Ignore:
Timestamp:
May 13, 2016 9:15:26 AM (7 years ago)
Author:
vondreele
Message:

make visible as html

Location:
Tutorials/CFXraySingleCrystal
Files:
11 deleted
8 edited

Legend:

Unmodified
Added
Removed

  • Tutorials/CFXraySingleCrystal/CFSingleCrystal.htm

    • Property svn:mime-type set to text/html
    r2099 r2262  
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     139
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    … …  
    1041150
    1042151<p class=MsoNormal>In this exercise we will use a set of X-ray single crystal
    1043 structure factors to solve the structure of <span class=SpellE>dipyridyl</span>
    1044 disulfide by charge flipping and then refine the structure by least-squares.
    1045 The structure will be completed by adding the requisite hydrogen atoms and by
    1046 using anisotropic thermal parameters for the heavier atoms. The structure was
    1047 originally solved by <span class=SpellE>Raghavan</span> &amp; <span
    1048 class=SpellE>Seff</span>, <span class=SpellE>Acta</span> <span class=SpellE>Cryst</span>.
    1049 B33, 386-391 (1977) in the space group P2<sub>1</sub>/c with one disordered
    1050 pyridine ring with indications that the true space group was P2<sub>1</sub>. It
    1051 was subsequently reinvestigated by Young (2014
    1052 .) who found that the true space
    1053 group was P2<sub>1</sub> with 4 molecules in the asymmetric unit. The data used
    1054 in the latter analysis is what is used here and is provided as <span
    1055 class=GramE>a</span> “<span class=SpellE>fcf</span>” file obtained after
    1056 structure analysis by Shelx-97; the structure factors are scaled to those
    1057 calculated from the structure. We will solve the P 2<sub>1</sub>/c structure
    1058 first.</p>
    1059 
    1060 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
     152structure factors to solve the structure of dipyridyl disulfide by charge flipping
     153and then refine the structure by least-squares. The structure will be completed
     154by adding the requisite hydrogen atoms and by using anisotropic thermal
     155parameters for the heavier atoms. The structure was originally solved by
     156Raghavan &amp; Seff, Acta Cryst. B33, 386-391 (1977) in the space group P2<sub>1</sub>/c
     157with one disordered pyridine ring with indications that the true space group
     158was P2<sub>1</sub>. It was subsequently reinvestigated by Young (2014
     159.) who
     160found that the true space group was P2<sub>1</sub> with 4 molecules in the
     161asymmetric unit. The data used in the latter analysis is what is used here and
     162is provided as a “fcf” file obtained after structure analysis by Shelx-97; the
     163structure factors are scaled to those calculated from the structure. We will
     164solve the P 2<sub>1</sub>/c structure first.</p>
     165
     166<p class=MsoNormal>&nbsp;</p>
    1061167
    1062168<p class=MsoNormal>Note that menu entries and user input are shown in bold face
    1063 below as <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1064 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1065 Calibri;mso-bidi-theme-font:minor-latin'>Help/About GSAS-II</span></b>, which
    1066 lists first the name of the menu (here <b style='mso-bidi-font-weight:normal'><span
    1067 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1068 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1069 minor-latin'>Help</span></b>) and second the name of the entry in the menu
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    1072 Calibri;mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>). If you have
    1073 not done so already, start GSAS-II</p>
     169below as <b><span style='font-family:"Calibri",sans-serif'>Help/About GSAS-II</span></b>,
     170which lists first the name of the menu (here <b><span style='font-family:"Calibri",sans-serif'>Help</span></b>)
     171and second the name of the entry in the menu (here <b><span style='font-family:
     172"Calibri",sans-serif'>About GSAS-II</span></b>). If you have not done so
     173already, start GSAS-II</p>
    1074174
    1075175<h2>Step 1. Input phase information</h2>
    1076176
    1077 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
    1078 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    1079 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
    1080 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1081 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1082 Calibri;mso-bidi-theme-font:minor-latin'>Data/Add phase</span></b> menu item
    1083 add a new phase into the current GSAS-II project. A popup window will appear
    1084 asking for a phase name; I entered <b style='mso-bidi-font-weight:normal'><span
    1085 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1086 mso-hansi-theme-font:minor-latin'>SS <span class=SpellE>dipyridyl</span></span></b>;
    1087 press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1088 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>
    1089 when done. Select <b style='mso-bidi-font-weight:normal'><span
    1090 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1091 mso-hansi-theme-font:minor-latin'>Loaded Data/Phases/SS <span class=SpellE>dipyridyl</span></span></b>
    1092 from the GSAS-II Data tree window. The General tab for Phase Data will appear.</p>
    1093 
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    1107   <v:f eqn="prod @7 21600 pixelWidth"/>
    1108   <v:f eqn="sum @8 21600 0"/>
    1109   <v:f eqn="prod @7 21600 pixelHeight"/>
    1110   <v:f eqn="sum @10 21600 0"/>
    1111  </v:formulas>
    1112  <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    1113  <o:lock v:ext="edit" aspectratio="t"/>
    1114 </v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1042" type="#_x0000_t75"
    1115  style='width:393pt;height:230.25pt;visibility:visible;mso-wrap-style:square'>
    1116  <v:imagedata src="CFSingleCrystal_files/image001.png" o:title=""/>
    1117 </v:shape></span></p>
    1118 
    1119 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
    1120 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    1121 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
    1122 the space group <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1123 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1124 minor-latin'>P 21/c</span></b> (don’t forget the space between P &amp; 21/c)
    1125 &amp; press <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1126 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1127 minor-latin'>Enter</span></b>. A Space Group Information popup window will
    1128 appear; press <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1129 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1130 minor-latin'>OK</span></b>. The General window will be refreshed showing only
    1131 the needed lattice <span style='mso-no-proof:yes'>parameters for P 21/c.</span></p>
    1132 
    1133 <p class=MsoListParagraph><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_3"
    1134  o:spid="_x0000_i1041" type="#_x0000_t75" style='width:391.5pt;height:270.75pt;
    1135  visibility:visible;mso-wrap-style:square'>
    1136  <v:imagedata src="CFSingleCrystal_files/image002.png" o:title=""/>
    1137 </v:shape></span></p>
    1138 
    1139 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
    1140 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    1141 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
    1142 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1143 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>15.8489</span></b>,
    1144 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1145 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5.5008</span></b>,
    1146 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1147 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>23.118</span></b>,
    1148 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1149 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>96.9160</span></b>
    1150 for a, b, c and beta, respectively; the unit cell volume will be recalculated
    1151 at each entry.</p>
     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>
     179menu item add a new phase into the current GSAS-II project. A popup window will
     180appear asking for a phase name; I entered <b><span style='font-family:"Calibri",sans-serif'>SS
     181dipyridyl</span></b>; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>
     182when done. Select <b><span style='font-family:"Calibri",sans-serif'>Loaded
     183Data/Phases/SS dipyridyl</span></b> from the GSAS-II Data tree window. The
     184General tab for Phase Data will appear.</p>
     185
     186<p class=MsoListParagraph><img width=524 height=307 id="Picture 1"
     187src="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
     19121/c</span></b> (don’t forget the space between P &amp; 21/c) &amp; press <b><span
     192style='font-family:"Calibri",sans-serif'>Enter</span></b>. A Space Group
     193Information popup window will appear; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
     194The General window will be refreshed showing only the needed lattice parameters
     195for P 21/c.</p>
     196
     197<p class=MsoListParagraph><img width=522 height=361 id="Picture 3"
     198src="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
     203style='font-family:"Calibri",sans-serif'>23.118</span></b>, and <b><span
     204style='font-family:"Calibri",sans-serif'>96.9160</span></b> for a, b, c and
     205beta, respectively; the unit cell volume will be recalculated at each entry.</p>
    1152206
    1153207<h2>Step 2. Import structure factors </h2>
    … …  
    1156210and the second is to connect the data with the phase within GSAS-II.</p>
    1157211
    1158 <p class=MsoNormal>To do these, do <b style='mso-bidi-font-weight:normal'><span
    1159 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1160 mso-hansi-theme-font:minor-latin'>Import/Structure factor/from CIF file</span></b>
    1161 from the main GSAS-II data tree window menu. A file selection dialog will
    1162 appear; find <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1163 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1164 minor-latin'>exercises\CF <span class=SpellE>Xray</span> single
    1165 crystal\S2dipyridyl.fcf</span></b> and press <b style='mso-bidi-font-weight:
    1166 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1167 minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>. A popup window
    1168 asking if this is the file you want; press <span class=GramE><b
    1169 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1170 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b></span>.
