:yes'>  </span>The sample
     4126rotation angles are defined so that with the goniometer angles at zero <span
    40194127style='font-family:Symbol'>W</span><sub>s</sub> and <span style='font-family:
    40204128Symbol'>F</span><sub>s</sub> are rotations about K and <span style='font-family:
     
    40354143normal'><span style='font-family:Symbol'>F</span>+</b><b style='mso-bidi-font-weight:
    40364144normal'><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><span
    4038 class=SpellE><sub>s</sub><span style='font-family:Symbol'>W</span><sub>s</sub></span><o:p></o:p></b></p>
     4145style='mso-bidi-font-weight:normal'><span style='font-family:Symbol'>C</span><sub>s</sub></b><b
     4146style='mso-bidi-font-weight:normal'><span style='font-family:Symbol'>W</span><sub>s</sub><o:p></o:p></b></p>
    40394147
    40404148<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
     
    40454153
    40464154<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'><span
    4048 class=GramE><i>cos</i>(</span><span style='font-family:Symbol'>y</span>) = <!--[if gte msEquation 12]><m:oMath><i
     4155margin-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
     4156style='font-family:Symbol'>y</span>) = <!--[if gte msEquation 12]><m:oMath><i
    40494157 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
    40504158   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
     
    40974205top:15.0pt;mso-text-raise:-15.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    40984206EN-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'>
    41004208 <v:imagedata src="gsasII-phase_files/image015.png" o:title="" chromakey="white"/>
    41014209</v:shape><![endif]--><![if !vml]><img width=107 height=67
     
    41164224top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    41174225EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
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    41194227 <v:imagedata src="gsasII-phase_files/image017.png" o:title="" chromakey="white"/>
    41204228</v:shape><![endif]--><![if !vml]><img width=61 height=35
     
    41324240top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    41334241EN-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'>
    41354243 <v:imagedata src="gsasII-phase_files/image019.png" o:title="" chromakey="white"/>
    41364244</v:shape><![endif]--><![if !vml]><img width=58 height=35
     
    41484256top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    41494257EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
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    41514259 <v:imagedata src="gsasII-phase_files/image017.png" o:title="" chromakey="white"/>
    41524260</v:shape><![endif]--><![if !vml]><img width=61 height=35
     
    42024310"Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US;
    42034311mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
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    42054313 <v:imagedata src="gsasII-phase_files/image021.png" o:title="" chromakey="white"/>
    42064314</v:shape><![endif]--><![if !vml]><img width=211 height=56
     
    42244332top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    42254333EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
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    42274335 <v:imagedata src="gsasII-phase_files/image023.png" o:title="" chromakey="white"/>
    42284336</v:shape><![endif]--><![if !vml]><img width=41 height=35
     
    42744382"Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US;
    42754383mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
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    42774385 <v:imagedata src="gsasII-phase_files/image025.png" o:title="" chromakey="white"/>
    42784386</v:shape><![endif]--><![if !vml]><img width=199 height=70
     
    43274435"Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US;
    43284436mso-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'>
    43304438 <v:imagedata src="gsasII-phase_files/image027.png" o:title="" chromakey="white"/>
    43314439</v:shape><![endif]--><![if !vml]><img width=205 height=70
     
    43344442<p class=gsastext style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;
    43354443margin-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 Fourier coefficients, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
     4444n odd.<span style='mso-spacerun:yes'>  </span>Each sum is only over either the
     4445even or odd values of s, respectively, because of the properties of the Fourier
     4446coefficients, <!--[if gte msEquation 12]><m:oMath><m:sSubSup><m:sSubSupPr><span
    43394447   style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
    43404448   mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
     
    43484456top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
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    43514459 <v:imagedata src="gsasII-phase_files/image029.png" o:title="" chromakey="white"/>
    43524460</v:shape><![endif]--><![if !vml]><img width=29 height=35
     
    44734581"Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US;
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    47824890of this correction. In one, a suite of spherical harmonics coefficients is
    47834891defined 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 sample symmetry for each phase in each powder pattern (“histogram”) and is
    4787 usually used to accommodate preferred orientation effects in a Rietveld
    4788 refinement. The former description allows refinement of the sample orientation
    4789 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 <span style='font-family:Symbol'>C</span>, <span style='font-family:Symbol'>F) </span>are
     4892possible sample symmetries and is the usual result desired for texture analysis.
     4893The other is the suite of spherical harmonics terms for cylindrical sample
     4894symmetry for each phase in each powder pattern (“histogram”) and is usually
     4895used to accommodate preferred orientation effects in a Rietveld refinement. The
     4896former description allows refinement of the sample orientation zeros, <span
     4897style='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
     4899description does not (they are assumed to be zero and not refinable). The
     4900sample orientation angles, (<span style='font-family:Symbol'>W</span>, <span
     4901style='font-family:Symbol'>C</span>, <span style='font-family:Symbol'>F) </span>are
    47944902specified in the Sample Parameters table in the GSAS-II data tree structure and
    47954903are applied for either description.</p>
     
