Changeset 3047 for Tutorials


Ignore:
Timestamp:
Sep 5, 2017 3:57:42 PM (4 years ago)
Author:
vondreele
Message:

update to 2 frame version

Location:
Tutorials/CFXraySingleCrystal
Files:
30 added
7 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/CFXraySingleCrystal/CFSingleCrystal.htm

    r2386 r3047  
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    958962in the latter analysis is what is used here and is provided as a “<span
    959963class=SpellE>fcf</span>” file obtained after structure analysis by Shelx-97;
    960 the structure factors are scaled to those calculated from the structure. We
    961 will solve the P 2<sub>1</sub>/c structure first.</p>
     964the structure factors are scaled to those calculated from the structure. We will
     965solve the P 2<sub>1</sub>/c structure first.</p>
    962966
    963967<p class=MsoNormal>&nbsp;</p>
     
    975979<p class=MsoListParagraph style='text-indent:-.25in'>1.<span style='font-size:
    9769807.0pt'>&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
    978 the current GSAS-II project. A popup window will appear asking for a phase
     981"Calibri",sans-serif'>Data/Add new phase</span></b> menu item add a new phase
     982into the current GSAS-II project. A popup window will appear asking for a phase
    979983name; I entered <b><span style='font-family:"Calibri",sans-serif'>SS <span
    980984class=SpellE>dipyridyl</span></span></b>; press <b><span style='font-family:
     
    984988General tab for Phase Data will appear.</p>
    985989
    986 <p class=MsoListParagraph><span style='mso-no-proof:yes'><img width=524
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    9881015
    9891016<p class=MsoListParagraph style='text-indent:-.25in'>2.<span style='font-size:
     
    9951022be refreshed showing only the needed lattice parameters for P 21/c.</p>
    9961023
    997 <p class=MsoListParagraph><span style='mso-no-proof:yes'><img width=522
    998 height=361 id="_x0000_i1041" src="CFSingleCrystal_files/image002.png"></span></p>
     1024<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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    9991030
    10001031<p class=MsoListParagraph style='text-indent:-.25in'>3.<span style='font-size:
     
    10131044<p class=MsoNormal>To do these, do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure
    10141045factor/from CIF file</span></b> from the main GSAS-II data tree window menu. A
    1015 file 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>
    1017 and press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>. A
     1046file selection dialog will appear; find <span class=SpellE><b><span
     1047style='font-family:"Calibri",sans-serif'>CFXraySingleCrystal</span></b></span><b><span
     1048style='font-family:"Calibri",sans-serif'>\data\S2dipyridyl.fcf</span></b> and
     1049press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>. A
    10181050popup window asking if this is the file you want; press <b><span
    10191051style='font-family:"Calibri",sans-serif'>Yes</span></b>. After a pause while
    10201052the file is read a new popup will appear offering the chance to rename the
    10211053structure factor set; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
    1022 After some <span class=GramE>time</span> a new popup will appear to Add the new
    1023 structure factor set to the SS <span class=SpellE>dipyridyl</span> phase.
    1024 Select the phase and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
    1025 The plot will show a rectangular array of circles for the hk0 reflection layer;
    1026 select the plot &amp; press <b><span style='font-family:"Calibri",sans-serif'>k</span></b>
    1027 to get an h0l layer.</p>
    1028 
    1029 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=412
    1030 id="_x0000_i1040" src="CFSingleCrystal_files/image003.png"></span></p>
     1054After some time a new popup will appear to Add the new structure factor set to
     1055the SS <span class=SpellE>dipyridyl</span> phase. Select the phase and press <b><span
     1056style='font-family:"Calibri",sans-serif'>OK</span></b>. The plot will show a
     1057rectangular array of circles for the hk0 reflection layer; select the plot
     1058&amp; press <b><span style='font-family:"Calibri",sans-serif'>k</span></b> to
     1059get an h0l layer.</p>
     1060
     1061<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1062 id="Picture_x0020_21" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
     1063 height:401.25pt;visibility:visible;mso-wrap-style:square'>
     1064 <v:imagedata src="CFSingleCrystal_files/image005.png" o:title=""/>
     1065</v:shape><![endif]--><![if !vml]><img width=624 height=535
     1066src="CFSingleCrystal_files/image006.gif" v:shapes="Picture_x0020_21"><![endif]></span></p>
    10311067
    10321068<p class=MsoNormal>Because the <span class=SpellE>fcf</span> file has both
     
