Changeset 2386 for Tutorials


Ignore:
Timestamp:
Jul 28, 2016 2:17:19 PM (5 years ago)
Author:
vondreele
Message:
 
File:
1 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/CFXraySingleCrystal/CFSingleCrystal.htm

    r2262 r2386  
    1 <html>
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     2xmlns:o="urn:schemas-microsoft-com:office:office"
     3xmlns:w="urn:schemas-microsoft-com:office:word"
     4xmlns:m="http://schemas.microsoft.com/office/2004/12/omml"
     5xmlns="http://www.w3.org/TR/REC-html40">
    26
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     10<meta name=Generator content="Microsoft Word 15">
     11<meta name=Originator content="Microsoft Word 15">
     12<link rel=File-List href="CFSingleCrystal_files/filelist.xml">
     13<link rel=Edit-Time-Data href="CFSingleCrystal_files/editdata.mso">
     14<!--[if !mso]>
     15<style>
     16v\:* {behavior:url(#default#VML);}
     17o\:* {behavior:url(#default#VML);}
     18w\:* {behavior:url(#default#VML);}
     19.shape {behavior:url(#default#VML);}
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     30  <w:ValidateAgainstSchemas/>
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     40   <w:SplitPgBreakAndParaMark/>
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     86  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     87   Name="index 7"/>
     88  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     89   Name="index 8"/>
     90  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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     98  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     99   UnhideWhenUsed="true" Name="toc 4"/>
     100  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     101   UnhideWhenUsed="true" Name="toc 5"/>
     102  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     103   UnhideWhenUsed="true" Name="toc 6"/>
     104  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     105   UnhideWhenUsed="true" Name="toc 7"/>
     106  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     107   UnhideWhenUsed="true" Name="toc 8"/>
     108  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
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     110  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     111   Name="Normal Indent"/>
     112  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     113   Name="footnote text"/>
     114  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     115   Name="annotation text"/>
     116  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     117   Name="header"/>
     118  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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     121   Name="index heading"/>
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     123   UnhideWhenUsed="true" QFormat="true" Name="caption"/>
     124  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     125   Name="table of figures"/>
     126  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     127   Name="envelope address"/>
     128  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     129   Name="envelope return"/>
     130  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     131   Name="footnote reference"/>
     132  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     133   Name="annotation reference"/>
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     145   Name="macro"/>
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     147   Name="toa heading"/>
     148  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     149   Name="List"/>
     150  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     151   Name="List Bullet"/>
     152  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     153   Name="List Number"/>
     154  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     155   Name="List 2"/>
     156  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     157   Name="List 3"/>
     158  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     159   Name="List 4"/>
     160  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     161   Name="List 5"/>
     162  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     163   Name="List Bullet 2"/>
     164  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     165   Name="List Bullet 3"/>
     166  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     167   Name="List Bullet 4"/>
     168  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     169   Name="List Bullet 5"/>
     170  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     171   Name="List Number 2"/>
     172  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     173   Name="List Number 3"/>
     174  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     175   Name="List Number 4"/>
     176  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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     181  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     182   Name="Signature"/>
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     190   Name="List Continue"/>
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     209   Name="Body Text First Indent 2"/>
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     232  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     233   Name="E-mail Signature"/>
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     241   Name="HTML Acronym"/>
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     315   Name="Table Grid 7"/>
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     339   Name="Table 3D effects 3"/>
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     341   Name="Table Contemporary"/>
     342  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     343   Name="Table Elegant"/>
     344  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     345   Name="Table Professional"/>
     346  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     347   Name="Table Subtle 1"/>
     348  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     349   Name="Table Subtle 2"/>
     350  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     351   Name="Table Web 1"/>
     352  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     353   Name="Table Web 2"/>
     354  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     355   Name="Table Web 3"/>
     356  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     357   Name="Balloon Text"/>
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     359  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     360   Name="Table Theme"/>
     361  <w:LsdException Locked="false" SemiHidden="true" Name="Placeholder Text"/>
     362  <w:LsdException Locked="false" Priority="1" QFormat="true" Name="No Spacing"/>
     363  <w:LsdException Locked="false" Priority="60" Name="Light Shading"/>
     364  <w:LsdException Locked="false" Priority="61" Name="Light List"/>
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     367  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2"/>
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     371  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2"/>
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    143938
    144939<div class=WordSection1>
    145940
    146 <h1>Single crystal structure determination and refinement with X-ray data in
    147 GSAS-II</h1>
    148 
    149 <h2>Introduction</h2>
     941<h1><span style='mso-fareast-font-family:"Times New Roman"'>Single crystal
     942structure determination and refinement with X-ray data in GSAS-II<o:p></o:p></span></h1>
     943
     944<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction<o:p></o:p></span></h2>
    150945
    151946<p class=MsoNormal>In this exercise we will use a set of X-ray single crystal
    152 structure factors to solve the structure of dipyridyl disulfide by charge flipping
    153 and then refine the structure by least-squares. The structure will be completed
    154 by adding the requisite hydrogen atoms and by using anisotropic thermal
    155 parameters for the heavier atoms. The structure was originally solved by
    156 Raghavan &amp; Seff, Acta Cryst. B33, 386-391 (1977) in the space group P2<sub>1</sub>/c
    157 with one disordered pyridine ring with indications that the true space group
    158 was P2<sub>1</sub>. It was subsequently reinvestigated by Young (2014
    159 .) who
    160 found that the true space group was P2<sub>1</sub> with 4 molecules in the
    161 asymmetric unit. The data used in the latter analysis is what is used here and
    162 is provided as a “fcf” file obtained after structure analysis by Shelx-97; the
    163 structure factors are scaled to those calculated from the structure. We will
    164 solve the P 2<sub>1</sub>/c structure first.</p>
     947structure factors to solve the structure of <span class=SpellE>dipyridyl</span>
     948disulfide by charge flipping and then refine the structure by least-squares.
     949The structure will be completed by adding the requisite hydrogen atoms and by
     950using anisotropic thermal parameters for the heavier atoms. The structure was
     951originally solved by <span class=SpellE>Raghavan</span> &amp; <span
     952class=SpellE>Seff</span>, <span class=SpellE>Acta</span> <span class=SpellE>Cryst</span>.
     953B33, 386-391 (1977) in the space group P2<sub>1</sub>/c with one disordered
     954pyridine ring with indications that the true space group was P2<sub>1</sub>. It
     955was subsequently reinvestigated by Young (2014
     956.) who found that the true space
     957group was P2<sub>1</sub> with 4 molecules in the asymmetric unit. The data used
     958in the latter analysis is what is used here and is provided as a “<span
     959class=SpellE>fcf</span>” file obtained after structure analysis by Shelx-97;
     960the structure factors are scaled to those calculated from the structure. We
     961will solve the P 2<sub>1</sub>/c structure first.</p>
    165962
    166963<p class=MsoNormal>&nbsp;</p>
     