    48054913incident and diffracted beams at equal angles (theta) on opposite sides of the
    48064914sample. 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 &amp; 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><span
     4915statistics and impose cylindrical symmetry on any preferred orientation
     4916(texture). Thus, the diffraction plane (source, diffraction vector &amp;
     4917detector) 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
    48114919style='mso-bookmark:_Hlk74813217'><span style='font-family:Symbol'>C</span>, </span><span
    48124920style='mso-bookmark:_Hlk74813217'><span style='font-family:Symbol'>F = 0.</span></span><span
     
    48294937
    48304938<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 beam
    4832 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-axis
     4939area detector is presumed to be directly behind the sample with the incident
     4940beam 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
    48344942vertical “up”; one views the detector image as if looking from the x-ray
    48354943source. The sample is assumed to be a capillary (which may be spun to impose
     
    48464954<p class=MsoNormal style='margin-left:.75in'>1. Menu ‘<b>Texture/Refine
    48474955texture’ </b>– refines the spherical harmonics texture model using the
    4848 predetermined values of <span class=SpellE>Prfo</span> for all histogram
    4849 reflection sets as demonstrated in <a
     4956predetermined values of Prfo for all histogram reflection sets as demonstrated
     4957in <a
    48504958href="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>
     4959tutorial.</p>
    48544960
    48554961<p class=MsoNormal style='margin-left:.75in'>2. Texture settings:</p>
     
    48714977
    48724978<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 lfo14;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
     4979margin-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
    48744980style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    48754981mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    48764982style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    48774983</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>as
    4878 an &quot;Axial pole distribution&quot; which simulates the intensity of a
    4879 reflection during a phi scan.<o:p></o:p></span></p>
     4984an &quot;Axial pole distribution&quot; which simulates the intensity of a reflection
     4985during a phi scan.<o:p></o:p></span></p>
    48804986
    48814987<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 lfo14;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
     4988margin-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
    48834989style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    48844990mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
     
    48864992</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>as
    48874993a &quot;pole figure,&quot; 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>
     4994pole (hkl) is plotted as a function of sample orientation.<o:p></o:p></span></p>
    48904995
    48914996<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 lfo14;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
     4997margin-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
    48934998style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    48944999mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
    48955000style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    48965001</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>as
    4897 <span class=GramE>a</span> &quot;inverse pole figure,&quot; 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>
     5002an &quot;inverse pole figure,&quot; where a projection of the probability of
     5003finding all poles (hkls) is plotted for a selected sample orientation.<o:p></o:p></span></p>
    49005004
    49015005<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 lfo14;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
     5006margin-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
    49035007style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Symbol;
    49045008mso-fareast-font-family:Symbol;mso-bidi-font-family:Symbol'><span
     
