Changeset 4891


Ignore:
Timestamp:
Apr 24, 2021 9:24:44 AM (6 months ago)
Author:
toby
Message:

update CIF tutorial

Location:
Tutorials/CIFtutorial
Files:
5 added
2 deleted
4 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/CIFtutorial/CIFtutorial.fld/filelist.xml

    r4872 r4891  
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  • Tutorials/CIFtutorial/CIFtutorial.html

    r4872 r4891  
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    12031016
    1204 <h1 align=center style='text-align:center'><a name="_GoBack"></a>Tutorial: Preparing
    1205 a Full CIF<o:p></o:p></h1>
    1206 
    1207 <p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><BL><![if !supportLists]><span
    1208 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1209 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1017<h1 align=center style='text-align:center'><a name="_GoBack"></a><span
     1018style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Tutorial:
     1019Preparing a Full CIF<o:p></o:p></span></h1>
     1020
     1021<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><BL><![if !supportLists]><span
     1022style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1023Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    12101024</span></span></span><![endif]><span dir=LTR></span>Exercise files are found <a
    1211 href="./data" target="_blank">here</a>. The data files are taken
    1212 from the conclusion of the “<a
    1213 href="../CWCombined/Combined%20refinement.htm">Combined X-ray/neutron
    1214 refinement – PbSO<sub>4</sub></a>” tutorial. <o:p></o:p></p>
     1025href="data" target="_blank">here</a>. The data files are taken from the
     1026conclusion of the “<a href="../CWCombined/Combined%20refinement.htm">Combined
     1027X-ray/neutron refinement – PbSO<sub>4</sub></a>” tutorial. <o:p></o:p></p>
    12151028
    12161029</BL>
    12171030
    1218 <h1>Background <o:p></o:p></h1>
     1031<h1><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Background
     1032<o:p></o:p></span></h1>
    12191033
    12201034<p class=MsoNormal>Crystallography has had a long tradition where experimental
    12211035data as well as results were reported numerically, so that results could be
    1222 verified independently as well as utilized. In the past two decades the field has
    1223 set the standard for data science compared to almost all other areas of
     1036verified independently as well as utilized. In the past two decades the field
     1037has set the standard for data science compared to almost all other areas of
    12241038physical and biological science through the development of the Crystallographic
    12251039Information Framework (CIF) which defines a universal format for the reporting
     