    173970already, start GSAS-II</p>
    174971
    175 <h2>Step 1. Input phase information</h2>
    176 
    177 <p class=MsoListParagraph style='text-indent:-.25in'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    178 </span>Use the <b><span style='font-family:"Calibri",sans-serif'>Data/Add phase</span></b>
    179 menu item add a new phase into the current GSAS-II project. A popup window will
    180 appear asking for a phase name; I entered <b><span style='font-family:"Calibri",sans-serif'>SS
    181 dipyridyl</span></b>; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>
    182 when done. Select <b><span style='font-family:"Calibri",sans-serif'>Loaded
    183 Data/Phases/SS dipyridyl</span></b> from the GSAS-II Data tree window. The
     972<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 1. Input phase
     973information<o:p></o:p></span></h2>
     974
     975<p class=MsoListParagraph style='text-indent:-.25in'>1.<span style='font-size:
     9767.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Use the <b><span style='font-family:
     977"Calibri",sans-serif'>Data/Add phase</span></b> menu item add a new phase into
     978the current GSAS-II project. A popup window will appear asking for a phase
     979name; I entered <b><span style='font-family:"Calibri",sans-serif'>SS <span
     980class=SpellE>dipyridyl</span></span></b>; press <b><span style='font-family:
     981"Calibri",sans-serif'>OK</span></b> when done. Select <b><span
     982style='font-family:"Calibri",sans-serif'>Loaded Data/Phases/SS <span
     983class=SpellE>dipyridyl</span></span></b> from the GSAS-II Data tree window. The
    184984General tab for Phase Data will appear.</p>
    185985
    186 <p class=MsoListParagraph><img width=524 height=307 id="Picture 1"
    187 src="CFSingleCrystal_files/image001.png"></p>
    188 
    189 <p class=MsoListParagraph style='text-indent:-.25in'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    190 </span>Enter the space group <b><span style='font-family:"Calibri",sans-serif'>P
    191 21/c</span></b> (don’t forget the space between P &amp; 21/c) &amp; press <b><span
    192 style='font-family:"Calibri",sans-serif'>Enter</span></b>. A Space Group
    193 Information popup window will appear; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
    194 The General window will be refreshed showing only the needed lattice parameters
    195 for P 21/c.</p>
    196 
    197 <p class=MsoListParagraph><img width=522 height=361 id="Picture 3"
    198 src="CFSingleCrystal_files/image002.png"></p>
    199 
    200 <p class=MsoListParagraph style='text-indent:-.25in'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    201 </span>Enter <b><span style='font-family:"Calibri",sans-serif'>15.8489</span></b>,
    202 <b><span style='font-family:"Calibri",sans-serif'>5.5008</span></b>, <b><span
    203 style='font-family:"Calibri",sans-serif'>23.118</span></b>, and <b><span
     986<p class=MsoListParagraph><span style='mso-no-proof:yes'><img width=524
     987height=307 id="_x0000_i1042" src="CFSingleCrystal_files/image001.png"></span></p>
     988
     989<p class=MsoListParagraph style='text-indent:-.25in'>2.<span style='font-size:
     9907.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Enter the space group <b><span
     991style='font-family:"Calibri",sans-serif'>P 21/c</span></b> (don’t forget the
     992space between P &amp; 21/c) &amp; press <b><span style='font-family:"Calibri",sans-serif'>Enter</span></b>.
     993A Space Group Information popup window will appear; press <b><span
     994style='font-family:"Calibri",sans-serif'>OK</span></b>. The General window will
     995be refreshed showing only the needed lattice parameters for P 21/c.</p>
     996
     997<p class=MsoListParagraph><span style='mso-no-proof:yes'><img width=522
     998height=361 id="_x0000_i1041" src="CFSingleCrystal_files/image002.png"></span></p>
     999
     1000<p class=MsoListParagraph style='text-indent:-.25in'>3.<span style='font-size:
     10017.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Enter <b><span style='font-family:
     1002"Calibri",sans-serif'>15.8489</span></b>, <b><span style='font-family:"Calibri",sans-serif'>5.5008</span></b>,
     1003<b><span style='font-family:"Calibri",sans-serif'>23.118</span></b>, and <b><span
    2041004style='font-family:"Calibri",sans-serif'>96.9160</span></b> for a, b, c and
    2051005beta, respectively; the unit cell volume will be recalculated at each entry.</p>
    2061006
    207 <h2>Step 2. Import structure factors </h2>
     1007<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 2. Import
     1008structure factors <o:p></o:p></span></h2>
    2081009
    2091010<p class=MsoNormal>There are two parts to this step: one is to import the data
     