    10351071calculated ones as green rings and a small green or red dot may appear at each
    10361072ring center showing <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>. If
    1037 the reflection data file had only observed structure <span class=GramE>factors</span>
    1038 then only blue rings will be seen. You can explore the plot options in the ‘<b><span
     1073the reflection data file had only observed structure factors then only blue
     1074rings will be seen. You can explore the plot options in the ‘<b><span
    10391075style='font-family:"Calibri",sans-serif'>K</span></b>’ box in the plot toolbar.</p>
    10401076
     
    10561092from the GSAS-II data tree; the General tab will be shown</p>
    10571093
    1058 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=401
    1059 id="_x0000_i1039" src="CFSingleCrystal_files/image004.png"></span></p>
     1094<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1095 id="Picture_x0020_22" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
     1096 height:162.75pt;visibility:visible;mso-wrap-style:square'>
     1097 <v:imagedata src="CFSingleCrystal_files/image007.png" o:title=""/>
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     1099src="CFSingleCrystal_files/image008.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
    10601100
    10611101<p class=MsoNormal>Find the <b><span style='font-family:"Calibri",sans-serif'>Fourier
     
    11101150<p class=MsoNormal>The console window will show something like</p>
    11111151
    1112 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=166
    1113 id="_x0000_i1037" src="CFSingleCrystal_files/image006.png"></span></p>
     1152<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1153 id="Picture_x0020_23" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
     1154 height:125.25pt;visibility:visible;mso-wrap-style:square'>
     1155 <v:imagedata src="CFSingleCrystal_files/image009.png" o:title=""/>
     1156</v:shape><![endif]--><![if !vml]><img width=624 height=167
     1157src="CFSingleCrystal_files/image010.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>
    11141158
    11151159<p class=MsoNormal>There may be a pause at <b><span style='font-family:"Calibri",sans-serif'>Begin
    1116 <span class=SpellE>fourier</span> map search</span></b> before it finishes.
    1117 Provided is a summary of the charge flip calculation (time, map size, density
    1118 range &amp; structure factor residual). The map offset is discovered by an
    1119 analysis of the reflection phases with respect to how they should be
    1120 distributed for your chosen space group. These offsets are then applied to
    1121 shift the map so that the symmetry elements are properly located in the unit
    1122 cell. The quality of this fit (chi**2) is given. This process is not
    1123 necessarily perfect; you are given an opportunity to hand-tune the offset. <span
    1124 class=GramE>Finally</span> the number of peaks found in the map is listed, the
    1125 structure 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
    1128 id="_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
    1133 id="_x0000_i1035" src="CFSingleCrystal_files/image008.png"></span></p>
     1160<span class=SpellE><span class=GramE>fourier</span></span> map search</span></b>
     1161before it finishes. Provided is a summary of the charge flip calculation (time,
     1162map size, density range &amp; structure factor residual). The map offset is
     1163discovered by an analysis of the reflection phases with respect to how they
     1164should be distributed for your chosen space group. These offsets are then
     1165applied to shift the map so that the symmetry elements are properly located in
     1166the unit cell. The quality of this fit (chi**2) is given. This process is not
     1167necessarily perfect; you are given an opportunity to hand-tune the offset.
     1168Finally the number of peaks found in the map is listed, the structure is drawn
     1169(I’ve made the view down the b-axis)</p>
     1170
     1171<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1172 id="Picture_x0020_24" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:450pt;
     1173 height:387.75pt;visibility:visible;mso-wrap-style:square'>
     1174 <v:imagedata src="CFSingleCrystal_files/image011.png" o:title=""/>
     1175</v:shape><![endif]--><![if !vml]><img width=600 height=517
     1176src="CFSingleCrystal_files/image012.gif" v:shapes="Picture_x0020_24"><![endif]></span></p>
     1177
     1178<p class=MsoNormal>&nbsp;<span class=GramE>and</span> the Phase data window
     1179will show the map peaks tab</p>
     1180
     1181<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1182 id="Picture_x0020_25" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:450pt;
     1183 height:219.75pt;visibility:visible;mso-wrap-style:square'>
     1184 <v:imagedata src="CFSingleCrystal_files/image013.png" o:title=""/>
     1185</v:shape><![endif]--><![if !vml]><img width=600 height=293
     1186src="CFSingleCrystal_files/image014.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
    11341187
    11351188<p class=MsoNormal>These are listed in order of magnitude; a double click on
     