    12321046
    12331047<p class=MsoNormal>Within GSAS-II, a CIF for a phase <span class=GramE>are</span>
    1234 available as “quick” coordinate-only file, which provides atom coordinates and
    1235 displacement parameters, but no uncertainties or other supporting information from
    1236 the refinement. This is indeed easy with a single menu command. Likewise, a CIF
    1237 containing only a dataset without phase information can be easily created from
    1238 the Export menu, but the real power of CIF comes after a project has been completed.
    1239 Using the “Entire project as
” a “Full CIF” menu command in the Export menu,
    1240 all results can be reported in a machine and human readable. There are a few
    1241 steps in generating a full project CIF. This tutorial goes through them and
    1242 explains what is being done and why. </p>
     1048available as “quick” coordinate-only file, which provides atom coordinates and
     1049displacement parameters, but no uncertainties or other supporting information
     1050from the refinement. This is indeed easy with a single menu command. Likewise,
     1051a CIF containing only a dataset without phase information can be easily created
     1052from the Export menu, but the real power of CIF comes after a project has been
     1053completed. Using the “Entire project as…” a “Full CIF” menu command in the
     1054Export menu, all results can be reported in a machine and human readable. There
     1055are a few steps in generating a full project CIF. This tutorial goes through
     1056them and explains what is being done and why. </p>
    12431057
    12441058<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    12451059
    12461060<p class=MsoNormal>A bit of background on CIF: The format allows a label (a CIF
    1247 data item, such as _cell_length_a or _publ_author_name) to be associated with either a single value or a column
    1248 in a table. A collection of data items is placed in a block. For a single-crystal
    1249 structure, a block will usually contain the coordinates for a phase and the
    1250 structure factors (experimental data and the matching simulated values) as well
    1251 as supporting information and derived results. With multiple temperatures, a block
    1252 would be needed for each setting because, for example, only one set of unit
    1253 cell dimensions and coordinates can be defined in a block. With powder diffraction,
    1254 if a single dataset (histogram) is used and only one phase is present, a single
    1255 block can be used. If either more than one phase is present, or more than one
    1256 histogram is used, multiple blocks are required. GSAS-II will create single-block
    1257 CIFs when possible, but otherwise will create a block for the overall
    1258 refinement plus a block for each histogram and a block for each phase. Referencing
    1259 information between different blocks requires that each block be labeled with a
    1260 unique name. These block labels are assembled from a number of fields supplied
    1261 by the user and a timestamp when the file is created. </p>
     1061data item, such as _cell_length_a or _publ_author_name) to be associated with
     1062either a single value or a column in a table. A collection of data items is
     1063placed in a block. For a single-crystal structure, a block will usually contain
     1064the coordinates for a phase and the structure factors (experimental data and
     1065the matching simulated values) as well as supporting information and derived
     1066results. With multiple temperatures, a block would be needed for each setting
     1067because, for example, only one set of unit cell dimensions and coordinates can
     1068be defined in a block. With powder diffraction, if a single dataset (histogram)
     1069is used and only one phase is present, a single block can be used. If either
     1070more than one phase is present, or more than one histogram is used, multiple
     1071blocks are required. GSAS-II will create single-block CIFs when possible, but
     1072otherwise will create a block for the overall refinement plus a block for each
     1073histogram and a block for each phase. Referencing information between different
     1074blocks requires that each block be labeled with a unique name. These block
     1075labels are assembled from a number of fields supplied by the user and a
     1076timestamp when the file is created. </p>
    12621077
    12631078<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    12641079
    12651080<p class=MsoNormal>A tremendous amount of information can be placed into a CIF
    1266 file. No one is likely to specify all of the field in the IUCr-supplied template,
    1267 which itself does not include all data items defined in CIF. Some information can
    1268 be supplied by GSAS-II from what is defined inside a project, data such as
    1269 symmetry and lattice parameters, but other information, for example synthesis
    1270 conditions or sample color, must be supplied by the user. This could be done
    1271 with a simple text editor once the file is created, but the problem that arises
    1272 from that approach is that it is common that after one has produced the “final”
    1273 refinement, another idea occurs for a slightly better fit. The approach used in
    1274 GSAS-II is that as the CIF is generated, copies of template files are made that
    1275 contain all the user-supplied information. Thus, the CIF can be recreated from
    1276 the updated project without having to repeat all the work in supplying that information.
    1277 Also, by saving template files that have setting information that will be
    1278 common amongst multiple projects (for example, diffraction instrumentation
    1279 descriptions) these files can be reused, avoiding repetitive tasks. <span
    1280 style='mso-spacerun:yes'> </span></p>
    1281 
    1282 <h1>Prerequisite <o:p></o:p></h1>
     1081file. No one is likely to specify all of the field in the IUCr-supplied
     1082template, which itself does not include all data items defined in CIF. Some
     1083information can be supplied by GSAS-II from what is defined inside a project,
     1084data such as symmetry and lattice parameters, but other information, for
     1085example synthesis conditions or sample color, must be supplied by the user.
     1086This could be done with a simple text editor once the file is created, but the
     1087problem that arises from that approach is that it is common that after one has
     1088produced the “final” refinement, another idea occurs for a slightly better fit.
     1089The approach used in GSAS-II is that as the CIF is generated, copies of
     1090template files are made that contain all the user-supplied information. Thus,
     1091the CIF can be recreated from the updated project without having to repeat all
     1092the work in supplying that information. Also, by saving template files that
     1093have setting information that will be common amongst multiple projects (for
     1094example, diffraction instrumentation descriptions) these files can be reused,
     1095avoiding repetitive tasks.<span style='mso-spacerun:yes'>  </span></p>
     1096
     1097<h1><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Prerequisite
     1098<o:p></o:p></span></h1>
    12831099
    12841100<p class=MsoNormal>Before beginning this tutorial, either complete the
    1285 refinement in the “<a href="../../../CWCombined/Combined%20refinement.htm">Combined
    1286 X-ray/neutron refinement – PbSO<sub>4</sub></a>” tutorial or download the GSAS-II
    1287 project file provided <a href="../../../Scratch/data" target="_blank">here</a>,
     1101refinement in the <a href="../../../CWCombined/Combined%20refinement.htm">Combined
     1102X-ray/neutron refinement – PbSO<sub>4</sub></a>” tutorial or download the
     1103GSAS-II project file provided <a href="../../../Scratch/data" target="_blank">here</a>,
    12881104which provides a two histogram, one phase refinement. </p>
    12891105
    12901106<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    12911107
    1292 <h2>Part 1. Enter a name for the author of the CIF file. </h2>
    1293 
    1294 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1295 
    1296 <p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1297 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1298 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1108<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
     11091. Enter a name for the author of the CIF file. <o:p></o:p></span></h2>
     1110
     1111<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1112
     1113<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1114style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1115Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    12991116</span></span></span><![endif]><span dir=LTR></span>Select the Controls entry
    13001117on the data tree and enter the name for the main author for the project and
     
    13231140 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    13241141 <o:lock v:ext="edit" aspectratio="t"/>
    1325 </v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1042" type="#_x0000_t75"
     1142</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1045" type="#_x0000_t75"
    13261143 alt="GSAS-II Graphical user interface: Entering author name on Controls panel"
    13271144 style='width:351pt;height:272pt;visibility:visible;mso-wrap-style:square'>
     