    2121013<p class=MsoNormal>To do these, do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure
    2131014factor/from CIF file</span></b> from the main GSAS-II data tree window menu. A
    214 file selection dialog will appear; find <b><span style='font-family:"Calibri",sans-serif'>exercises\CF
    215 Xray single crystal\S2dipyridyl.fcf</span></b> and press <b><span
    216 style='font-family:"Calibri",sans-serif'>Open</span></b>. A popup window asking
    217 if this is the file you want; press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b>.
    218 After a pause while the file is read a new popup will appear offering the
    219 chance to rename the structure factor set; press <b><span style='font-family:
    220 "Calibri",sans-serif'>OK</span></b>. After some time a new popup will appear to
    221 Add the new structure factor set to the SS dipyridyl phase. Select the phase
    222 and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. The
    223 plot will show a rectangular array of circles for the hk0 reflection layer;
     1015file selection dialog will appear; find <b><span style='font-family:"Calibri",sans-serif'>CF
     1016<span class=SpellE>Xray</span> single crystal\data\S2dipyridyl.fcf</span></b>
     1017and press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>. A
     1018popup window asking if this is the file you want; press <b><span
     1019style='font-family:"Calibri",sans-serif'>Yes</span></b>. After a pause while
     1020the file is read a new popup will appear offering the chance to rename the
     1021structure factor set; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
     1022After some <span class=GramE>time</span> a new popup will appear to Add the new
     1023structure factor set to the SS <span class=SpellE>dipyridyl</span> phase.
     1024Select the phase and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
     1025The plot will show a rectangular array of circles for the hk0 reflection layer;
    2241026select the plot &amp; press <b><span style='font-family:"Calibri",sans-serif'>k</span></b>
    2251027to get an h0l layer.</p>
    2261028
    227 <p class=MsoNormal><img width=480 height=412 id="Picture 2"
    228 src="CFSingleCrystal_files/image003.png"></p>
    229 
    230 <p class=MsoNormal>Because the fcf file has both observed and calculated
    231 structure factors, the plot shows a small R value for the layer. The observed
    232 structure factors are shown as blue rings, the calculated ones as green rings
    233 and a small green or red dot may appear at each ring center showing F<sub>o</sub>-F<sub>c</sub>.
    234 If the reflection data file had only observed structure factors then only blue
    235 rings will be seen. You can explore the plot options in the ‘<b><span
     1029<p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=412
     1030id="_x0000_i1040" src="CFSingleCrystal_files/image003.png"></span></p>
     1031
     1032<p class=MsoNormal>Because the <span class=SpellE>fcf</span> file has both
     1033observed and calculated structure factors, the plot shows a small R value for
     1034the layer. The observed structure factors are shown as blue rings, the
     1035calculated ones as green rings and a small green or red dot may appear at each
     1036ring center showing <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>. If
     1037the reflection data file had only observed structure <span class=GramE>factors</span>
     1038then only blue rings will be seen. You can explore the plot options in the ‘<b><span
    2361039style='font-family:"Calibri",sans-serif'>K</span></b>’ box in the plot toolbar.</p>
    2371040
    238 <h2>Step 3. Setup for charge flipping</h2>
     1041<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Setup for
     1042charge flipping<o:p></o:p></span></h2>
    2391043
    2401044<p class=MsoNormal>To solve (again) this crystal structure we will use charge
     