    49065010</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>or
    49075011as a &quot;3D pole distribution&quot; 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>
     5012pole (hkl) is plotted as a function of sample orientation. <o:p></o:p></span></p>
    49105013
    49115014<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
    49125015margin-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
    49135016style='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 0 1).<o:p></o:p></span></p>
     5017figure and 3D pole distribution one must next select the hkl of the desired
     5018pole, for Inverse pole figure one must select a sample direction (typically 0 0
     50191).<o:p></o:p></span></p>
    49175020
    49185021<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     
    49445047magnitude. The crystal structure plot shows each peak position as a white to
    49455048dark 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>
     5049relative to the maximum peak magnitude; some are connected by white sticks as
     5050possible bonds. Negative peaks are shown in orange.</p>
    49475051
    49485052<h5 style='margin-left:.5in'>What can I do here?</h5>
    49495053
    49505054<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    4951 text-indent:-.25in;mso-list:l10 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]><span
     5055text-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
    49525056style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    49535057style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    49625066
    49635067<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4964 auto;text-indent:-.25in;mso-list:l10 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'><a
     5068auto;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
    49655069name=Phase-Pawley><![if !supportLists]><span style='mso-fareast-font-family:
    49665070"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    49695073
    49705074<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4971 auto;text-indent:-.25in;mso-list:l10 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'><a
     5075auto;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
    49725076name=Pawley><![if !supportLists]><span style='mso-fareast-font-family:"Times New Roman"'><span
    49735077style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    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>
     5079column – the entries will be sorted with the smallest (distance from origin) at
     5080the top.</a></p>
    49785081
    49795082<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4980 auto;text-indent:-.25in;mso-list:l10 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'><span
     5083auto;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
    49815084style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    49825085"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    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
     5087will be sorted with the smallest distance from the unit cell center at the top.</span></p>
    49865088
    49875089<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    4988 auto;text-indent:-.25in;mso-list:l10 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'><span
     5090auto;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
    49895091style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    49905092"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    49915093</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
     5094peaks’ </b><span style='mso-spacerun:yes'> </span>–</span></p>
     5095
     5096<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5097auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    49975098style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    49985099"Times New Roman"'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    50115112
    50125113<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5013 auto;text-indent:-.25in;mso-list:l10 level2 lfo16;tab-stops:list 1.0in'><span
     5114auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    50145115style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    50155116"Times New Roman"'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    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
     5118point </b>– this positions the viewpoint (large 3D RGB cross) at the 1<sup>st</sup>
     5119selected peak.</span></p>
     5120
     5121<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5122auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    50235123style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    50245124"Times New Roman"'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    50255125</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>View pt</b>.
    50265126<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:l10 level2 lfo16;tab-stops:list 1.0in'><span
     5127from viewpoint to all selected map peaks.</span></p>
     5128
     5129<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5130auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    50315131style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    50325132"Times New Roman"'><span style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    50355135
    50365136<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5037 auto;text-indent:-.25in;mso-list:l10 level2 lfo16;tab-stops:list 1.0in'><span
     5137auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    50385138style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    50395139"Times New Roman"'><span style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5040 </span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Calc <span
    5041 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:l10 level2 lfo16;tab-stops:list 1.0in'><span
     5140</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Calc
     5141dist/ang </b>– if 2 peaks are selected, this calculates the distance between
     5142them. If 3 peaks are selected this calculates the angle between them; NB:
     5143selection order matters. If selection is not 2 or 3 peaks this is ignored.
     5144Output is on the console window.</span></p>
     5145
     5146<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5147auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    50485148style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    50495149"Times New Roman"'><span style='mso-list:Ignore'>f.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    50535153
    50545154<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5055 auto;text-indent:-.25in;mso-list:l10 level2 lfo16;tab-stops:list 1.0in'><span
     5155auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    50565156style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    50575157"Times New Roman"'><span style='mso-list:Ignore'>g.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    50605160
    50615161<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5062 auto;text-indent:-.25in;mso-list:l10 level2 lfo16;tab-stops:list 1.0in'><span
     5162auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    50635163style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    50645164"Times New Roman"'><span style='mso-list:Ignore'>h.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    50685168
    50695169<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5070 auto;text-indent:-.25in;mso-list:l10 level2 lfo16;tab-stops:list 1.0in'><span
     5170auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    50715171style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    50725172"Times New Roman"'><span style='mso-list:Ignore'>i.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    50775177
    50785178<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5079 auto;text-indent:-.25in;mso-list:l10 level2 lfo16;tab-stops:list 1.0in'><span
     5179auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    50805180style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    50815181"Times New Roman"'><span style='mso-list:Ignore'>j.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    50845184
    50855185<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5086 auto;text-indent:-.25in;mso-list:l10 level2 lfo16;tab-stops:list 1.0in'><span
     5186auto;text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    50875187style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    50885188"Times New Roman"'><span style='mso-list:Ignore'>k.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    50895189</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 changed
    5091 to reflect any change in the maximum after deletion.</span></p>
     5190peaks </b>– this deletes selected peaks. The shading on the remaining peaks is
     5191changed to reflect any change in the maximum after deletion.</span></p>
    50925192
    50935193<p class=MsoListParagraphCxSpLast style='margin-left:1.5in;mso-add-space:auto;
    5094 text-indent:-.25in;mso-list:l10 level2 lfo16;tab-stops:list 1.0in'><span
     5194text-indent:-.25in;mso-list:l9 level2 lfo13;tab-stops:list 1.0in'><span
    50955195style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    50965196"Times New Roman"'><span style='mso-list:Ignore'>l.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    51105210style='mso-bookmark:Pawley'>).</span></p>
    51115211
    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
     5213here?</span></h5>
    51135214
    51145215<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    5115 text-indent:-.25in;mso-list:l3 level1 lfo18;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
     5216text-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
    51165217style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    51175218"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    51205221
    51215222<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5122 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
     5223auto;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
    51235224style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    51245225"Times New Roman"'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    51295230
    51305231<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5131 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
     5232auto;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
    51325233style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    51335234"Times New Roman"'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    51345235</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
     5236create</b> – this creates a new set of Pawley reflections, over writing any preexisting
     5237Pawley 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
     5239are not set and the Fsq(hkl) = 100.0.</span></p>
     5240
     5241<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5242auto;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
    51435243style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    51445244"Times New Roman"'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    51455245</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
     5246estimate</b> – this attempts an estimate of Fsq(hkl) from the peak heights of
     5247the reflection as seen in the 1<sup>st</sup> powder pattern of those selected
     5248in the </span><a href="#_Data"><span style='mso-bookmark:Pawley'>Data</span><span
     5249style='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:
     5252auto;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
    51545253style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    51555254"Times New Roman"'><span style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    51565255</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Pawley
    51575256update </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 repeat
    5160 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 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Refine all</span></b>
    5163 and an additional refinement. Repeat as needed to remove negative intensities.
    5164 Set </span><span style='mso-bookmark:Pawley'><b><span style='font-family:"Calibri",sans-serif;
     5257set to ½ its absolute value for noncentrosymmetric space groups (0.3
     5258otherwise); the refine flag is turned off. One should repeat Pawley refinement
     5259and 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:
     5261minor-latin;mso-bidi-theme-font:minor-latin'>Refine all</span></b> and an
     5262additional refinement. Repeat as needed to remove negative intensities. Set </span><span
     5263style='mso-bookmark:Pawley'><b><span style='font-family:"Calibri",sans-serif;
    51655264mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    51665265minor-latin'>Pawley neg. wt.</span></b> (see </span><span style='mso-bookmark:
     