    13351152<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    13361153
    1337 <h2>Part 2: Start the export process</h2>
    1338 
    1339 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1340 
    1341 <p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1342 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1343 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1154<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
     11552: Start the export process<o:p></o:p></span></h2>
     1156
     1157<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1158
     1159<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1160style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1161Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    13441162</span></span></span><![endif]><span dir=LTR></span>Using the Export menu,
    1345 select the “Entire project as” menu item and the “Full CIF” submenu option. </p>
     1163select the “Entire project as” menu item and the “Full CIF” submenu option. </p>
    13461164
    13471165<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    13481166
    13491167<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1350  id="Picture_x0020_2" o:spid="_x0000_i1041" type="#_x0000_t75" alt="Graphical user interface: menu item for export poject as CIF"
     1168 id="Picture_x0020_2" o:spid="_x0000_i1044" type="#_x0000_t75" alt="Graphical user interface: menu item for export poject as CIF"
    13511169 style='width:231pt;height:34pt;visibility:visible;mso-wrap-style:square'>
    13521170 <v:imagedata src="CIFtutorial.fld/image003.png" o:title=" menu item for export poject as CIF"/>
     
    13621180
    13631181<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1364  id="Picture_x0020_3" o:spid="_x0000_i1040" type="#_x0000_t75" alt="Graphical user interface, application&#10;&#10;Description automatically generated"
     1182 id="Picture_x0020_3" o:spid="_x0000_i1043" type="#_x0000_t75" alt="Graphical user interface, application&#10;&#10;Description automatically generated"
    13651183 style='width:356pt;height:226pt;visibility:visible;mso-wrap-style:square'>
    13661184 <v:imagedata src="CIFtutorial.fld/image004.png" o:title="Graphical user interface, application&#10;&#10;Description automatically generated"
     
    13731191<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    13741192
    1375 <p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1376 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1377 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1193<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1194style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1195Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    13781196</span></span></span><![endif]><span dir=LTR></span>Enter a name for the file
    1379 if you wish to override the default name and press Save. If that file exists,
    1380 you will need to agree to overwrite it or to select a new name. </p>
    1381 
    1382 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1383 
    1384 <h2>Part 3: Select instrument name(s)</h2>
    1385 
    1386 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1387 
    1388 <p class=MsoNormal>Before a CIF can be created, each histogram must have associated
    1389 with it an instrument name. Note that the instrument name appears in the Sample
    1390 Parameters tree entry for each histogram. If any instrument does not have a
    1391 name, the dialog below is displayed. </p>
     1197if you wish to override the default name and press Save. If that file exists, you
     1198will need to agree to overwrite it or to select a new name. </p>
     1199
     1200<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1201
     1202<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
     12033: Select instrument name(s)<o:p></o:p></span></h2>
     1204
     1205<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1206
     1207<p class=MsoNormal>Before a CIF can be created, each histogram must have
     1208associated with it an instrument name. Note that the instrument name appears in
     1209the Sample Parameters tree entry for each histogram. If any instrument does not
     1210have a name, the dialog below is displayed. </p>
    13921211
    13931212<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    13941213
    13951214<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1396  id="Picture_x0020_4" o:spid="_x0000_i1039" type="#_x0000_t75" alt="Graphical user interface: enter instrument name&#10;"
    1397  style='width:199pt;height:188pt;visibility:visible;mso-wrap-style:square'>
    1398  <v:imagedata src="CIFtutorial.fld/image006.png" o:title=" enter instrument name&#10;"/>
    1399 </v:shape><![endif]--><![if !vml]><img border=0 width=199 height=188
    1400 src="CIFtutorial.fld/image006.png"
    1401 alt="Graphical user interface: enter instrument name&#10;" v:shapes="Picture_x0020_4"><![endif]></span></p>
    1402 
    1403 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1404 
    1405 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1406 