     212<p class=MsoNormal>To do these, do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure
     213factor/from CIF file</span></b> from the main GSAS-II data tree window menu. A
     214file selection dialog will appear; find <b><span style='font-family:"Calibri",sans-serif'>exercises\CF
     215Xray single crystal\S2dipyridyl.fcf</span></b> and press <b><span
     216style='font-family:"Calibri",sans-serif'>Open</span></b>. A popup window asking
     217if this is the file you want; press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b>.
    1171218After a pause while the file is read a new popup will appear offering the
    1172 chance to rename the structure factor set; press <b style='mso-bidi-font-weight:
    1173 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1174 minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. After some time a
    1175 new popup will appear to <span style='mso-bidi-font-family:"Times New Roman"'>Add
    1176 the new structure factor set</span> to the SS <span class=SpellE>dipyridyl</span>
    1177 phase. Select the phase and press <b style='mso-bidi-font-weight:normal'><span
    1178 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1179 mso-hansi-theme-font:minor-latin'>OK</span></b>. The plot will show a rectangular
    1180 array of circles for the hk0 reflection layer; select the plot &amp; press <b
    1181 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1182 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k</span></b>
     219chance 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
     221Add the new structure factor set to the SS dipyridyl phase. Select the phase
     222and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. The
     223plot will show a rectangular array of circles for the hk0 reflection layer;
     224select the plot &amp; press <b><span style='font-family:"Calibri",sans-serif'>k</span></b>
    1183225to get an h0l layer.</p>
    1184226
    1185 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_2"
    1186  o:spid="_x0000_i1040" type="#_x0000_t75" style='width:5in;height:309pt;
    1187  visibility:visible;mso-wrap-style:square'>
    1188  <v:imagedata src="CFSingleCrystal_files/image003.png" o:title=""/>
    1189 </v:shape></span></p>
    1190 
    1191 <p class=MsoNormal>Because the <span class=SpellE>fcf</span> file has both
    1192 observed and calculated structure factors, the plot shows a small R value for
    1193 the layer. The observed structure factors are shown as blue rings, the
    1194 calculated ones as green rings and a small green or red dot may appear at each
    1195 ring center showing <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>. If
    1196 the reflection data file had only observed structure factors then only blue
    1197 rings will be seen. You can explore the plot options in the ‘<b
    1198 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1199 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>K</span></b>’
    1200 box in the plot toolbar.</p>
     227<p class=MsoNormal><img width=480 height=412 id="Picture 2"
     228src="CFSingleCrystal_files/image003.png"></p>
     229
     230<p class=MsoNormal>Because the fcf file has both observed and calculated
     231structure factors, the plot shows a small R value for the layer. The observed
     232structure factors are shown as blue rings, the calculated ones as green rings
     233and a small green or red dot may appear at each ring center showing F<sub>o</sub>-F<sub>c</sub>.
     234If the reflection data file had only observed structure factors then only blue
     235rings will be seen. You can explore the plot options in the ‘<b><span
     236style='font-family:"Calibri",sans-serif'>K</span></b>’ box in the plot toolbar.</p>
    1201237
    1202238<h2>Step 3. Setup for charge flipping</h2>
    … …  
    1205241flipping. Charge flipping in GSAS-II is implemented to solve the crystal
    1206242structure without consideration of space group symmetry. To do this it operates
    1207 on the entire unit cell volume to a selected resolution (usually 0.5<span
    1208 style='mso-bidi-font-family:"Times New Roman"'>Å</span>) using fast <span
    1209 class=SpellE><span class=GramE>fourier</span></span> transform techniques. This
    1210 requires a set of structure factors in an array of the same dimensions as the
    1211 density array covering the unit cell (i.e. a box bounded by ~0.5<span
    1212 style='mso-bidi-font-family:"Times New Roman"'>Å</span> resolution). The space
    1213 group symmetry is applied to the observed structure factors to create a full
    1214 sphere which is then zero filled out to the 0.5<span style='mso-bidi-font-family:
    1215 "Times New Roman"'>Å</span> resolution bounded box. To be reasonably assured of
    1216 success, the observed structure factors should extend to ~1<span
    1217 style='mso-bidi-font-family:"Times New Roman"'>Å</span> resolution; we have
    1218 that here for this example. To begin select <b style='mso-bidi-font-weight:
    1219 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1220 minor-latin;mso-hansi-theme-font:minor-latin'>Phases/SS <span class=SpellE>dipyridyl</span></span></b>
    1221 from the GSAS-II data tree; the General tab will be shown</p>
    1222 
    1223 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_4"
    1224  o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;height:300.75pt;
    1225  visibility:visible;mso-wrap-style:square'>
    1226  <v:imagedata src="CFSingleCrystal_files/image004.png" o:title=""/>
    1227 </v:shape></span></p>
    1228 
    1229 <p class=MsoNormal>Find the <b style='mso-bidi-font-weight:normal'><span
    1230 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1231 mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> and change
    1232 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1233 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak cutoff
    1234 %</span></b> to <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1235 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1236 minor-latin'>10</span></b>; then immediately below find the <b
    1237 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1238 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Charge flip
    1239 controls</span></b>. Press <b style='mso-bidi-font-weight:normal'><span
    1240 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1241 mso-hansi-theme-font:minor-latin'>Select reflection sets</span></b>, pick <b
    1242 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1243 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>HKLF
    1244 S2dipyridyl.fcf:1a</span></b> from the list (the only one) and press <b
    1245 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1246 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1247 If you had multiple data sets for this phase, you can pick more than one and
    1248 GSAS-II will use a “last one in” process for assembling the reflection set to
    1249 use for charge flipping. There are four more settings to consider: 1) <span
    1250 class=SpellE>kMax</span> controls the upper cutoff for charge flipping; if the
    1251 density is &gt; k-Max*<span style='font-family:Symbol'>s</span><sub><span
    1252 style='font-family:Symbol;mso-bidi-font-family:"Times New Roman"'>r</span></sub>
     243on the entire unit cell volume to a selected resolution (usually 0.5Å) using
     244fast fourier transform techniques. This requires a set of structure factors in
     245an 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
     247to the observed structure factors to create a full sphere which is then zero
     248filled out to the 0.5Å resolution bounded box. To be reasonably assured of
     249success, the observed structure factors should extend to ~1Å resolution; we
     250have 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
     252tree; the General tab will be shown</p>
     253
     254<p class=MsoNormal><img width=624 height=401 id="Picture 4"
     255src="CFSingleCrystal_files/image004.png"></p>
     256
     257<p class=MsoNormal>Find the <b><span style='font-family:"Calibri",sans-serif'>Fourier