    2421046structure without consideration of space group symmetry. To do this it operates
    2431047on the entire unit cell volume to a selected resolution (usually 0.5Å) using
    244 fast fourier transform techniques. This requires a set of structure factors in
    245 an array of the same dimensions as the density array covering the unit cell
    246 (i.e. a box bounded by ~0.5Å resolution). The space group symmetry is applied
    247 to the observed structure factors to create a full sphere which is then zero
    248 filled out to the 0.5Å resolution bounded box. To be reasonably assured of
    249 success, the observed structure factors should extend to ~1Å resolution; we
    250 have that here for this example. To begin select <b><span style='font-family:
    251 "Calibri",sans-serif'>Phases/SS dipyridyl</span></b> from the GSAS-II data
    252 tree; the General tab will be shown</p>
    253 
    254 <p class=MsoNormal><img width=624 height=401 id="Picture 4"
    255 src="CFSingleCrystal_files/image004.png"></p>
     1048fast <span class=SpellE>fourier</span> transform techniques. This requires a
     1049set of structure factors in an array of the same dimensions as the density
     1050array covering the unit cell (i.e. a box bounded by ~0.5Å resolution). The
     1051space group symmetry is applied to the observed structure factors to create a
     1052full sphere which is then zero filled out to the 0.5Å resolution bounded box.
     1053To be reasonably assured of success, the observed structure factors should
     1054extend to ~1Å resolution; we have that here for this example. To begin select <b><span
     1055style='font-family:"Calibri",sans-serif'>Phases/SS <span class=SpellE>dipyridyl</span></span></b>
     1056from the GSAS-II data tree; the General tab will be shown</p>
     1057
     1058<p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=401
     1059id="_x0000_i1039" src="CFSingleCrystal_files/image004.png"></span></p>
    2561060
    2571061<p class=MsoNormal>Find the <b><span style='font-family:"Calibri",sans-serif'>Fourier
     
    2651069data sets for this phase, you can pick more than one and GSAS-II will use a
    2661070“last one in” process for assembling the reflection set to use for charge
    267 flipping. There are four more settings to consider: 1) kMax controls the upper
    268 cutoff for charge flipping; if the density is &gt; k-Max*<span
    269 style='font-family:Symbol'>s</span><sub><span style='font-family:Symbol'>r</span></sub>
    270 (map standard deviation) then flip the charge. This prevents the “Uranium
    271 solution” sometimes found where all the density is concentrated in a single
    272 peak. A useful guide is to use twice the largest atomic number of any element
    273 in your structure. For equal atom problems use 12-15; adjust upward for
    274 structures with heavy &amp; light atoms. In this case, set <b><span
    275 style='font-family:"Calibri",sans-serif'>k-Max</span></b> to <b><span
    276 style='font-family:"Calibri",sans-serif'>30.0</span></b> to allow the S atom to
    277 appear. 2) k-Factor controls the lower level for charge flipping; if the
    278 density is &lt; k-Factor*<span style='font-family:Symbol'>s</span><sub><span
    279 style='font-family:Symbol'>r</span></sub> then flip the charge. The default
    280 value seems to work pretty well; I’d only change it if the charge flipping is
    281 having trouble solving the structure. 3) Resolution selects the spacing between
    282 map points. 0.5Å is sufficient in most cases. Choosing a smaller value requires
    283 more map points (NB: GSAS-II uses the entire unit cell volume for charge
    284 flipping) and thus will require more structure factors since the fast fourier
    285 algorithm requires the same size arrays in both real space and reciprocal
    286 space. This will slow down the charge flip process. 4) Normalizing element
    287 selects a form factor to rescale the structure factors thus “sharpening” the
    288 density map. I suggest trying <b><span style='font-family:"Calibri",sans-serif'>None</span></b>
     1071flipping. There are four more settings to consider: 1) <span class=SpellE>kMax</span>
     1072controls the upper cutoff for charge flipping; if the density is &gt; k-Max*<span
     1073style='font-family:Symbol'>s<sub>r</sub></span> (map standard deviation) then
     1074flip the charge. This prevents the “Uranium solution” sometimes found where all
     1075the density is concentrated in a single peak. A useful guide is to use twice
     1076the largest atomic number of any element in your structure. For equal atom
     1077problems use 12-15; adjust upward for structures with heavy &amp; light atoms.
     1078In this case, set <b><span style='font-family:"Calibri",sans-serif'>k-Max</span></b>
     1079to <b><span style='font-family:"Calibri",sans-serif'>30.0</span></b> to allow
     1080the S atom to appear. 2) k-Factor controls the lower level for charge flipping;
     1081if the density is &lt; k-Factor*<span style='font-family:Symbol'>s<sub>r</sub></span>
     1082then flip the charge. The default value seems to work pretty well; I’d only
     1083change it if the charge flipping is having trouble solving the structure. 3)
     1084Resolution selects the spacing between map points. 0.5Å is sufficient in most
     1085cases. Choosing a smaller value requires more map points (NB: GSAS-II uses the
     1086entire unit cell volume for charge flipping) and thus will require more
     1087structure factors since the fast <span class=SpellE>fourier</span> algorithm
     1088requires the same size arrays in both real space and reciprocal space. This
     1089will slow down the charge flip process. 4) Normalizing element selects a form
     1090factor to rescale the structure factors thus “sharpening” the density map. I
     1091suggest trying <b><span style='font-family:"Calibri",sans-serif'>None</span></b>
    2891092first, otherwise select a representative element (really doesn’t matter which).</p>
    2901093
    291 <h2 style='page-break-after:avoid'>Step 4. Charge flipping</h2>
     1094<h2 style='page-break-after:avoid'><span style='mso-fareast-font-family:"Times New Roman"'>Step
     10954. Charge flipping<o:p></o:p></span></h2>
    2921096
    2931097<p class=MsoNormal>With the controls all set you can now do charge flipping;
     