    1407 <p class=MsoNormal>Ideally the instrument name will be unique, so the combination
    1408 of the name and a timestamp will create an identifier that is unlikely to be
    1409 repeated. The instrument name should also allow the data source to be
    1410 identified should there be several similar instruments within an institution,
    1411 but the details for naming are left as a local decision. Inclusion of an institution
    1412 name is a good idea, so an ideal name might be “Univ. of Mars, Curiosity II”.
    1413 While in this case the two histograms are from different instruments, the down
    1414 arrow (<span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
    1415 mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
    1416 Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Ú</span></span>)
    1417 button will copy the entered name to all fields below, simplifying the data
    1418 entry task, when appropriate. <o:p></o:p></p>
    1419 
    1420 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1421 
    1422 <p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1423 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1424 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    1425 </span></span></span><![endif]><span dir=LTR></span>Enter names for each instrument
    1426 and then press OK.</p>
    1427 
    1428 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1429 
    1430 <h2>Part 4: Bond distance/Angle criteria</h2>
     1215 id="Picture_x0020_20" o:spid="_x0000_i1042" type="#_x0000_t75" alt="Graphical user interface, application&#10;&#10;Description automatically generated"
     1216 style='width:165pt;height:155pt;visibility:visible;mso-wrap-style:square'>
     1217 <v:imagedata src="CIFtutorial.fld/image024.png" o:title="Graphical user interface, application&#10;&#10;Description automatically generated"/>
     1218</v:shape><![endif]--><![if !vml]><img border=0 width=165 height=155
     1219src="CIFtutorial.fld/image024.png"
     1220alt="Graphical user interface, application&#10;&#10;Description automatically generated"
     1221v:shapes="Picture_x0020_20"><![endif]></span></p>
     1222
     1223<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1224
     1225<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1226
     1227<p class=MsoNormal>Ideally the instrument name will be unique, so the
     1228combination of the name and a timestamp will create an identifier that is
     1229unlikely to be repeated. The instrument name should also allow the data source
     1230to be identified should there be several similar instruments within an
     1231institution, but the details for naming are left as a local decision. Inclusion
     1232of an institution name is a good idea, so an ideal name might be “Univ. of
     1233Mars, Curiosity II”. While in this case the two histograms are from different
     1234instruments, the down arrow (<span style='font-family:Symbol;mso-ascii-font-family:
     1235"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
     1236mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
     1237Symbol'>Ú</span></span>) button will copy the entered name to all fields below,
     1238simplifying the data entry task, when appropriate. </p>
     1239
     1240<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1241
     1242<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1243style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1244Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1245</span></span></span><![endif]><span dir=LTR></span>Enter names for each
     1246instrument and then press OK.</p>
     1247
     1248<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
     1249
     1250<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1251 id="Picture_x0020_22" o:spid="_x0000_i1041" type="#_x0000_t75" alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
     1252 style='width:202pt;height:192pt;visibility:visible;mso-wrap-style:square'>
     1253 <v:imagedata src="CIFtutorial.fld/image025.png" o:title="Graphical user interface, text, application&#10;&#10;Description automatically generated"/>
     1254</v:shape><![endif]--><![if !vml]><img border=0 width=202 height=192
     1255src="CIFtutorial.fld/image025.png"
     1256alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
     1257v:shapes="Picture_x0020_22"><![endif]></span></p>
     1258
     1259<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
     12604: Bond distance/Angle criteria<o:p></o:p></span></h2>
    14311261
    14321262<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    14401270
    14411271<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1442  id="Picture_x0020_5" o:spid="_x0000_i1038" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
     1272 id="Picture_x0020_5" o:spid="_x0000_i1040" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
    14431273 style='width:180pt;height:164pt;visibility:visible;mso-wrap-style:square'>
    14441274 <v:imagedata src="CIFtutorial.fld/image007.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
     