    11881241will be highlighted and the corresponding peaks in the drawing will be green
    11891242(NB: if you navigate away from this tab, this selection will be lost and you’ll
    1190 have to repeat it!). Next, do <b><span style='font-family:"Calibri",sans-serif'>Map
     1243have to repeat it!). The console will show a summary giving the number &amp;
     1244fraction of unique peaks found; in this case 28 &amp; 0.25 are the correct
     1245values. Next, do <b><span style='font-family:"Calibri",sans-serif'>Map
    11911246peaks/Move peaks</span></b>; these peaks will be transferred to the <b><span
    11921247style='font-family:"Calibri",sans-serif'>Atoms</span></b> list as H-atoms named
    11931248according to their position in the magnitude column.</p>
    11941249
    1195 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=267
    1196 id="_x0000_i1034" src="CFSingleCrystal_files/image009.png"></span></p>
     1250<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1251 id="Picture_x0020_26" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
     1252 height:198.75pt;visibility:visible;mso-wrap-style:square'>
     1253 <v:imagedata src="CFSingleCrystal_files/image015.png" o:title=""/>
     1254</v:shape><![endif]--><![if !vml]><img width=624 height=265
     1255src="CFSingleCrystal_files/image016.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
    11971256
    11981257<p class=MsoNormal>The drawing will show white balls at the atom positions
    11991258scattered over several molecules.</p>
    12001259
    1201 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=474 height=409
    1202 id="_x0000_i1033" src="CFSingleCrystal_files/image010.jpg"></span></p>
     1260<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1261 id="Picture_x0020_27" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
     1262 height:405pt;visibility:visible;mso-wrap-style:square'>
     1263 <v:imagedata src="CFSingleCrystal_files/image017.png" o:title=""/>
     1264</v:shape><![endif]--><![if !vml]><img width=624 height=540
     1265src="CFSingleCrystal_files/image018.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
    12031266
    12041267<p class=MsoNormal>Notice that 4 atoms have magnitudes ~90+, these are the S
    12051268atoms. The rest are C &amp; N atoms. In the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
    12061269tab select the first 4 atoms (press LB on the 1<sup>st</sup> &amp; shift LB on
    1207 the 4<sup>th</sup> one). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
    1208 atom parameters</span></b>; a popup window will appear. Select <b><span
    1209 style='font-family:"Calibri",sans-serif'>Type</span></b> &amp; press <b><span
    1210 style='font-family:"Calibri",sans-serif'>OK</span></b>; a Periodic Table will
    1211 appear. Select <b><span style='font-family:"Calibri",sans-serif'>S</span></b>;
    1212 the atoms will be <span class=GramE>renames</span> and their Type changed to S.
    1213 Next select the remaining H atoms (a quick way it to double LB click the <b><span
    1214 style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and
    1215 select <b><span style='font-family:"Calibri",sans-serif'>H</span></b> from the
    1216 popup window). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
    1217 atom parameters</span></b> and <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
    1218 from the popup; select <b><span style='font-family:"Calibri",sans-serif'>C</span></b>
    1219 from the Periodic Table as we don’t know which ones are N. The drawing will
    1220 change (you may have to wiggle it a bit to force the update).</p>
    1221 
    1222 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=390
    1223 id="_x0000_i1032" src="CFSingleCrystal_files/image011.jpg"></span></p>
     1270the 4<sup>th</sup> one). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit
     1271Atoms/On selected atoms
     1272/Modify parameters</span></b>; a popup window will
     1273appear. Select <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
     1274&amp; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; a
     1275Periodic Table will appear. Select <b><span style='font-family:"Calibri",sans-serif'>S</span></b>;
     1276the atoms will be renamed and their Type changed to S. The structure will be
     1277redrawn with yellow balls for the S atoms. Next select the remaining H atoms (a
     1278quick way it to double LB click the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
     1279column heading and select <b><span style='font-family:"Calibri",sans-serif'>H</span></b>
     1280from the popup window). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit
     1281Atoms/On selected atoms
     1282/Modify parameters</span></b> and <b><span
     1283style='font-family:"Calibri",sans-serif'>Type</span></b> from the popup; select
     1284<b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the
     1285Periodic Table as we don’t know which ones are N. The drawing will change (you
     1286may have to wiggle it a bit to force the update).</p>
     1287
     1288<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1289 id="Picture_x0020_28" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
     1290 height:405pt;visibility:visible;mso-wrap-style:square'>
     1291 <v:imagedata src="CFSingleCrystal_files/image019.png" o:title=""/>
     1292</v:shape><![endif]--><![if !vml]><img width=624 height=540
     1293src="CFSingleCrystal_files/image020.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
    12241294
    12251295<p class=MsoNormal>Notice that the atoms are scattered over several molecules;
    12261296we want to assemble them into 2 conveniently placed ones. Begin by selecting an
    12271297atom (make sure the <b><span style='font-family:"Calibri",sans-serif'>Atom</span></b>
    1228 tab is displayed &amp; do shift LB on an atom in the drawing – I chose the S
    1229 atom near the upper middle); it will turn green and a line in the Atom table
    1230 will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Assemble
    1231 molecule</span></b>; a popup window will appear. Change the <b><span
    1232 style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span
    1233 style='font-family:"Calibri",sans-serif'>0.90</span></b> to be sure all S-C
    1234 bonds are found.</p>
     1298tab is displayed &amp; do <b style='mso-bidi-font-weight:normal'><span
     1299style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1300mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>shift LB</span></b>
     1301on an atom in the drawing – I chose the S atom on the left side of the drawing);
     1302it will turn green and a line in the Atom table will be highlighted. Next do <b><span
     1303style='font-family:"Calibri",sans-serif'>Edit Atoms/Assemble molecule</span></b>;
     1304a popup window will appear. Change the <b><span style='font-family:"Calibri",sans-serif'>Bond
     1305search factor</span></b> to <b><span style='font-family:"Calibri",sans-serif'>0.90</span></b>
     1306to be sure all S-C bonds are found.</p>
    12351307
    12361308<p class=MsoNormal><span style='mso-no-proof:yes'><img width=265 height=223
     