    51705269
    51715270<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5172 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
     5271auto;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
    51735272style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    51745273"Times New Roman"'><span style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    51775276
    51785277<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5179 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
     5278auto;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
    51805279style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    51815280"Times New Roman"'><span style='mso-list:Ignore'>f.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    51845283
    51855284<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5186 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
     5285auto;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
    51875286style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    51885287"Times New Roman"'><span style='mso-list:Ignore'>g.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    51915290
    51925291<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5193 auto;text-indent:-.25in;mso-list:l3 level1 lfo18;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
     5292auto;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
    51945293style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    51955294"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5196 </span></span></span><![endif]>You can change the refine flags either by clicking
    5197 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
     5296clicking on the box or by selecting one and then selecting the column (a single
     5297click on the column heading). Then type ‘y’ to set the refine flags or ‘n’ to
     5298clear the flags. You should not refine those reflections that fall below the
     5299lower limit or above the upper limit of the powder pattern otherwise you may
     5300have a singular matrix error in your Pawley refinement.</span></p>
    52025301
    52035302<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    5204 auto;text-indent:-.25in;mso-list:l3 level1 lfo18;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
     5303auto;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
    52055304style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    52065305style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>You
    52075306can delete an individual reflection from the Pawley set by selecting its row
    52085307(will be highlighted) and then pressing the Delete key (this is not reversable
    5209 &amp; only <span class=GramE>deletes</span> the 1<sup>st</sup> one selected).</p>
     5308&amp; only deletes the 1<sup>st</sup> one selected).</p>
    52105309
    52115310<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    5212 text-indent:-.25in;mso-list:l3 level1 lfo18;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
     5311text-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
    52135312style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    52145313style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </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>
     5314can change the individual Fsq(hkl) values by selecting it, typing in the new
     5315value and then pressing enter or selecting somewhere else in the table.</p>
    52185316
    52195317<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
    52205318name=Phase-Layers>Layers</a></h4>
    52215319
    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 <a
     5320<p class=MsoNormal style='margin-left:.5in'>This is used to set up stacking
     5321fault models for simulations of x-ray diffraction patterns. See for example the
     5322<a
    52255323href="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>
     5324Faults-I</a> tutorial. The computations are done by a modified version of
     5325DIFFaX. See M.M.J. Treacy, J.M. Newsam and M.W. Deem, Proc. Roy. Soc. Lond.
     5326433A, 499-520 (1991) for more information on DIFFaX and please cite this if you
     5327use this section of GSAS-II.</p>
    52315328
    52325329<h5 style='margin-left:.5in'>What can I do here?</h5>
    52335330
    52345331<p class=MsoListParagraphCxSpFirst style='margin-left:63.8pt;mso-add-space:
    5235 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]><span
     5332auto;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
    52365333style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    52375334style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     
    52395336
    52405337<p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space:
    5241 auto;text-indent:-.25in;mso-list:l6 level2 lfo22;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
     5338auto;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
    52425339style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    52435340style='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>
     5341style='mso-bidi-font-weight:normal'>Load from DIFFaX file – </b><span
     5342style='mso-bidi-font-weight:bold'>load parameters from a DIFFaX input file</span></p>
    52475343
    52485344<p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space:
    5249 auto;text-indent:-.25in;mso-list:l6 level2 lfo22;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
     5345auto;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
    52505346style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    52515347style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b
     