     258map controls</span></b> and change the <b><span style='font-family:"Calibri",sans-serif'>Peak
     259cutoff %</span></b> to <b><span style='font-family:"Calibri",sans-serif'>10</span></b>;
     260then immediately below find the <b><span style='font-family:"Calibri",sans-serif'>Charge
     261flip controls</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Select
     262reflection sets</span></b>, pick <b><span style='font-family:"Calibri",sans-serif'>HKLF
     263S2dipyridyl.fcf:1a</span></b> from the list (the only one) and press <b><span
     264style='font-family:"Calibri",sans-serif'>OK</span></b>. If you had multiple
     265data sets for this phase, you can pick more than one and GSAS-II will use a
     266“last one in” process for assembling the reflection set to use for charge
     267flipping. There are four more settings to consider: 1) kMax controls the upper
     268cutoff for charge flipping; if the density is &gt; k-Max*<span
     269style='font-family:Symbol'>s</span><sub><span style='font-family:Symbol'>r</span></sub>
    1253270(map standard deviation) then flip the charge. This prevents the “Uranium
    1254271solution” sometimes found where all the density is concentrated in a single
    1255272peak. A useful guide is to use twice the largest atomic number of any element
    1256273in your structure. For equal atom problems use 12-15; adjust upward for
    1257 structures with heavy &amp; light atoms. In this case, set <b style='mso-bidi-font-weight:
    1258 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1259 minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b> to <b
    1260 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1261 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>30.0</span></b>
    1262 to allow the S atom to appear. 2) k-Factor controls the lower level for charge
    1263 flipping; if the density is &lt; k-Factor*<span style='font-family:Symbol'>s</span><sub><span
    1264 style='font-family:Symbol;mso-bidi-font-family:"Times New Roman"'>r</span></sub><span
    1265 style='mso-bidi-font-family:"Times New Roman"'> then flip the charge. The
    1266 default value seems to work pretty well; I’d only change it if the charge
    1267 flipping is having trouble solving the structure. 3) Resolution selects the
    1268 spacing between map points. 0.5Å is sufficient in most cases. Choosing a
    1269 smaller value requires more map points (NB: GSAS-II uses the entire unit cell
    1270 volume for charge flipping) and thus will require more structure factors since
    1271 the fast <span class=SpellE>fourier</span> algorithm requires the same size
    1272 arrays in both real space and reciprocal space. This will slow down the charge
    1273 flip process. 4) Normalizing element selects a form factor to rescale the
    1274 structure factors thus “sharpening” the density map. I suggest trying </span><span
    1275 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1276 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1277 minor-latin;mso-bidi-font-family:"Times New Roman"'>None</span></b></span><span
    1278 style='mso-bidi-font-family:"Times New Roman"'> first, otherwise select a
    1279 representative element (really doesn’t matter which).<o:p></o:p></span></p>
     274structures with heavy &amp; light atoms. In this case, set <b><span
     275style='font-family:"Calibri",sans-serif'>k-Max</span></b> to <b><span
     276style='font-family:"Calibri",sans-serif'>30.0</span></b> to allow the S atom to
     277appear. 2) k-Factor controls the lower level for charge flipping; if the
     278density is &lt; k-Factor*<span style='font-family:Symbol'>s</span><sub><span
     279style='font-family:Symbol'>r</span></sub> then flip the charge. The default
     280value seems to work pretty well; I’d only change it if the charge flipping is
     281having trouble solving the structure. 3) Resolution selects the spacing between
     282map points. 0.5Å is sufficient in most cases. Choosing a smaller value requires
     283more map points (NB: GSAS-II uses the entire unit cell volume for charge
     284flipping) and thus will require more structure factors since the fast fourier
     285algorithm requires the same size arrays in both real space and reciprocal
     286space. This will slow down the charge flip process. 4) Normalizing element
     287selects a form factor to rescale the structure factors thus “sharpening” the
     288density map. I suggest trying <b><span style='font-family:"Calibri",sans-serif'>None</span></b>
     289first, otherwise select a representative element (really doesn’t matter which).</p>
    1280290
    1281291<h2 style='page-break-after:avoid'>Step 4. Charge flipping</h2>
    1282292
    1283293<p class=MsoNormal>With the controls all set you can now do charge flipping;
    1284 from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1285 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    1286 tab do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1287 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge
     294from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
     295tab do <b><span style='font-family:"Calibri",sans-serif'>Compute/Charge
    1288296flipping</span></b>. A progress bar popup will appear showing the residual
    1289 between the observed structure factors and those obtained from the inverse <span
    1290 class=SpellE><span class=GramE>fourier</span></span> transform of the last
    1291 flipped density map. It should quickly decrease to the ~20% range and level out
    1292 indicating a good charge flip solution. When it has reached this, press <span
    1293 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1294 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1295 minor-latin'>Cancel</span></b></span> to stop the process.</p>
    1296 
    1297 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_6"
    1298  o:spid="_x0000_i1038" type="#_x0000_t75" style='width:274.5pt;height:135pt;
    1299  visibility:visible;mso-wrap-style:square'>
    1300  <v:imagedata src="CFSingleCrystal_files/image005.png" o:title=""/>
    1301 </v:shape></span></p>
     297between the observed structure factors and those obtained from the inverse
     298fourier transform of the last flipped density map. It should quickly decrease
     299to the ~20% range and level out indicating a good charge flip solution. When it
     300has reached this, press <b><span style='font-family:"Calibri",sans-serif'>Cancel</span></b>
     301to stop the process.</p>
     302
     303<p class=MsoNormal><img width=366 height=180 id="Picture 6"
     304src="CFSingleCrystal_files/image005.png"></p>
    1302305
    1303306<p class=MsoNormal>The console window will show something like</p>
    1304307
    1305 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_7"
    1306  o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;height:124.5pt;
    1307  visibility:visible;mso-wrap-style:square'>
    1308  <v:imagedata src="CFSingleCrystal_files/image006.png" o:title=""/>
    1309 </v:shape></span></p>
    1310 
    1311 <p class=MsoNormal>There may be a pause at <b style='mso-bidi-font-weight:normal'><span
    1312 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1313 mso-hansi-theme-font:minor-latin'>Begin <span class=SpellE><span class=GramE>fourier</span></span>
    1314 map search</span></b> before it finishes. Provided is a summary of the charge
    1315 flip calculation (time, map size, density range &amp; structure factor
     308<p class=MsoNormal><img width=624 height=166 id="Picture 7"
     309src="CFSingleCrystal_files/image006.png"></p>
     310
     311<p class=MsoNormal>There may be a pause at <b><span style='font-family:"Calibri",sans-serif'>Begin
     312fourier map search</span></b> before it finishes. Provided is a summary of the
     313charge flip calculation (time, map size, density range &amp; structure factor
    1316314residual). The map offset is discovered by an analysis of the reflection phases
    1317315with respect to how they should be distributed for your chosen space group.