    14501280<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    14511281
    1452 <p class=MsoNormal>This dialog will not be shown again, unless invoked manually.
    1453 To explain what these numbers mean, distances between Pb and O atoms will be
    1454 reported when their interatomic distance is less than or equal to (1.95+1.09)*0.85
    1455 Ã
    1456  (=2.584 Ã
    1457 ) and O-Pb-X or X-O-Pb angles will be reported if the Pb-O distance is
    1458 less than or equal to (1.75+0.89)*0.85 Ã
    1459  (=2.244 Ã
    1460 ) <i>and</i> the O-X or Pb-X
    1461 is within the requirement for that pair of atoms as well (in this case X could
    1462 be O, Pb or S). </p>
    1463 
    1464 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1465 
    1466 <p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1467 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1468 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    1469 </span></span></span><![endif]><span dir=LTR></span>In this case no changes are
    1470 needed, so simply press OK.</p>
    1471 
    1472 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1473 
    1474 <h2>Part 5. <span class=GramE>Conditions</span> warning</h2>
     1282<p class=MsoNormal>This dialog will not be shown again, unless invoked
     1283manually. To explain what these numbers mean, distances between Pb and O atoms
     1284will be reported when their interatomic distance is less than or equal to
     1285(1.95+1.09)*0.85 Å (=2.584 Å) and O-Pb-X or X-O-Pb angles will be reported if
     1286the Pb-O distance is less than or equal to (1.75+0.89)*0.85 Å (=2.244 Å) <i>and</i>
     1287the O-X or Pb-X is within the requirement for that pair of atoms as well (in
     1288this case X could be O, Pb or S). </p>
     1289
     1290<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1291
     1292<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1293style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1294Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1295</span></span></span><![endif]><span dir=LTR></span>At this point no changes
     1296are needed, so simply press OK.</p>
     1297
     1298<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1299
     1300<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
     13015. <span class=GramE>Conditions</span> warning<o:p></o:p></span></h2>
    14751302
    14761303<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    14861313
    14871314<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1488  id="Picture_x0020_6" o:spid="_x0000_i1037" type="#_x0000_t75" alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
    1489  style='width:352pt;height:185pt;visibility:visible;mso-wrap-style:square'>
    1490  <v:imagedata src="CIFtutorial.fld/image008.png" o:title="Graphical user interface, text, application&#10;&#10;Description automatically generated"/>
    1491 </v:shape><![endif]--><![if !vml]><img border=0 width=352 height=185
    1492 src="CIFtutorial.fld/image008.png"
    1493 alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
    1494 v:shapes="Picture_x0020_6"><![endif]></span></p>
    1495 
    1496 <p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1497 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1498 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    1499 </span></span></span><![endif]><span dir=LTR></span>Press OK to continue.</p>
    1500 
    1501 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1502 
    1503 <p class=MsoNormal>This warning is shown every time the code is CIF generation
    1504 code is initiated unless the sample temperature has been set to a value other
    1505 than 300 K for each histogram. Note that the Command<span class=GramE>/“</span>Copy
    1506 Selected” may be useful to change a value in multiple histograms in one
    1507 operation. Note that this warning may be ignored if the histogram values are
    1508 correct. </p>
    1509 
    1510 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1511 
    1512 <h2>Part 6. Specifying CIF Contents. </h2>
     1315 id="Picture_x0020_23" o:spid="_x0000_i1039" type="#_x0000_t75" alt="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"
     1316 style='width:220pt;height:87pt;visibility:visible;mso-wrap-style:square'>
     1317 <v:imagedata src="CIFtutorial.fld/image026.png" o:title="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"/>
     1318</v:shape><![endif]--><![if !vml]><img border=0 width=220 height=87
     1319src="CIFtutorial.fld/image026.png"
     1320alt="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"
     1321v:shapes="Picture_x0020_23"><![endif]></span></p>
     1322
     1323<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1324
     1325<p class=MsoNormal>The warning above will be shown every time the code for CIF
     1326generation code is initiated, unless the sample temperature has been set to a
     1327value other than 300 K for each histogram. If indeed the histogram temperature/pressure
     1328values are correct, this warning may be ignored. Note that the Command<span
     1329class=GramE>/“</span>Copy Selected” menu command may be useful to change a
     1330value in multiple histograms in one operation. <o:p></o:p></p>
     1331
     1332<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1333
     1334<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1335style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1336Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1337</span></span></span><![endif]><span dir=LTR></span>Press Cancel to stop the
     1338export</p>
     1339
     1340<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1341
     1342<p class=MsoNormal>In this case it is of particular importance to note the data
     1343collection temperatures. The neutron dataset was collected at cryogenic
     1344temperatures, while the x-ray data were collected under ambient conditions. </p>
     1345
     1346<p class=MsoListParagraphCxSpFirst style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
     1347
     1348<p class=MsoListParagraphCxSpLast style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1349style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1350Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1351</span></span></span><![endif]><span dir=LTR></span>Change the temperature
     1352values in each histogram, as shown below. Note that ideally, temperature and
     1353pressure values will be available to GSAS-II in a data file’s metadata and will
     1354be set in the Sample Parameters automatically, but this is seldom the case.</p>
     1355
     1356<p class=MsoNormal style='margin-left:0in'><o:p>&nbsp;</o:p></p>
     1357
     1358<p class=MsoNormal style='margin-left:0in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1359 id="Picture_x0020_24" o:spid="_x0000_i1038" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
     1360 style='width:292pt;height:279pt;visibility:visible;mso-wrap-style:square'>
     1361 <v:imagedata src="CIFtutorial.fld/image027.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
     1362</v:shape><![endif]--><![if !vml]><img border=0 width=292 height=279
     1363src="CIFtutorial.fld/image027.png"
     1364alt="Graphical user interface&#10;&#10;Description automatically generated"
     1365v:shapes="Picture_x0020_24"><![endif]></span></p>
     1366
     1367<p class=MsoNormal style='margin-left:0in'><o:p>&nbsp;</o:p></p>
     1368
     1369<p class=MsoNormal style='margin-left:0in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1370 id="Picture_x0020_25" o:spid="_x0000_i1037" type="#_x0000_t75" alt="Graphical user interface, table&#10;&#10;Description automatically generated"