    2951099tab do <b><span style='font-family:"Calibri",sans-serif'>Compute/Charge
    2961100flipping</span></b>. A progress bar popup will appear showing the residual
    297 between the observed structure factors and those obtained from the inverse
    298 fourier transform of the last flipped density map. It should quickly decrease
    299 to the ~20% range and level out indicating a good charge flip solution. When it
    300 has reached this, press <b><span style='font-family:"Calibri",sans-serif'>Cancel</span></b>
    301 to stop the process.</p>
    302 
    303 <p class=MsoNormal><img width=366 height=180 id="Picture 6"
    304 src="CFSingleCrystal_files/image005.png"></p>
     1101between the observed structure factors and those obtained from the inverse <span
     1102class=SpellE>fourier</span> transform of the last flipped density map. It
     1103should quickly decrease to the ~20% range and level out indicating a good
     1104charge flip solution. When it has reached this, press <b><span
     1105style='font-family:"Calibri",sans-serif'>Cancel</span></b> to stop the process.</p>
     1106
     1107<p class=MsoNormal><span style='mso-no-proof:yes'><img width=366 height=180
     1108id="_x0000_i1038" src="CFSingleCrystal_files/image005.png"></span></p>
    3051109
    3061110<p class=MsoNormal>The console window will show something like</p>
    3071111
    308 <p class=MsoNormal><img width=624 height=166 id="Picture 7"
    309 src="CFSingleCrystal_files/image006.png"></p>
     1112<p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=166
     1113id="_x0000_i1037" src="CFSingleCrystal_files/image006.png"></span></p>
    3101114
    3111115<p class=MsoNormal>There may be a pause at <b><span style='font-family:"Calibri",sans-serif'>Begin
    312 fourier map search</span></b> before it finishes. Provided is a summary of the
    313 charge flip calculation (time, map size, density range &amp; structure factor
    314 residual). The map offset is discovered by an analysis of the reflection phases
    315 with respect to how they should be distributed for your chosen space group.
    316 These offsets are then applied to shift the map so that the symmetry elements
    317 are properly located in the unit cell. The quality of this fit (chi**2) is
    318 given. This process is not necessarily perfect; you are given an opportunity to
    319 hand-tune the offset. Finally the number of peaks found in the map is listed,
    320 the structure is drawn (I’ve made the view down the b-axis)</p>
    321 
    322 <p class=MsoNormal><img width=478 height=402 id="Picture 11"
    323 src="CFSingleCrystal_files/image007.jpg"></p>
    324 
    325 <p class=MsoNormal> and the Phase data window will show the map peaks tab</p>
    326 
    327 <p class=MsoNormal><img width=500 height=300 id="Picture 12"
    328 src="CFSingleCrystal_files/image008.png"></p>
     1116<span class=SpellE>fourier</span> map search</span></b> before it finishes.
     1117Provided is a summary of the charge flip calculation (time, map size, density
     1118range &amp; structure factor residual). The map offset is discovered by an
     1119analysis of the reflection phases with respect to how they should be
     1120distributed for your chosen space group. These offsets are then applied to
     1121shift the map so that the symmetry elements are properly located in the unit
     1122cell. The quality of this fit (chi**2) is given. This process is not
     1123necessarily perfect; you are given an opportunity to hand-tune the offset. <span
     1124class=GramE>Finally</span> the number of peaks found in the map is listed, the
     1125structure is drawn (I’ve made the view down the b-axis)</p>
     1126
     1127<p class=MsoNormal><span style='mso-no-proof:yes'><img width=478 height=402
     1128id="_x0000_i1036" src="CFSingleCrystal_files/image007.jpg"></span></p>
     1129
     1130<p class=MsoNormal>&nbsp;and the Phase data window will show the map peaks tab</p>
     1131
     1132<p class=MsoNormal><span style='mso-no-proof:yes'><img width=500 height=300
     1133id="_x0000_i1035" src="CFSingleCrystal_files/image008.png"></span></p>
    3291134
    3301135<p class=MsoNormal>These are listed in order of magnitude; a double click on
    3311136any of the table headings will sort the list according to that parameter. My
    332 list has 112 entries; dipyridyl disulfide has 14 C &amp; S atoms so this list
    333 is appropriate for 8 molecules in the unit cell and thus all atoms were found
    334 in this charge flipping result.</p>
     1137list has 112 entries; <span class=SpellE>dipyridyl</span> disulfide has 14 C
     1138&amp; S atoms so this list is appropriate for 8 molecules in the unit cell and
     1139thus all atoms were found in this charge flipping result.</p>
    3351140
    3361141<p class=MsoNormal>If all went well then the drawing should nicely show all the
     
    3711176style='font-family:"Calibri",sans-serif'>Compute/Search map</span></b>.</p>
    3721177
    373 <h2>Step 5. Extract solution and make molecules</h2>
     1178<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 5. Extract
     1179solution and make molecules<o:p></o:p></span></h2>
    3741180
    3751181<p class=MsoNormal>Assuming that the map &amp; peak positions are properly
     