    … …  
    1322320the structure is drawn (I’ve made the view down the b-axis)</p>
    1323321
    1324 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_11"
    1325  o:spid="_x0000_i1036" type="#_x0000_t75" style='width:358.5pt;height:301.5pt;
    1326  visibility:visible;mso-wrap-style:square'>
    1327  <v:imagedata src="CFSingleCrystal_files/image007.png" o:title="" croptop="12490f"
    1328   cropbottom="16795f" cropleft="47577f" cropright="3045f"/>
    1329 </v:shape></span></p>
    1330 
    1331 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>and</span>
    1332 the Phase data window will show the map peaks tab</p>
    1333 
    1334 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_12"
    1335  o:spid="_x0000_i1035" type="#_x0000_t75" style='width:375pt;height:225pt;
    1336  visibility:visible;mso-wrap-style:square'>
    1337  <v:imagedata src="CFSingleCrystal_files/image008.png" o:title=""/>
    1338 </v:shape></span></p>
    1339 
    1340 <p class=MsoNormal>These are listed in order of magnitude; a double click on any
    1341 of the table headings will sort the list according to that parameter. My list
    1342 has 112 entries; <span class=SpellE>dipyridyl</span> disulfide has 14 C &amp; S
    1343 atoms so this list is appropriate for 8 molecules in the unit cell and thus all
    1344 atoms were found in this charge flipping result.</p>
     322<p class=MsoNormal><img width=478 height=402 id="Picture 11"
     323src="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"
     328src="CFSingleCrystal_files/image008.png"></p>
     329
     330<p class=MsoNormal>These are listed in order of magnitude; a double click on
     331any of the table headings will sort the list according to that parameter. My
     332list has 112 entries; dipyridyl disulfide has 14 C &amp; S atoms so this list
     333is appropriate for 8 molecules in the unit cell and thus all atoms were found
     334in this charge flipping result.</p>
    1345335
    1346336<p class=MsoNormal>If all went well then the drawing should nicely show all the
    1347 atoms in the structure placed properly with respect to the locations of the inversion
    1348 centers (they are at all the corners, edge centers, face centers and cell
    1349 center). If not then you can shift the map &amp; peaks with the <b
    1350 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1351 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>,
    1352 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1353 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>,
    1354 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1355 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
    1356 &amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1357 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
    1358 keys (NB: rotate the drawing so the axes are ~horizontal/vertical); the
    1359 map/peaks will move in resolution steps (0.5A). The table is also updated with
    1360 new peak positions. You could also just repeat the charge flipping and hope to
    1361 get a better map offset solution (examine the map offset chi**2 to get a sense
    1362 of this). You can also show the map density (highest point is shown as a green
    1363 dot somewhere in the map – on <span class=GramE>a</span> S-atom position);
    1364 select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1365 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1366 minor-latin'>Draw Options</span></b> tab and use the <b style='mso-bidi-font-weight:
    1367 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1368 minor-latin;mso-hansi-theme-font:minor-latin'>Contour level</span></b> slider.
    1369 The drawing will show green dots at each set map point with size in proportion
    1370 to the density. The mouse <b style='mso-bidi-font-weight:normal'><span
    1371 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1372 mso-hansi-theme-font:minor-latin'>RB</span></b> can be used to slide the
    1373 structure around; the density is always drawn in a space surrounding the view
    1374 point (multicolored cross at the center). While here you can also change the <b
    1375 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1376 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond search
    1377 factor</span></b> to <b style='mso-bidi-font-weight:normal'><span
    1378 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1379 mso-hansi-theme-font:minor-latin'>0.90</span></b> to ensure all S-C bonds are
    1380 shown.</p>
     337atoms in the structure placed properly with respect to the locations of the
     338inversion centers (they are at all the corners, edge centers, face centers and
     339cell center). If not then you can shift the map &amp; peaks with the <b><span
     340style='font-family:"Calibri",sans-serif'>L</span></b>, <b><span
     341style='font-family:"Calibri",sans-serif'>R</span></b>, <b><span
     342style='font-family:"Calibri",sans-serif'>U</span></b> &amp; <b><span
     343style='font-family:"Calibri",sans-serif'>D</span></b> keys (NB: rotate the
     344drawing so the axes are ~horizontal/vertical); the map/peaks will move in
     345resolution steps (0.5A). The table is also updated with new peak positions. You
     346could also just repeat the charge flipping and hope to get a better map offset
     347solution (examine the map offset chi**2 to get a sense of this). You can also
     348show the map density (highest point is shown as a green dot somewhere in the
     349map – on a S-atom position); select the <b><span style='font-family:"Calibri",sans-serif'>Draw
     350Options</span></b> tab and use the <b><span style='font-family:"Calibri",sans-serif'>Contour
     351level</span></b> slider. The drawing will show green dots at each set map point
     352with size in proportion to the density. The mouse <b><span style='font-family:
     353"Calibri",sans-serif'>RB</span></b> can be used to slide the structure around;
     354the density is always drawn in a space surrounding the view point (multicolored
     355cross at the center). While here you can also change the <b><span
     356style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span
     357style='font-family:"Calibri",sans-serif'>0.90</span></b> to ensure all S-C
     358bonds are shown.</p>
    1381359
    1382360<p class=MsoNormal>If the charge flipping has failed (high residual &amp; no
    … …  
    1384362new random start for the structure factor phases which may lead to a good
    1385363solution. After a few attempts, you can try different control settings to see
    1386 if that will coax out a good solution; first be sure <b style='mso-bidi-font-weight:
    1387 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1388 minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b> is properly set
    1389 and then perhaps try different <b style='mso-bidi-font-weight:normal'><span
    1390 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1391 mso-hansi-theme-font:minor-latin'>k-Factors</span></b> and do <b
    1392 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1393 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing</span></b>
     364if that will coax out a good solution; first be sure <b><span style='font-family:
     365"Calibri",sans-serif'>k-Max</span></b> is properly set and then perhaps try
     366different <b><span style='font-family:"Calibri",sans-serif'>k-Factors</span></b>
     367and do <b><span style='font-family:"Calibri",sans-serif'>Normalizing</span></b>
    1394368by some element form factor. If it seemed to work but very few peaks were
    1395 found, make sure <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1396 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1397 minor-latin'>Peak cutoff</span></b> was properly set; you can then repeat the
    1398 peak search by doing <b style='mso-bidi-font-weight:normal'><span
    1399 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1400 mso-hansi-theme-font:minor-latin'>Compute/Search map</span></b>.</p>
     369found, make sure <b><span style='font-family:"Calibri",sans-serif'>Peak cutoff</span></b>
     370was properly set; you can then repeat the peak search by doing <b><span
     371style='font-family:"Calibri",sans-serif'>Compute/Search map</span></b>.</p>
    1401372
    1402373<h2>Step 5. Extract solution and make molecules</h2>
    … …  
    1404375<p class=MsoNormal>Assuming that the map &amp; peak positions are properly
    1405376placed with respect to the symmetry elements of the space group, we can now
    1406 select those peaks which describe the structure. Select the <b
    1407 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1408 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
    1409 tab and double LB click the blank upper left corner of the table; all entries
    1410 will be highlighted in blue. Then do <b style='mso-bidi-font-weight:normal'><span
    1411 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1412 mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>; after a
    1413 bit of time 1/4 of the peaks in the list will be highlighted and the
    1414 corresponding peaks in the drawing will be green (NB: if you navigate away from
    1415 this tab, this selection will be lost and you’ll have to repeat it!). Next, do <b
    1416 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1417 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
    1418 peaks/Move peaks</span></b>; these peaks will be transferred to the <b
    1419 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1420 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