    12411313but others are not. Next select one of the unassembled atoms (I chose a C-atom
    12421314in a nearby SS-<span class=SpellE>dipyridyl</span>) and do <b><span
    1243 style='font-family:"Calibri",sans-serif'>Edit/Assemble molecule</span></b>;
     1315style='font-family:"Calibri",sans-serif'>Edit Atoms/Assemble molecule</span></b>;
    12441316there will be two nicely assembled SS-<span class=SpellE>dipyridyls</span>.</p>
    12451317
    1246 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=384
    1247 id="_x0000_i1030" src="CFSingleCrystal_files/image013.jpg"></span></p>
     1318<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1319 id="Picture_x0020_29" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
     1320 height:405pt;visibility:visible;mso-wrap-style:square'>
     1321 <v:imagedata src="CFSingleCrystal_files/image021.png" o:title=""/>
     1322</v:shape><![endif]--><![if !vml]><img width=624 height=540
     1323src="CFSingleCrystal_files/image022.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
    12481324
    12491325<p class=MsoNormal>You should probably save this project as it contains your
     
    12541330
    12551331<p class=MsoNormal>Since we now have a structural model, we can do the initial
    1256 structure refinement. By <span class=GramE>default</span> this will only refine
    1257 the scale factor; do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
    1258 from the main GSAS-II data tree window. Convergence will quickly occur with <span
     1332structure refinement. By default this will only refine the scale factor; do <b><span
     1333style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> from the
     1334main GSAS-II data tree window. Convergence will quickly occur with <span
    12591335class=SpellE>Rw</span> ~35%. More useful is to refine the atom positions and
    12601336isotropic thermal parameters. Select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
     
    12671343style='font-family:"Calibri",sans-serif'>XU</span></b> for each atom in the
    12681344refine column. Then do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
    1269 (twice to get convergence) and the <span class=SpellE>Rw</span> ~12%.</p>
     1345(2-3 times to get convergence) and the <span class=SpellE>Rw</span> ~12%.</p>
    12701346
    12711347<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 7. Determine
     
    12961372<p class=MsoNormal>&nbsp;</p>
    12971373
    1298 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=474 height=386
    1299 id="_x0000_i1029" src="CFSingleCrystal_files/image014.jpg"></span></p>
     1374<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1375 id="Picture_x0020_30" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:453pt;
     1376 height:393pt;visibility:visible;mso-wrap-style:square'>
     1377 <v:imagedata src="CFSingleCrystal_files/image023.png" o:title=""/>
     1378</v:shape><![endif]--><![if !vml]><img width=604 height=524
     1379src="CFSingleCrystal_files/image024.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
    13001380
    13011381<p class=MsoNormal>Now go to the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
     