    3871193according to their position in the magnitude column.</p>
    3881194
    389 <p class=MsoNormal><img width=624 height=267 id="Picture 13"
    390 src="CFSingleCrystal_files/image009.png"></p>
     1195<p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=267
     1196id="_x0000_i1034" src="CFSingleCrystal_files/image009.png"></span></p>
    3911197
    3921198<p class=MsoNormal>The drawing will show white balls at the atom positions
    3931199scattered over several molecules.</p>
    3941200
    395 <p class=MsoNormal><img width=474 height=409 id="Picture 14"
    396 src="CFSingleCrystal_files/image010.jpg"></p>
     1201<p class=MsoNormal><span style='mso-no-proof:yes'><img width=474 height=409
     1202id="_x0000_i1033" src="CFSingleCrystal_files/image010.jpg"></span></p>
    3971203
    3981204<p class=MsoNormal>Notice that 4 atoms have magnitudes ~90+, these are the S
     
    4041210style='font-family:"Calibri",sans-serif'>OK</span></b>; a Periodic Table will
    4051211appear. Select <b><span style='font-family:"Calibri",sans-serif'>S</span></b>;
    406 the atoms will be renames and their Type changed to S. Next select the
    407 remaining H atoms (a quick way it to double LB click the <b><span
     1212the atoms will be <span class=GramE>renames</span> and their Type changed to S.
     1213Next select the remaining H atoms (a quick way it to double LB click the <b><span
    4081214style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and
    4091215select <b><span style='font-family:"Calibri",sans-serif'>H</span></b> from the
     
    4141220change (you may have to wiggle it a bit to force the update).</p>
    4151221
    416 <p class=MsoNormal><img width=480 height=390 id="Picture 17"
    417 src="CFSingleCrystal_files/image011.jpg"></p>
     1222<p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=390
     1223id="_x0000_i1032" src="CFSingleCrystal_files/image011.jpg"></span></p>
    4181224
    4191225<p class=MsoNormal>Notice that the atoms are scattered over several molecules;
     
    4281234bonds are found.</p>
    4291235
    430 <p class=MsoNormal><img width=265 height=223 id="Picture 16"
    431 src="CFSingleCrystal_files/image012.png"> </p>
     1236<p class=MsoNormal><span style='mso-no-proof:yes'><img width=265 height=223
     1237id="_x0000_i1031" src="CFSingleCrystal_files/image012.png"></span>&nbsp;</p>
    4321238
    4331239<p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>;
    434 atoms will be collected into a well positioned group, but others are not. Next
    435 select one of the unassembled atoms (I chose a C-atom in a nearby SS-dipyridyl)
    436 and do <b><span style='font-family:"Calibri",sans-serif'>Edit/Assemble molecule</span></b>;
    437 there will be two nicely assembled SS-dipyridyls.</p>
    438 
    439 <p class=MsoNormal><img width=480 height=384 id="Picture 5"
    440 src="CFSingleCrystal_files/image013.jpg"></p>
     1240atoms will be collected into a <span class=SpellE>well positioned</span> group,
     1241but others are not. Next select one of the unassembled atoms (I chose a C-atom
     1242in a nearby SS-<span class=SpellE>dipyridyl</span>) and do <b><span
     1243style='font-family:"Calibri",sans-serif'>Edit/Assemble molecule</span></b>;
     1244there will be two nicely assembled SS-<span class=SpellE>dipyridyls</span>.</p>
     1245
     1246<p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=384
     1247id="_x0000_i1030" src="CFSingleCrystal_files/image013.jpg"></span></p>
    4411248
    4421249<p class=MsoNormal>You should probably save this project as it contains your
    4431250solved crystal structure.</p>
    4441251
    445 <h2>Step 6. Initial refinement</h2>
     1252<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 6. Initial
     1253refinement<o:p></o:p></span></h2>
    4461254
    4471255<p class=MsoNormal>Since we now have a structural model, we can do the initial
    448 structure refinement. By default this will only refine the scale factor; do <b><span
    449 style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> from the
    450 main GSAS-II data tree window. Convergence will quickly occur with Rw ~35%.
    451 More useful is to refine the atom positions and isotropic thermal parameters.
    452 Select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
     1256structure refinement. By <span class=GramE>default</span> this will only refine
     1257the scale factor; do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
     1258from the main GSAS-II data tree window. Convergence will quickly occur with <span
     1259class=SpellE>Rw</span> ~35%. More useful is to refine the atom positions and
     1260isotropic thermal parameters. Select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
    4531261tab from the Phase window. Then LB double click the <b><span style='font-family:
    4541262"Calibri",sans-serif'>refine</span></b> column heading; a popup window will
     
    4591267style='font-family:"Calibri",sans-serif'>XU</span></b> for each atom in the
    4601268refine column. Then do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
    461 (twice to get convergence) and the Rw ~12%.</p>
    462 
    463 <h2>Step 7. Determine C/N choice</h2>
     1269(twice to get convergence) and the <span class=SpellE>Rw</span> ~12%.</p>
     1270
     1271<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 7. Determine
     1272C/N choice<o:p></o:p></span></h2>
    4641273
    4651274<p class=MsoNormal>We know from the chemistry that the N atom is in the 2
    466 position of the pyridine ring, i.e. next to the point of attachment to the S-atom.
    467 However, we don’t know which one that is and we have 8 atoms of which 4 are C
    468 and 4 are N.</p>
     1275position of the pyridine ring, i.e. next to the point of attachment to the
     1276S-atom. However, we don’t know which one that is and we have 8 atoms of which 4
     1277are C and 4 are N.</p>
    4691278
    4701279<p class=MsoNormal>To work out the C/N problem above we need the atoms to be in
     