    1421 list as H-atoms named according to their position in the magnitude column.</p>
    1422 
    1423 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_13"
    1424  o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;height:200.25pt;
    1425  visibility:visible;mso-wrap-style:square'>
    1426  <v:imagedata src="CFSingleCrystal_files/image009.png" o:title=""/>
    1427 </v:shape></span></p>
     377select those peaks which describe the structure. Select the <b><span
     378style='font-family:"Calibri",sans-serif'>Map peaks</span></b> tab and double LB
     379click the blank upper left corner of the table; all entries will be highlighted
     380in blue. Then do <b><span style='font-family:"Calibri",sans-serif'>Map
     381peaks/Unique peaks</span></b>; after a bit of time 1/4 of the peaks in the list
     382will be highlighted and the corresponding peaks in the drawing will be green
     383(NB: if you navigate away from this tab, this selection will be lost and you’ll
     384have to repeat it!). Next, do <b><span style='font-family:"Calibri",sans-serif'>Map
     385peaks/Move peaks</span></b>; these peaks will be transferred to the <b><span
     386style='font-family:"Calibri",sans-serif'>Atoms</span></b> list as H-atoms named
     387according to their position in the magnitude column.</p>
     388
     389<p class=MsoNormal><img width=624 height=267 id="Picture 13"
     390src="CFSingleCrystal_files/image009.png"></p>
    1428391
    1429392<p class=MsoNormal>The drawing will show white balls at the atom positions
    1430393scattered over several molecules.</p>
    1431394
    1432 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_14"
    1433  o:spid="_x0000_i1033" type="#_x0000_t75" style='width:355.5pt;height:306.75pt;
    1434  visibility:visible;mso-wrap-style:square'>
    1435  <v:imagedata src="CFSingleCrystal_files/image010.png" o:title="" croptop="9479f"
    1436   cropbottom="18319f" cropleft="42631f" cropright="7857f"/>
    1437 </v:shape></span></p>
     395<p class=MsoNormal><img width=474 height=409 id="Picture 14"
     396src="CFSingleCrystal_files/image010.jpg"></p>
    1438397
    1439398<p class=MsoNormal>Notice that 4 atoms have magnitudes ~90+, these are the S
    1440 atoms. The rest are C &amp; N atoms. In the <b style='mso-bidi-font-weight:
    1441 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1442 minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab select the
    1443 first 4 atoms (press LB on the 1<sup>st</sup> &amp; shift LB on the 4<sup>th</sup>
    1444 one). Then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1445 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1446 minor-latin'>Edit/Modify atom parameters</span></b>; a popup window will
    1447 appear. Select <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1448 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1449 minor-latin'>Type</span></b> &amp; press <b style='mso-bidi-font-weight:normal'><span
    1450 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1451 mso-hansi-theme-font:minor-latin'>OK</span></b>; a Periodic Table will appear.
    1452 Select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1453 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>S</span></b>;
    1454 the atoms will be renames and their Type changed to S. Next select the remaining
    1455 H atoms (a quick way it to double LB click the <b style='mso-bidi-font-weight:
    1456 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1457 minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column heading
    1458 and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1459 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1460 minor-latin'>H</span></b> from the popup window). Then do <b style='mso-bidi-font-weight:
    1461 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1462 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b>
    1463 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1464 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b>
    1465 from the popup; select <b style='mso-bidi-font-weight:normal'><span
    1466 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1467 mso-hansi-theme-font:minor-latin'>C</span></b> from the Periodic Table as we
    1468 don’t know which ones are N. The drawing will change (you may have to wiggle it
    1469 a bit to force the update).</p>
    1470 
    1471 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_17"
    1472  o:spid="_x0000_i1032" type="#_x0000_t75" style='width:5in;height:292.5pt;
    1473  visibility:visible;mso-wrap-style:square'>
    1474  <v:imagedata src="CFSingleCrystal_files/image011.png" o:title="" croptop="12086f"
    1475   cropbottom="17505f" cropleft="42193f" cropright="8105f"/>
    1476 </v:shape></span></p>
     399atoms. The rest are C &amp; N atoms. In the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
     400tab select the first 4 atoms (press LB on the 1<sup>st</sup> &amp; shift LB on
     401the 4<sup>th</sup> one). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
     402atom parameters</span></b>; a popup window will appear. Select <b><span
     403style='font-family:"Calibri",sans-serif'>Type</span></b> &amp; press <b><span
     404style='font-family:"Calibri",sans-serif'>OK</span></b>; a Periodic Table will
     405appear. Select <b><span style='font-family:"Calibri",sans-serif'>S</span></b>;
     406the atoms will be renames and their Type changed to S. Next select the
     407remaining H atoms (a quick way it to double LB click the <b><span
     408style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and
     409select <b><span style='font-family:"Calibri",sans-serif'>H</span></b> from the
     410popup window). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
     411atom parameters</span></b> and <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
     412from the popup; select <b><span style='font-family:"Calibri",sans-serif'>C</span></b>
     413from the Periodic Table as we don’t know which ones are N. The drawing will
     414change (you may have to wiggle it a bit to force the update).</p>
     415
     416<p class=MsoNormal><img width=480 height=390 id="Picture 17"
     417src="CFSingleCrystal_files/image011.jpg"></p>
    1477418
    1478419<p class=MsoNormal>Notice that the atoms are scattered over several molecules;
    1479420we want to assemble them into 2 conveniently placed ones. Begin by selecting an
    1480 atom (make sure the <b style='mso-bidi-font-weight:normal'><span
    1481 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1482 mso-hansi-theme-font:minor-latin'>Atom</span></b> tab is displayed &amp; do
    1483 shift LB on an atom in the drawing – I chose the S atom near the upper middle);
    1484 it will turn green and a line in the Atom table will be highlighted. Next do <b
    1485 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1486 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assemble
    1487 molecule</span></b>; a popup window will appear. Change the <b
    1488 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1489 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond search
    1490 factor</span></b> to <b style='mso-bidi-font-weight:normal'><span
    1491 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1492 mso-hansi-theme-font:minor-latin'>0.90</span></b> to be sure all S-C bonds are
    1493 found.</p>
    1494 
    1495 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_16"
    1496  o:spid="_x0000_i1031" type="#_x0000_t75" style='width:198.75pt;height:167.25pt;
    1497  visibility:visible;mso-wrap-style:square'>
    1498  <v:imagedata src="CFSingleCrystal_files/image012.png" o:title=""/>
    1499 </v:shape></span><span style='mso-spacerun:yes'> </span></p>
    1500 
    1501 <p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
    1502 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1503 mso-hansi-theme-font:minor-latin'>OK</span></b>; atoms will be collected into a
    1504 <span class=SpellE>well positioned</span> group, but others are not. Next
    1505 select one of the unassembled atoms (I chose a C-atom in a nearby SS-<span
    1506 class=SpellE>dipyridyl</span>) and do <b style='mso-bidi-font-weight:normal'><span
    1507 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1508 mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b>; there will
    1509 be two nicely assembled SS-<span class=SpellE>dipyridyls</span>.</p>
    1510 
    1511 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_5"
    1512  o:spid="_x0000_i1030" type="#_x0000_t75" style='width:5in;height:4in;
    1513  visibility:visible;mso-wrap-style:square'>
    1514  <v:imagedata src="CFSingleCrystal_files/image013.png" o:title="" croptop="11447f"
    1515   cropbottom="19102f" cropleft="41491f" cropright="8984f"/>
    1516 </v:shape></span></p>
     421atom (make sure the <b><span style='font-family:"Calibri",sans-serif'>Atom</span></b>
     422tab is displayed &amp; do shift LB on an atom in the drawing – I chose the S
     423atom near the upper middle); it will turn green and a line in the Atom table
     424will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Assemble
     425molecule</span></b>; a popup window will appear. Change the <b><span
     426style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span
     427style='font-family:"Calibri",sans-serif'>0.90</span></b> to be sure all S-C
     428bonds are found.</p>
     429
     430<p class=MsoNormal><img width=265 height=223 id="Picture 16"
     431src="CFSingleCrystal_files/image012.png"> </p>
     432
     433<p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>;