     1371 style='width:291pt;height:280pt;visibility:visible;mso-wrap-style:square'>
     1372 <v:imagedata src="CIFtutorial.fld/image028.png" o:title="Graphical user interface, table&#10;&#10;Description automatically generated"/>
     1373</v:shape><![endif]--><![if !vml]><img border=0 width=291 height=280
     1374src="CIFtutorial.fld/image028.png"
     1375alt="Graphical user interface, table&#10;&#10;Description automatically generated"
     1376v:shapes="Picture_x0020_25"><![endif]></span></p>
     1377
     1378<p class=MsoNormal style='margin-left:0in'><o:p>&nbsp;</o:p></p>
     1379
     1380<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1381
     1382<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
     13836. Restart the export process<o:p></o:p></span></h2>
     1384
     1385<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></h2>
     1386
     1387<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1388style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1389Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1390</span></span></span><![endif]><span dir=LTR></span>As before, use the Export
     1391menu and select the “Entire project as” menu item and the “Full CIF” submenu
     1392option. If you use the same file name as in Part 2, you will likely need to say
     1393yes to overwrite the file. </p>
     1394
     1395<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1396
     1397<p class=MsoNormal>Note that the windows opened previously in steps 3-5 will
     1398not occur again, since the requested information has been provided. <o:p></o:p></p>
     1399
     1400<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1401
     1402<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
     14037. Specifying CIF Contents. <o:p></o:p></span></h2>
    15131404
    15141405<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    15151406
    15161407<p class=MsoNormal>Once the previous steps have been performed, a window such
    1517 as the one below is shown. Note that the “Edit CIF Author” button opens a
    1518 dialog window, where the information supplied in Part 1 can be changed. The â€œEdit
    1519 Instrument Name(s)” button reopens the window shown in Part 3.</p>
     1408as the one below is shown. Note that the “Edit CIF Author” button opens a
     1409dialog window, where the information supplied in Part 1 can be changed. The
     1410“Edit Instrument Name(s)” button reopens the window shown in Part 3.</p>
    15201411
    15211412<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    15321423<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    15331424
    1534 <p class=MsoNormal>Note that for every other section of the window, there is are
    1535 a pair of buttons labeled “Select Template File” and “Edit Template.” A default
    1536 template file is selected initially, and information can be included in that
    1537 template with the “Edit Template” button, as will be shown below. Note that there
    1538 are four types of template files for (1) overall information; (2) phase
    1539 information; (3) powder diffraction data and instrumentation details; and (4) single-crystal
    1540 diffraction data and instrumentation details. Note that data items that are set
    1541 by GSAS-II directly (for example, lattice parameters and space group
    1542 information for a phase) are not included in the template. </p>
    1543 
    1544 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1545 
    1546 <p class=MsoNormal>The information you specify to place in a template is included
    1547 in the GSAS-II project (.<span class=SpellE>gpx</span>) file so that if you
    1548 perform a new refinement, all of the template edits you have made are used
    1549 automatically when a new CIF is created. </p>
     1425<p class=MsoNormal>Note that for every other section of the window, there is
     1426are a pair of buttons labeled “Select Template File” and “Edit Template.” A
     1427default template file is selected initially, and information can be included in
     1428that template with the “Edit Template” button, as will be shown below. Note
     1429that there are four types of template files for (1) overall information; (2)
     1430phase information; (3) powder diffraction data and instrumentation details; and
     1431(4) single-crystal diffraction data and instrumentation details. Note that data
     1432items that are set by GSAS-II directly (for example, lattice parameters and
     1433space group information for a phase) are not included in the template. </p>
     1434
     1435<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1436
     1437<p class=MsoNormal>The information you specify to place in a template is
     1438included in the GSAS-II project (.<span class=SpellE>gpx</span>) file so that
     1439if you perform a new refinement, all of the template edits you have made are
     1440used automatically when a new CIF is created. </p>
    15501441
    15511442<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    15541445information in a file. There are two reasons for doing this. One is that by
    15551446saving the information as a file you potentially create a customized template
    1556 file. Use of this file in the future for a different project can save you considerable
    1557 time, as an example, when documenting a diffractometer. Also, if a file is
    1558 saved, instead of keeping all of the template contents in the .<span
     1447file. Use of this file in the future for a different project can save you
     1448considerable time, as an example, when documenting a diffractometer. Also, if a
     1449file is saved, instead of keeping all of the template contents in the .<span
    15591450class=SpellE>gpx</span> file, only the name of the template file is saved,
    15601451reducing the project file size slightly. (The default template files range from
    1561 1K to 4K bytes in size, so this not usually very significant savings.) Once a customized
    1562 template file has been created, use the “Select Template File” button to select
    1563 it in place of the default. </p>
    1564 
    1565 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1566 
    1567 <p class=MsoListParagraphCxSpFirst style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1568 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1569 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     14521K to 4K bytes in size, so this not usually very significant savings.) Once a
     1453customized template file has been created, use the “Select Template File”
     1454button to select it in place of the default. </p>
     1455
     1456<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1457
     1458<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1459style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1460Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    15701461</span></span></span><![endif]><span dir=LTR></span>Edit the Publication
    1571 template by pressing the “Edit Template” button closest to the top of the
    1572 window [just below the “Publication (overall) template” heading] a window similar
    1573 to the one below is created. </p>
     1462template by pressing the “Edit Template” button closest to the top of the
     1463window [just below the “Publication (overall) template” heading] a window
     1464similar to the one below is created. </p>
    15741465
    15751466<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
     