    4871296<p class=MsoNormal>&nbsp;</p>
    4881297
    489 <p class=MsoNormal><img width=474 height=386 id="Picture 9"
    490 src="CFSingleCrystal_files/image014.jpg"></p>
     1298<p class=MsoNormal><span style='mso-no-proof:yes'><img width=474 height=386
     1299id="_x0000_i1029" src="CFSingleCrystal_files/image014.jpg"></span></p>
    4911300
    4921301<p class=MsoNormal>Now go to the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
    493 tab. If you look carefully, you can see that the atoms in each SS-dipyridyl are
    494 grouped together in the table but they are not in chemically sensible order.
    495 The atoms can be reordered by selecting one row with the <b><span
    496 style='font-family:"Calibri",sans-serif'>Alt</span></b> key down (the status
    497 line will tell which atom is selected to move) and then with the <b><span
    498 style='font-family:"Calibri",sans-serif'>Alt</span></b> key still down pick a
    499 row below where you want to insert it. I ordered them so each S-atom was
    500 followed by the C-atoms in order around the ring; my list looked like (I show
    501 just the 1<sup>st</sup> SS dipyridyl molecule)</p>
    502 
    503 <p class=MsoNormal><img width=624 height=408 id="Picture 10"
    504 src="CFSingleCrystal_files/image015.png"></p>
     1302tab. If you look carefully, you can see that the atoms in each SS-<span
     1303class=SpellE>dipyridyl</span> are grouped together in the table but they are
     1304not in chemically sensible order. The atoms can be reordered by selecting one
     1305row with the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b>
     1306key down (the status line will tell which atom is selected to move) and then
     1307with the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b> key
     1308still down pick a row below where you want to insert it. I ordered them so each
     1309S-atom was followed by the C-atoms in order around the ring; my list looked
     1310like (I show just the 1<sup>st</sup> SS <span class=SpellE>dipyridyl</span>
     1311molecule)</p>
     1312
     1313<p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=408
     1314id="_x0000_i1028" src="CFSingleCrystal_files/image015.png"></span></p>
    5051315
    5061316<p class=MsoNormal>Once you have reordered the atoms to your satisfaction they
     
    5181328<b><span style='font-family:"Calibri",sans-serif'>X</span></b> &amp; <b><span
    5191329style='font-family:"Calibri",sans-serif'>U</span></b> for these. Do <b><span
    520 style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the Rw
    521 will drop to ~10% and 4 of the atom <b><span style='font-family:"Calibri",sans-serif'>frac</span></b>
    522 values will be ~1.25 while the others are ~1.0. The former are N-atoms and the
    523 latter are C-atoms. Change the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
     1330style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the <span
     1331class=SpellE>Rw</span> will drop to ~10% and 4 of the atom <span class=SpellE><b><span
     1332style='font-family:"Calibri",sans-serif'>frac</span></b></span> values will be
     1333~1.25 while the others are ~1.0. The former are N-atoms and the latter are
     1334C-atoms. Change the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
    5241335for the N-atoms and repeat <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
    525 the Rw will be high to start, but immediately fall to ~10%. In the Atom table
    526 all 8 refined frac values are be now ~1.0. To finish this part of the
    527 refinement, set all <b><span style='font-family:"Calibri",sans-serif'>frac</span></b>
    528 values to <b><span style='font-family:"Calibri",sans-serif'>1.0</span></b> and
    529 all refine flags to <b><span style='font-family:"Calibri",sans-serif'>XU</span></b>.
    530 Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
    531 the final Rw ~10.5%</p>
    532 
    533 <h2>Step 8. Anisotropic thermal motion refinement</h2>
     1336the <span class=SpellE>Rw</span> will be high to start, but immediately fall to
     1337~10%. In the Atom table all 8 refined <span class=SpellE>frac</span> values are
     1338be now ~1.0. To finish this part of the refinement, set all <span class=SpellE><b><span
     1339style='font-family:"Calibri",sans-serif'>frac</span></b></span> values to <b><span
     1340style='font-family:"Calibri",sans-serif'>1.0</span></b> and all refine flags to
     1341<b><span style='font-family:"Calibri",sans-serif'>XU</span></b>. Do <b><span
     1342style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the final
     1343<span class=SpellE>Rw</span> ~10.5%</p>
     1344
     1345<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 8. Anisotropic
     1346thermal motion refinement<o:p></o:p></span></h2>
    5341347
    5351348<p class=MsoNormal>Given reasonable measured structure factors one can improve
    536 a crystal model by using anisotropic thermal motion models for all the
    537 nonhydrogen atoms. To convert all the atoms here select the Atoms tab and then
    538 do a double LB click on the I/A column heading. Select Anisotropic from the
    539 popup and press OK; the Atom table will be redrawn with Uij values equivalent
    540 to the corresponding Uiso (now hidden). Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
    541 the final Rw ~8.2%</p>
    542 
    543 <h2 style='page-break-after:avoid'>Step 9. H-atom placement &amp; final
    544 refinement</h2>
    545 
    546 <p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per
    547 pyridine ring (16 in all). One could do this (painfully) by hand by looking for
    548 them in <span style='font-family:Symbol'>D</span>F maps, but it is simpler to just
    549 place them knowing the bonding chemistry of the rings. To start this select the
    550 <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b> tab for the
    551 phase. Then select the C-atoms by a double LB click on the <b><span
     1349a crystal model by using anisotropic thermal motion models for all the <span
     1350class=SpellE>nonhydrogen</span> atoms. To convert all the atoms here select the
     1351Atoms tab and then do a double LB click on the I/A column heading. Select
     1352Anisotropic from the popup and press OK; the Atom table will be redrawn with <span
     1353class=SpellE>Uij</span> values equivalent to the corresponding <span
     1354class=SpellE>Uiso</span> (now hidden). Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
     1355the final <span class=SpellE>Rw</span> ~8.2%</p>
     1356
     1357<h2 style='page-break-after:avoid'><span style='mso-fareast-font-family:"Times New Roman"'>Step
     13589. H-atom placement &amp; final refinement<o:p></o:p></span></h2>
     1359
     1360<p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per pyridine
     1361ring (16 in all). One could do this (painfully) by hand by looking for them in <span
     1362style='font-family:Symbol'>D</span>F maps, but it is simpler to just place them
     1363knowing the bonding chemistry of the rings. To start <span class=GramE>this</span>
     1364select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
     1365tab for the phase. Then select the C-atoms by a double LB click on the <b><span
    5521366style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and
    5531367select <b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the
     