     434atoms will be collected into a well positioned group, but others are not. Next
     435select one of the unassembled atoms (I chose a C-atom in a nearby SS-dipyridyl)
     436and do <b><span style='font-family:"Calibri",sans-serif'>Edit/Assemble molecule</span></b>;
     437there will be two nicely assembled SS-dipyridyls.</p>
     438
     439<p class=MsoNormal><img width=480 height=384 id="Picture 5"
     440src="CFSingleCrystal_files/image013.jpg"></p>
    1517441
    1518442<p class=MsoNormal>You should probably save this project as it contains your
    … …  
    1522446
    1523447<p class=MsoNormal>Since we now have a structural model, we can do the initial
    1524 structure refinement. By default this will only refine the scale factor; do <b
    1525 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1526 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1527 from the main GSAS-II data tree window. Convergence will quickly occur with <span
    1528 class=SpellE>Rw</span> ~35%. More useful is to refine the atom positions and
    1529 isotropic thermal parameters. Select the <b style='mso-bidi-font-weight:normal'><span
    1530 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1531 mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab from the Phase window.
    1532 Then LB double click the <b style='mso-bidi-font-weight:normal'><span
    1533 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1534 mso-hansi-theme-font:minor-latin'>refine</span></b> column heading; a popup
    1535 window will appear. Select <b style='mso-bidi-font-weight:normal'><span
    1536 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1537 mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
    1538 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1539 minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> and press <b
    1540 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1541 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1542 The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1543 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
    1544 window will show <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1545 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1546 minor-latin'>XU</span></b> for each atom in the refine column. Then do <b
    1547 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1548 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1549 (twice to get convergence) and the <span class=SpellE>Rw</span> ~12%.</p>
     448structure refinement. By default this will only refine the scale factor; do <b><span
     449style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> from the
     450main GSAS-II data tree window. Convergence will quickly occur with Rw ~35%.
     451More useful is to refine the atom positions and isotropic thermal parameters.
     452Select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
     453tab from the Phase window. Then LB double click the <b><span style='font-family:
     454"Calibri",sans-serif'>refine</span></b> column heading; a popup window will
     455appear. Select <b><span style='font-family:"Calibri",sans-serif'>X</span></b>
     456and <b><span style='font-family:"Calibri",sans-serif'>U</span></b> and press <b><span
     457style='font-family:"Calibri",sans-serif'>OK</span></b>. The <b><span
     458style='font-family:"Calibri",sans-serif'>Atoms</span></b> window will show <b><span
     459style='font-family:"Calibri",sans-serif'>XU</span></b> for each atom in the
     460refine 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>
    1550462
    1551463<h2>Step 7. Determine C/N choice</h2>
    1552464
    1553465<p class=MsoNormal>We know from the chemistry that the N atom is in the 2
    1554 position of the pyridine ring, i.e. next to the point of attachment to the
    1555 S-atom. However, we don’t know which one that is and we have 8 atoms of which 4
    1556 are C and 4 are N.</p>
     466position of the pyridine ring, i.e. next to the point of attachment to the S-atom.
     467However, we don’t know which one that is and we have 8 atoms of which 4 are C
     468and 4 are N.</p>
    1557469
    1558470<p class=MsoNormal>To work out the C/N problem above we need the atoms to be in
    1559471a chemically sensible order. The assemble molecule routine did construct chains
    1560472of atoms but this ordering is not really satisfactory. The ordering can quickly
    1561 be done by hand by following a labelled drawing. First go to the <b
    1562 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1563 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
    1564 tab and double LB click the <b style='mso-bidi-font-weight:normal'><span
    1565 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1566 mso-hansi-theme-font:minor-latin'>Style</span></b> column; select <b
    1567 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1568 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>balls &amp;
    1569 sticks</span></b> from the popup box. Press <b style='mso-bidi-font-weight:
    1570 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1571 minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. Next, double LB
    1572 click the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1573 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Label</span></b>
    1574 column and select <b style='mso-bidi-font-weight:normal'><span
    1575 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1576 mso-hansi-theme-font:minor-latin'>name</span></b> from the popup box; press <b
    1577 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1578 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1579 Then go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1580 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1581 minor-latin'>Draw options</span></b> tab and adjust the <b style='mso-bidi-font-weight:
    1582 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1583 minor-latin;mso-hansi-theme-font:minor-latin'>Ball scale</span></b> &amp; <b
    1584 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1585 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond radius </span></b>to
     473be done by hand by following a labelled drawing. First go to the <b><span
     474style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and double
     475LB click the <b><span style='font-family:"Calibri",sans-serif'>Style</span></b>
     476column; select <b><span style='font-family:"Calibri",sans-serif'>balls &amp;
     477sticks</span></b> from the popup box. Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
     478Next, double LB click the <b><span style='font-family:"Calibri",sans-serif'>Label</span></b>
     479column and select <b><span style='font-family:"Calibri",sans-serif'>name</span></b>
     480from the popup box; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
     481Then go to the <b><span style='font-family:"Calibri",sans-serif'>Draw options</span></b>
     482tab and adjust the <b><span style='font-family:"Calibri",sans-serif'>Ball scale</span></b>
     483&amp; <b><span style='font-family:"Calibri",sans-serif'>Bond radius </span></b>to
    1586484allow the labels to be easily seen. After shifting the view point the drawing
    1587485should look something like</p>
    1588486
    1589 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1590 
    1591 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_9"
    1592  o:spid="_x0000_i1029" type="#_x0000_t75" style='width:355.5pt;height:289.5pt;
    1593  visibility:visible;mso-wrap-style:square'>
    1594  <v:imagedata src="CFSingleCrystal_files/image014.png" o:title="" croptop="11765f"
    1595   cropbottom="18146f" cropleft="38895f" cropright="11572f"/>
    1596 </v:shape></span></p>
    1597 
    1598 <p class=MsoNormal>Now go to the <b style='mso-bidi-font-weight:normal'><span
    1599 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1600 mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab. If you look carefully,
    1601 you can see that the atoms in each SS-<span class=SpellE>dipyridyl</span> are
    1602 grouped together in the table but they are not in chemically sensible order. The
    1603 atoms can be reordered by selecting one row with the <b style='mso-bidi-font-weight:
    1604 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1605 minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key down (the
    1606 status line will tell which atom is selected to move) and then with the <b
    1607 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1608 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b>
    1609 key still down pick a row below where you want to insert it. I ordered them so
    1610 each S-atom was followed by the C-atoms in order around the ring; my list
    1611 looked like (I show just the 1<sup>st</sup> SS <span class=SpellE>dipyridyl</span>
    1612 molecule)</p>
    1613 
    1614 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_10"
    1615  o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;height:306pt;
    1616  visibility:visible;mso-wrap-style:square'>
    1617  <v:imagedata src="CFSingleCrystal_files/image015.png" o:title=""/>
    1618 </v:shape></span></p>
     487<p class=MsoNormal>&nbsp;</p>
     488
     489<p class=MsoNormal><img width=474 height=386 id="Picture 9"
     490src="CFSingleCrystal_files/image014.jpg"></p>
     491
     492<p class=MsoNormal>Now go to the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
     493tab. If you look carefully, you can see that the atoms in each SS-dipyridyl are
     494grouped together in the table but they are not in chemically sensible order.