    15971488alt="Graphical user interface&#10;&#10;Description automatically generated"
    15981489v:shapes="Picture_x0020_10"><![endif]></span><span
    1599 style='mso-spacerun:yes'> </span></p>
     1490style='mso-spacerun:yes'> </span></p>
    16001491
    16011492<p class=MsoNormal>Note that this contains three CIF items, _<span
    16021493class=SpellE>publ_author_name</span>, _<span class=SpellE>publ_author_footnote</span>
    16031494and _<span class=SpellE>publ_author_address</span>, in a table (loop_). Note
    1604 the “Add row” button to the upper left which allows additional rows to be added
    1605 to the table. The remainder of this template is a series of CIF items that accept
    1606 a single value. Most CIF items are tagged with a help button, marked with a
    1607 question mark. That indicates that that CIF item is defined in a CIF
     1495the “Add row” button to the upper left which allows additional rows to be added
     1496to the table. The remainder of this template is a series of CIF items that
     1497accept a single value. Most CIF items are tagged with a help button, marked
     1498with a question mark. That indicates that that CIF item is defined in a CIF
    16081499dictionary. The definition can be looked up by pressing that help button or by
    16091500allowing the mouse to stay stationary on a CIF item name for a few seconds
     
    16351526<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    16361527
    1637 <p class=MsoNormal>Note that each text entry box has a small right-angle
    1638 bracket (looking a bit like an inverted L) at the lower right corner. This can
    1639 be used to resize the text entry box to allow viewing a longer line of text
    1640 and/or several lines of text. </p>
    1641 
    1642 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1643 
    1644 <p class=MsoListParagraphCxSpFirst style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1645 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1646 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    1647 </span></span></span><![endif]><span dir=LTR></span>Press the “Add row” button
    1648 to create entries for a second author. </p>
    1649 
    1650 <p class=MsoListParagraphCxSpMiddle style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1651 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1652 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1528<p class=MsoNormal>Note that each text entry box has a small right-angle bracket
     1529(looking a bit like an inverted L) at the lower right corner. This can be used
     1530to resize the text entry box to allow viewing a longer line of text and/or
     1531several lines of text. </p>
     1532
     1533<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1534
     1535<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1536style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1537Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1538</span></span></span><![endif]><span dir=LTR></span>Press the “Add row” button to
     1539create entries for a second author. </p>
     1540
     1541<p class=MsoListParagraphCxSpMiddle style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1542style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1543Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    16531544</span></span></span><![endif]><span dir=LTR></span>Enlarge the width of either
    1654 of the _<span class=SpellE>publ_author_name</span> entry boxes as well as the height
    1655 and width of the _<span class=SpellE>publ_author_address</span> item to accommodate
    1656 more text. </p>
    1657 
    1658 <p class=MsoListParagraphCxSpLast style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1659 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1660 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1545of the _<span class=SpellE>publ_author_name</span> entry boxes as well as the
     1546height and width of the _<span class=SpellE>publ_author_address</span> item to
     1547accommodate more text. </p>
     1548
     1549<p class=MsoListParagraphCxSpLast style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1550style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1551Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    16611552</span></span></span><![endif]><span dir=LTR></span>Add text to describe
    1662 authorship, such as what has been done below (authorship of the original Anglesite,
    1663 aka PbSO<sub>4</sub>, crystal structure). Note that as is described in the CIF
    1664 definition, author names are supplied as last name, first name. </p>
     1553authorship, such as what has been done below (authorship of the original
     1554Anglesite, aka PbSO<sub>4</sub>, crystal structure). Note that as is described
     1555in the CIF definition, author names are supplied as last name, first name. </p>
    16651556
    16661557<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16771568<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    16781569
    1679 <p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1680 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1681 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1570<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1571style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1572Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    16821573</span></span></span><![endif]><span dir=LTR></span>After completing all
    1683 appropriate CIF items that would be appropriate for this work, press the “Use”
     1574appropriate CIF items that would be appropriate for this work, press the “Use”
    16841575button to close the window, saving the entries into the project file. </p>
    16851576
     