    5591373popup will appear</p>
    5601374
    561 <p class=MsoNormal><img width=400 height=485 id="Picture 8"
    562 src="CFSingleCrystal_files/image016.png"></p>
     1375<p class=MsoNormal><span style='mso-no-proof:yes'><img width=400 height=485
     1376id="_x0000_i1027" src="CFSingleCrystal_files/image016.png"></span></p>
    5631377
    5641378<p class=MsoNormal>This is the hydrogen add control; it shows both the expected
     
    5661380determine the geometry of the C-H bond. Check to make sure that 4 H-atoms will
    5671381be added for each ring. Note that C2, C9, C16 &amp; C23 will not have an H-atom
    568 added as these are the S-atom attachment points in SS-dipyridyl. Press <b><span
    569 style='font-family:"Calibri",sans-serif'>Ok</span></b>; the H-atoms will be
    570 inserted immediately after the corresponding C-atoms and the drawing is updated
    571 showing van der Waals spheres for all atoms.</p>
    572 
    573 <p class=MsoNormal><img width=624 height=396 id="Picture 15"
    574 src="CFSingleCrystal_files/image017.png"></p>
     1382added as these are the S-atom attachment points in SS-<span class=SpellE>dipyridyl</span>.
     1383Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the
     1384H-atoms will be inserted immediately after the corresponding C-atoms and the
     1385drawing is updated showing van der Waals spheres for all atoms.</p>
     1386
     1387<p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=396
     1388id="_x0000_i1026" src="CFSingleCrystal_files/image017.png"></span></p>
    5751389
    5761390<p class=MsoNormal>&nbsp;</p>
    5771391
    578 <p class=MsoNormal><img width=483 height=394 id="Picture 18"
    579 src="CFSingleCrystal_files/image018.jpg"></p>
     1392<p class=MsoNormal><span style='mso-no-proof:yes'><img width=483 height=394
     1393id="_x0000_i1025" src="CFSingleCrystal_files/image018.jpg"></span></p>
    5801394
    5811395<p class=MsoNormal>Next, do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
    582 there will be an immediate drop in Rw ~3.2%. Note that we did not refine the
    583 H-atom positions or thermal parameters. The H-atom insertion process retains
    584 the mechanisms for creating them in the first place and these tools can be used
    585 to move them to reflect the changes in the C-atom parameters thus forcing them
    586 to ride on the C-atoms. Do <b><span style='font-family:"Calibri",sans-serif'>Edit/Update
    587 H atoms</span></b>; the H-atom positions &amp; Uisos will be revised. Repeat <b><span
     1396there will be an immediate drop in <span class=SpellE>Rw</span> ~3.2%. Note
     1397that we did not refine the H-atom positions or thermal parameters. The H-atom
     1398insertion process retains the mechanisms for creating them in the first place
     1399and these tools can be used to move them to reflect the changes in the C-atom
     1400parameters thus forcing them to ride on the C-atoms. Do <b><span
     1401style='font-family:"Calibri",sans-serif'>Edit/Update H atoms</span></b>; the
     1402H-atom positions &amp; <span class=SpellE>Uisos</span> will be revised. Repeat <b><span
    5881403style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; there
    589 will be a slight improvement in Rw. Repeat these two steps (twice); Rw should
    590 not change on the last round. This completes the refinement of the SS-dipyridyl
     1404will be a slight improvement in <span class=SpellE>Rw</span>. Repeat these two
     1405steps (twice); <span class=SpellE>Rw</span> should not change on the last
     1406round. This completes the refinement of the SS-<span class=SpellE>dipyridyl</span>
    5911407structure. You can generate a final <span style='font-family:Symbol'>D</span>F
    5921408map from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
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