     495The atoms can be reordered by selecting one row with the <b><span
     496style='font-family:"Calibri",sans-serif'>Alt</span></b> key down (the status
     497line will tell which atom is selected to move) and then with the <b><span
     498style='font-family:"Calibri",sans-serif'>Alt</span></b> key still down pick a
     499row below where you want to insert it. I ordered them so each S-atom was
     500followed by the C-atoms in order around the ring; my list looked like (I show
     501just the 1<sup>st</sup> SS dipyridyl molecule)</p>
     502
     503<p class=MsoNormal><img width=624 height=408 id="Picture 10"
     504src="CFSingleCrystal_files/image015.png"></p>
    1619505
    1620506<p class=MsoNormal>Once you have reordered the atoms to your satisfaction they
    1621507can be renamed to be in order. To do this select all the atoms (double LB click
    1622 the empty corner box) and then do <b style='mso-bidi-font-weight:normal'><span
    1623 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1624 mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b>.
    1625 Select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1626 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Name</span></b>
    1627 and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1628 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
    1629 press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
    1630 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1631 mso-hansi-theme-font:minor-latin'>Yes</span></b></span> to the popup question.
    1632 The atoms will be renamed in numerical order. Do <b style='mso-bidi-font-weight:
    1633 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1634 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>;
    1635 the labels will change. In my numbering scheme, half of the C3, C7, C10, C14,
    1636 C17, C21, C24 and C28 carbon atoms are really nitrogen (if they are ordered).
    1637 Select these and do <b style='mso-bidi-font-weight:normal'><span
    1638 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1639 mso-hansi-theme-font:minor-latin'>Edit/Set atom refinement flags</span></b>;
    1640 select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1641 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>F</span></b>,
    1642 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1643 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
    1644 &amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1645 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
    1646 for these. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1647 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1648 minor-latin'>Calculate/Refine</span></b>; the <span class=SpellE>Rw</span> will
    1649 drop to ~10% and 4 of the atom <span class=SpellE><b style='mso-bidi-font-weight:
    1650 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1651 minor-latin;mso-hansi-theme-font:minor-latin'>frac</span></b></span> values
    1652 will be ~1.25 while the others are ~1.0. The former are N-atoms and the latter
    1653 are C-atoms. Change the <b style='mso-bidi-font-weight:normal'><span
    1654 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1655 mso-hansi-theme-font:minor-latin'>Type</span></b> for the N-atoms and repeat <b
    1656 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1657 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    1658 the <span class=SpellE>Rw</span> will be high to start, but immediately fall to
    1659 ~10%. In the Atom table all 8 refined <span class=SpellE>frac</span> values are
    1660 be now ~1.0. To finish this part of the refinement, set all <span class=SpellE><b
    1661 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1662 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>frac</span></b></span>
    1663 values to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1664 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.0</span></b>
    1665 and all refine flags to <b style='mso-bidi-font-weight:normal'><span
    1666 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1667 mso-hansi-theme-font:minor-latin'>XU</span></b>. Do <b style='mso-bidi-font-weight:
    1668 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1669 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the
    1670 final <span class=SpellE>Rw</span> ~10.5%</p>
     508the empty corner box) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
     509atom parameters</span></b>. Select <b><span style='font-family:"Calibri",sans-serif'>Name</span></b>
     510and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>;
     511press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> to the
     512popup question. The atoms will be renamed in numerical order. Do <b><span
     513style='font-family:"Calibri",sans-serif'>Edit/Reload draw atoms</span></b>; the
     514labels will change. In my numbering scheme, half of the C3, C7, C10, C14, C17,
     515C21, C24 and C28 carbon atoms are really nitrogen (if they are ordered). Select
     516these and do <b><span style='font-family:"Calibri",sans-serif'>Edit/Set atom
     517refinement flags</span></b>; select <b><span style='font-family:"Calibri",sans-serif'>F</span></b>,
     518<b><span style='font-family:"Calibri",sans-serif'>X</span></b> &amp; <b><span
     519style='font-family:"Calibri",sans-serif'>U</span></b> for these. Do <b><span
     520style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the Rw
     521will drop to ~10% and 4 of the atom <b><span style='font-family:"Calibri",sans-serif'>frac</span></b>
     522values will be ~1.25 while the others are ~1.0. The former are N-atoms and the
     523latter are C-atoms. Change the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
     524for the N-atoms and repeat <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
     525the Rw will be high to start, but immediately fall to ~10%. In the Atom table
     526all 8 refined frac values are be now ~1.0. To finish this part of the
     527refinement, set all <b><span style='font-family:"Calibri",sans-serif'>frac</span></b>
     528values to <b><span style='font-family:"Calibri",sans-serif'>1.0</span></b> and
     529all refine flags to <b><span style='font-family:"Calibri",sans-serif'>XU</span></b>.