    52555351
    52565352<p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space:
    5257 auto;text-indent:-.25in;mso-list:l6 level2 lfo22;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
     5353auto;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
    52585354style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span
    52595355style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b
    52605356style='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>
     5357style='mso-bidi-font-weight:bold'>run DIFFaX to simulate selected pattern<o:p></o:p></span></p>
    52635358
    52645359<p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space:
    5265 auto;text-indent:-.25in;mso-list:l6 level2 lfo22;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
     5360auto;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
    52665361style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span
    52675362style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b
    52685363style='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 observed
    5270 pattern (not available yet)<o:p></o:p></span></p>
     5364bold'>refine stacking fult parameters to fit observed pattern (not available
     5365yet)<o:p></o:p></span></p>
    52715366
    52725367<p class=MsoListParagraphCxSpMiddle style='margin-left:99.8pt;mso-add-space:
    5273 auto;text-indent:-.25in;mso-list:l6 level2 lfo22;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
     5368auto;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
    52745369style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span
    52755370style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><b
     
    52795374
    52805375<p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space:
    5281 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]><span
     5376auto;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
    52825377style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span
    52835378style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    52865381
    52875382<p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space:
    5288 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]><span
     5383auto;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
    52895384style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span
    52905385style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    52935388
    52945389<p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space:
    5295 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]><span
     5390auto;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
    52965391style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span
    52975392style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    53015396
    53025397<p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space:
    5303 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]><span
     5398auto;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
    53045399style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span
    53055400style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    53095404
    53105405<p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space:
    5311 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]><span
     5406auto;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
    53125407style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span
    53135408style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    53145409</span></span></span><![endif]><span style='mso-bidi-font-weight:bold'>Next are
    53155410descriptions 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>
     5411atom-by-atom or imported from another GSAS-II gpx file. If a layer is already
     5412present, then the new layer can be the same; give it a different name.<o:p></o:p></span></p>
    53195413
    53205414<p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space:
    5321 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]><span
     5415auto;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
    53225416style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span
    53235417style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    53275421
    53285422<p class=MsoListParagraphCxSpMiddle style='margin-left:63.8pt;mso-add-space:
    5329 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]><span
     5423auto;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
    53305424style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span
    53315425style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    533454281).<o:p></o:p></span></p>
    53355429
    5336 <p class=MsoListParagraphCxSpMiddle 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]><span
     5430<p class=MsoListParagraphCxSpLast style='margin-left:63.8pt;mso-add-space:auto;
     5431text-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
    53385432style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-weight:bold'><span
    53395433style='mso-list:Ignore'>9.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    53425436simulation<o:p></o:p></span></p>
    53435437
    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
     5439sequences of layers to check on how they fit together; see the <b>Plot</b>
    53475440boxes for this.</p>
    53485441
    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
    53515444<h5 style='margin-left:.5in'>What can I do here?</h5>
    53525445
    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
    53555448<h5 style='margin-left:.5in'>What can I do here?</h5>
    53565449
    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
    53595452<h5 style='margin-left:.5in'>What can I do here?</h5>
    53605453
    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
    53635456<h5 style='margin-left:.5in'>What can I do here?</h5>
    53645457
    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
     5459style='mso-fareast-font-family:"Times New Roman"'>
    53705460
    53715461<hr size=3 width="100%" align=center>
    53725462
    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
     5466modified: Tue Jan 25 09:29:56 CST 2022 <!-- hhmts end --><o:p></o:p></span></p>
    53765467
    53775468</div>
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