    13031383class=SpellE>dipyridyl</span> are grouped together in the table but they are
    13041384not in chemically sensible order. The atoms can be reordered by selecting one
    1305 row with the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b>
    1306 key down (the status line will tell which atom is selected to move) and then
    1307 with the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b> key
    1308 still down pick a row below where you want to insert it. I ordered them so each
     1385row with the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b> key
     1386down (the status line will tell which atom is selected to move) and then with
     1387the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b> key still
     1388down pick a row below where you want to insert it. I ordered them so each
    13091389S-atom was followed by the C-atoms in order around the ring; my list looked
    13101390like (I show just the 1<sup>st</sup> SS <span class=SpellE>dipyridyl</span>
    13111391molecule)</p>
    13121392
    1313 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=408
    1314 id="_x0000_i1028" src="CFSingleCrystal_files/image015.png"></span></p>
     1393<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1394 id="Picture_x0020_31" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
     1395 height:248.25pt;visibility:visible;mso-wrap-style:square'>
     1396 <v:imagedata src="CFSingleCrystal_files/image025.png" o:title=""/>
     1397</v:shape><![endif]--><![if !vml]><img width=624 height=331
     1398src="CFSingleCrystal_files/image026.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
    13151399
    13161400<p class=MsoNormal>Once you have reordered the atoms to your satisfaction they
    13171401can be renamed to be in order. To do this select all the atoms (double LB click
    1318 the empty corner box) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
    1319 atom parameters</span></b>. Select <b><span style='font-family:"Calibri",sans-serif'>Name</span></b>
    1320 and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>;
    1321 press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> to the
    1322 popup question. The atoms will be renamed in numerical order. Do <b><span
    1323 style='font-family:"Calibri",sans-serif'>Edit/Reload draw atoms</span></b>; the
    1324 labels will change. In my numbering scheme, half of the C3, C7, C10, C14, C17,
    1325 C21, C24 and C28 carbon atoms are really nitrogen (if they are ordered). Select
    1326 these and do <b><span style='font-family:"Calibri",sans-serif'>Edit/Set atom
    1327 refinement flags</span></b>; select <b><span style='font-family:"Calibri",sans-serif'>F</span></b>,
     1402the empty corner box) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit
     1403Atoms/On selected atoms
     1404/Modify atom parameters</span></b>. Select <b><span
     1405style='font-family:"Calibri",sans-serif'>Name</span></b> and press <b><span
     1406style='font-family:"Calibri",sans-serif'>OK</span></b>; press <b><span
     1407style='font-family:"Calibri",sans-serif'>Yes</span></b> to the popup question.
     1408The atoms will be renamed in numerical order. Do <b><span style='font-family:
     1409"Calibri",sans-serif'>Edit/Reload draw atoms</span></b>; the labels will
     1410change. In my numbering scheme, half of the C3, C7, C10, C14, C17, C21, C24 and
     1411C28 carbon atoms are really nitrogen (if they are ordered). Select these and do
     1412<b><span style='font-family:"Calibri",sans-serif'>Edit Atoms/On selected atoms
     1413/Refine
     1414selected</span></b>; select <b><span style='font-family:"Calibri",sans-serif'>F</span></b>,
    13281415<b><span style='font-family:"Calibri",sans-serif'>X</span></b> &amp; <b><span
    13291416style='font-family:"Calibri",sans-serif'>U</span></b> for these. Do <b><span
     
    13461433thermal motion refinement<o:p></o:p></span></h2>
    13471434
    1348 <p class=MsoNormal>Given reasonable measured structure factors one can improve
    1349 a crystal model by using anisotropic thermal motion models for all the <span
     1435<p class=MsoNormal>Given reasonable measured structure factors one can improve a
     1436crystal model by using anisotropic thermal motion models for all the <span
    13501437class=SpellE>nonhydrogen</span> atoms. To convert all the atoms here select the
    13511438Atoms tab and then do a double LB click on the I/A column heading. Select
     