     530Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
     531the final Rw ~10.5%</p>
    1671532
    1672533<h2>Step 8. Anisotropic thermal motion refinement</h2>
    1673534
    1674535<p class=MsoNormal>Given reasonable measured structure factors one can improve
    1675 a crystal model by using anisotropic thermal motion models for all the <span
    1676 class=SpellE>nonhydrogen</span> atoms. To convert all the atoms here select the
    1677 Atoms tab and then do a double LB click on <span class=GramE>the I</span>/A
    1678 column heading. Select Anisotropic from the popup and press OK; the Atom table
    1679 will be redrawn with <span class=SpellE>Uij</span> values equivalent to the
    1680 corresponding <span class=SpellE>Uiso</span> (now hidden). Do <b
    1681 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1682 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    1683 the final <span class=SpellE>Rw</span> ~8.2%</p>
     536a crystal model by using anisotropic thermal motion models for all the
     537nonhydrogen atoms. To convert all the atoms here select the Atoms tab and then
     538do a double LB click on the I/A column heading. Select Anisotropic from the
     539popup and press OK; the Atom table will be redrawn with Uij values equivalent
     540to the corresponding Uiso (now hidden). Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
     541the final Rw ~8.2%</p>
    1684542
    1685543<h2 style='page-break-after:avoid'>Step 9. H-atom placement &amp; final
    … …  
    1688546<p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per
    1689547pyridine ring (16 in all). One could do this (painfully) by hand by looking for
    1690 them in <span style='font-family:Symbol'>D</span>F maps, but it is simpler to
    1691 just place them knowing the bonding chemistry of the rings. To start this
    1692 select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1693 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1694 minor-latin'>Atoms</span></b> tab for the phase. Then select the C-atoms by a
    1695 double LB click on the <b style='mso-bidi-font-weight:normal'><span
    1696 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1697 mso-hansi-theme-font:minor-latin'>Type</span></b> column heading and select <b
    1698 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1699 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b>
    1700 from the popup; press <b style='mso-bidi-font-weight:normal'><span
    1701 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1702 mso-hansi-theme-font:minor-latin'>OK</span></b>. The C-atoms will be
    1703 highlighted. Next do <b style='mso-bidi-font-weight:normal'><span
    1704 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1705 mso-hansi-theme-font:minor-latin'>Edit/Insert H atoms</span></b>; a <b
    1706 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1707 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Distance
     548them in <span style='font-family:Symbol'>D</span>F maps, but it is simpler to just
     549place 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
     551phase. Then select the C-atoms by a double LB click on the <b><span
     552style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and
     553select <b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the
     554popup; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
     555The C-atoms will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Insert
     556H atoms</span></b>; a <b><span style='font-family:"Calibri",sans-serif'>Distance
    1708557Angle Controls</span></b> popup will appear; the numbers should be as before.
    1709 Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1710 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
    1711 a new popup will appear</p>
    1712 
    1713 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_8"
    1714  o:spid="_x0000_i1027" type="#_x0000_t75" style='width:300pt;height:363.75pt;
    1715  visibility:visible;mso-wrap-style:square'>
    1716  <v:imagedata src="CFSingleCrystal_files/image016.png" o:title=""/>
    1717 </v:shape></span></p>
     558Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; a new
     559popup will appear</p>
     560
     561<p class=MsoNormal><img width=400 height=485 id="Picture 8"
     562src="CFSingleCrystal_files/image016.png"></p>
    1718563
    1719564<p class=MsoNormal>This is the hydrogen add control; it shows both the expected
    … …  
    1721566determine the geometry of the C-H bond. Check to make sure that 4 H-atoms will
    1722567be added for each ring. Note that C2, C9, C16 &amp; C23 will not have an H-atom
    1723 added as these are the S-atom attachment points in SS-<span class=SpellE>dipyridyl</span>.
    1724 Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1725 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>;
    1726 the H-atoms will be inserted immediately after the corresponding C-atoms and
    1727 the drawing is updated showing van der Waals spheres for all atoms.</p>
    1728 
    1729 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_15"
    1730  o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;height:297pt;
    1731  visibility:visible;mso-wrap-style:square'>
    1732  <v:imagedata src="CFSingleCrystal_files/image017.png" o:title=""/>
    1733 </v:shape></span></p>
    1734 
    1735 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1736 
    1737 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_18"
    1738  o:spid="_x0000_i1025" type="#_x0000_t75" style='width:362.25pt;height:295.5pt;
    1739  visibility:visible;mso-wrap-style:square'>
    1740  <v:imagedata src="CFSingleCrystal_files/image018.png" o:title="" croptop="12402f"
    1741   cropbottom="17514f" cropleft="39344f" cropright="11175f"/>
    1742 </v:shape></span></p>
    1743 
    1744 <p class=MsoNormal>Next, do <b style='mso-bidi-font-weight:normal'><span
    1745 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1746 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; there will be an
    1747 immediate drop in <span class=SpellE>Rw</span> ~3.2%. Note that we did not
    1748 refine the H-atom positions or thermal parameters. The H-atom insertion process
    1749 retains the mechanisms for creating them in the first place and these tools can
    1750 be used to move them to reflect the changes in the C-atom parameters thus
    1751 forcing them to ride on the C-atoms. Do <b style='mso-bidi-font-weight:normal'><span
    1752 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1753 mso-hansi-theme-font:minor-latin'>Edit/Update H atoms</span></b>; the H-atom
    1754 positions &amp; <span class=SpellE>Uisos</span> will be <span class=GramE>revised.</span>
    1755 Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1756 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    1757 there will be a slight improvement in <span class=SpellE>Rw</span>. Repeat
    1758 these two steps (twice); <span class=SpellE>Rw</span> should not change on the
    1759 last round. This completes the refinement of the SS-<span class=SpellE>dipyridyl</span>
     568added as these are the S-atom attachment points in SS-dipyridyl. Press <b><span
     569style='font-family:"Calibri",sans-serif'>Ok</span></b>; the H-atoms will be
     570inserted immediately after the corresponding C-atoms and the drawing is updated
     571showing van der Waals spheres for all atoms.</p>
     572
     573<p class=MsoNormal><img width=624 height=396 id="Picture 15"
     574src="CFSingleCrystal_files/image017.png"></p>
     575
     576<p class=MsoNormal>&nbsp;</p>
     577
     578<p class=MsoNormal><img width=483 height=394 id="Picture 18"
     579src="CFSingleCrystal_files/image018.jpg"></p>
     580
     581<p class=MsoNormal>Next, do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
     582there will be an immediate drop in Rw ~3.2%. Note that we did not refine the
     583H-atom positions or thermal parameters. The H-atom insertion process retains
     584the mechanisms for creating them in the first place and these tools can be used
     585to move them to reflect the changes in the C-atom parameters thus forcing them
     586to ride on the C-atoms. Do <b><span style='font-family:"Calibri",sans-serif'>Edit/Update
     587H atoms</span></b>; the H-atom positions &amp; Uisos will be revised. Repeat <b><span
     588style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; there
     589will be a slight improvement in Rw. Repeat these two steps (twice); Rw should
     590not change on the last round. This completes the refinement of the SS-dipyridyl
    1760591structure. You can generate a final <span style='font-family:Symbol'>D</span>F
    1761 map from the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1762 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1763 minor-latin'>General</span></b> tab; in <b style='mso-bidi-font-weight:normal'><span
    1764 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1765 mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> select the <b
    1766 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1767 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>
    1768 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1769 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
    1770 sets</span></b>, then do <b style='mso-bidi-font-weight:normal'><span
    1771 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1772 mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b>. The <span
    1773 style='font-family:Symbol'>r</span><sub>max</sub> (=0.33) and <span
     592map from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
     593tab; in <b><span style='font-family:"Calibri",sans-serif'>Fourier map controls</span></b>
     594select the <b><span style='font-family:"Calibri",sans-serif'>Map type</span></b>
     595and <b><span style='font-family:"Calibri",sans-serif'>Reflection sets</span></b>,
     596then do <b><span style='font-family:"Calibri",sans-serif'>Compute/Fourier map</span></b>.
     597The <span style='font-family:Symbol'>r</span><sub>max</sub> (=0.33) and <span
    1774598style='font-family:Symbol'>r</span><sub>min</sub> (=-0.31) are listed on the
    1775599console; these seem to be concentrated around the S-atoms.</p>
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