    135814459. H-atom placement &amp; final refinement<o:p></o:p></span></h2>
    13591446
    1360 <p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per pyridine
    1361 ring (16 in all). One could do this (painfully) by hand by looking for them in <span
    1362 style='font-family:Symbol'>D</span>F maps, but it is simpler to just place them
    1363 knowing the bonding chemistry of the rings. To start <span class=GramE>this</span>
     1447<p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per
     1448pyridine ring (16 in all). One could do this (painfully) by hand by looking for
     1449them in <span style='font-family:Symbol'>D</span>F maps, but it is simpler to
     1450just place them knowing the bonding chemistry of the rings. To start this
    13641451select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
    13651452tab for the phase. Then select the C-atoms by a double LB click on the <b><span
     
    13671454select <b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the
    13681455popup; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
    1369 The C-atoms will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Insert
    1370 H atoms</span></b>; a <b><span style='font-family:"Calibri",sans-serif'>Distance
    1371 Angle Controls</span></b> popup will appear; the numbers should be as before.
    1372 Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; a new
    1373 popup will appear</p>
    1374 
    1375 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=400 height=485
    1376 id="_x0000_i1027" src="CFSingleCrystal_files/image016.png"></span></p>
     1456The C-atoms will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit
     1457Atoms/On selected atoms
     1458/<span class=SpellE>Calc</span> H atoms</span></b>; a <b><span
     1459style='font-family:"Calibri",sans-serif'>Distance Angle Controls</span></b>
     1460popup will appear; the numbers should be as before. Press <b><span
     1461style='font-family:"Calibri",sans-serif'>OK</span></b>; a new popup will appear</p>
     1462
     1463<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1464 id="Picture_x0020_32" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:300pt;
     1465 height:187.5pt;visibility:visible;mso-wrap-style:square'>
     1466 <v:imagedata src="CFSingleCrystal_files/image027.png" o:title=""/>
     1467</v:shape><![endif]--><![if !vml]><img width=400 height=250
     1468src="CFSingleCrystal_files/image028.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
    13771469
    13781470<p class=MsoNormal>This is the hydrogen add control; it shows both the expected
     
    13851477drawing is updated showing van der Waals spheres for all atoms.</p>
    13861478
    1387 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=396
    1388 id="_x0000_i1026" src="CFSingleCrystal_files/image017.png"></span></p>
     1479<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1480 id="Picture_x0020_33" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:430.5pt;
     1481 height:249pt;visibility:visible;mso-wrap-style:square'>
     1482 <v:imagedata src="CFSingleCrystal_files/image029.png" o:title=""/>
     1483</v:shape><![endif]--><![if !vml]><img width=574 height=332
     1484src="CFSingleCrystal_files/image030.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
    13891485
    13901486<p class=MsoNormal>&nbsp;</p>
    13911487
    1392 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=483 height=394
    1393 id="_x0000_i1025" src="CFSingleCrystal_files/image018.jpg"></span></p>
     1488<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1489 id="Picture_x0020_34" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:430.5pt;
     1490 height:373.5pt;visibility:visible;mso-wrap-style:square'>
     1491 <v:imagedata src="CFSingleCrystal_files/image031.png" o:title=""/>
     1492</v:shape><![endif]--><![if !vml]><img width=574 height=498
     1493src="CFSingleCrystal_files/image032.gif" v:shapes="Picture_x0020_34"><![endif]></span></p>
    13941494
    13951495<p class=MsoNormal>Next, do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
     
    13991499and these tools can be used to move them to reflect the changes in the C-atom
    14001500parameters thus forcing them to ride on the C-atoms. Do <b><span
    1401 style='font-family:"Calibri",sans-serif'>Edit/Update H atoms</span></b>; the
    1402 H-atom positions &amp; <span class=SpellE>Uisos</span> will be revised. Repeat <b><span
    1403 style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; there
    1404 will be a slight improvement in <span class=SpellE>Rw</span>. Repeat these two
    1405 steps (twice); <span class=SpellE>Rw</span> should not change on the last
    1406 round. This completes the refinement of the SS-<span class=SpellE>dipyridyl</span>
     1501style='font-family:"Calibri",sans-serif'>Edit Atoms/Update H atoms</span></b>;
     1502the H-atom positions &amp; <span class=SpellE>Uisos</span> will be <span
     1503class=GramE>revised.</span> Repeat <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
     1504there will be a slight improvement in <span class=SpellE>Rw</span>. Repeat
     1505these two steps (twice); <span class=SpellE>Rw</span> should not change on the
     1506last round. This completes the refinement of the SS-<span class=SpellE>dipyridyl</span>
    14071507structure. You can generate a final <span style='font-family:Symbol'>D</span>F
    14081508map from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
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