    16951586  croptop="910f" cropbottom="38375f"/>
    16961587</v:shape><![endif]--><![if !vml]><img border=0 width=148 height=86
    1697 src="CIFtutorial.fld/image016.png"
     1588src="CIFtutorial.fld/image006.png"
    16981589alt="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"
    16991590v:shapes="Picture_x0020_14"><![endif]></span></p>
     
    17011592<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17021593
    1703 <h2>Part 7. Edit Phase Information including Distances and Angles. </h2>
     1594<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
     15958. Edit Phase Information including Distances and Angles. <o:p></o:p></span></h2>
    17041596
    17051597<p class=MsoNormal>The phase template contains a relatively small number of
    1706 items that can document information about a phase, as shown below. Note that _<span
    1707 class=SpellE>cell_measurement_temperature</span> is probably best used only
    1708 with single crystal fits. For powder data, the _<span class=SpellE>diffrn_ambient_temperature</span>
    1709 field will be set with the temperature supplied for Sample Parameters. If one
    1710 produced several projects all using the same sample, it might make sense to produce
    1711 a template file that might be used for that sample in all projects. </p>
     1598items that can document information about a phase, as shown below. If one
     1599produced several projects all using the same sample, it might make sense to
     1600produce a template file that might be used for that sample in all projects. </p>
     1601
     1602<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1603
     1604<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1605style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1606Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1607</span></span></span><![endif]><span dir=LTR></span>Press the “Edit Template”
     1608button in the Phase section of the “Edit CIF settings” window and the window
     1609below appears. Enter any information desired. Press “Use” when done.<o:p></o:p></p>
     1610
     1611<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17121612
    17131613<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17141614
    17151615<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1716  id="Picture_x0020_15" o:spid="_x0000_i1029" type="#_x0000_t75" alt="Diagram&#10;&#10;Description automatically generated with low confidence"
    1717  style='width:195pt;height:310pt;visibility:visible;mso-wrap-style:square'>
    1718  <v:imagedata src="CIFtutorial.fld/image017.png" o:title="Diagram&#10;&#10;Description automatically generated with low confidence"/>
    1719 </v:shape><![endif]--><![if !vml]><img border=0 width=195 height=310
    1720 src="CIFtutorial.fld/image017.png"
    1721 alt="Diagram&#10;&#10;Description automatically generated with low confidence"
    1722 v:shapes="Picture_x0020_15"><![endif]></span></p>
    1723 
    1724 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1725 
    1726 <p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1727 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1728 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    1729 </span></span></span><![endif]><span dir=LTR></span>Press the “Set distance/angle
    1730 publication flag” the window below appears. </p>
     1616 id="Picture_x0020_26" o:spid="_x0000_i1029" type="#_x0000_t75" alt="Diagram&#10;&#10;Description automatically generated with medium confidence"
     1617 style='width:214pt;height:316pt;visibility:visible;mso-wrap-style:square'>
     1618 <v:imagedata src="CIFtutorial.fld/image008.png" o:title="Diagram&#10;&#10;Description automatically generated with medium confidence"/>
     1619</v:shape><![endif]--><![if !vml]><img border=0 width=214 height=316
     1620src="CIFtutorial.fld/image008.png"
     1621alt="Diagram&#10;&#10;Description automatically generated with medium confidence"
     1622v:shapes="Picture_x0020_26"><![endif]></span></p>
     1623
     1624<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1625
     1626<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1627
     1628<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1629style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1630Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1631</span></span></span><![endif]><span dir=LTR></span>Press the “Set
     1632distance/angle publication flag” and the window below appears. </p>
    17311633
    17321634<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    17441646<p class=MsoNormal>This shows the interatomic distances and angles that that
    17451647occur within the radii specified above. Note that the Pb radius is too small to
    1746 pick up the coordination of that atom, so we should change that. </p>
    1747 
    1748 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1749 
    1750 <p class=MsoListParagraphCxSpFirst style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1751 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1752 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    1753 </span></span></span><![endif]><span dir=LTR></span>Press the “Done” button to
     1648pick up the coordination of that atom, so we should change that:</p>
     1649
     1650<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1651
     1652<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1653style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1654Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1655</span></span></span><![endif]><span dir=LTR></span>Press the “Done” button to
    17541656close this window</p>
    17551657
    1756 <p class=MsoListParagraphCxSpMiddle style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1757 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1758 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    1759 </span></span></span><![endif]><span dir=LTR></span>Press the “Edit distance/angle
    1760 ranges” button to bring up the screen below. Change the bond search factor from
    1761 0.85 to 0.9 to increase the search range, as below.</p>
     1658<p class=MsoListParagraphCxSpMiddle style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1659style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1660Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1661</span></span></span><![endif]><span dir=LTR></span>Press the “Edit
     1662distance/angle ranges” button to bring up the screen below. Change the bond
     1663search factor from 0.85 to 0.9 to increase the search range, as below.</p>
    17621664
    17631665<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
     
    17741676<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17751677
    1776 <p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1777 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1778 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    1779 </span></span></span><![endif]><span dir=LTR></span>Press the “Set distance/angle
    1780 publication flag” and note the additional distances (but not angles) in the
    1781 window below. <o:p></o:p></p>
     1678<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1679style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1680Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1681</span></span></span><![endif]><span dir=LTR></span>Press the “Set
     1682distance/angle publication flag” and note the additional distances (but not
     1683angles) in the window below. </p>
    17821684
    17831685<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    17941696
    17951697<p class=MsoNormal>Note that to obtain the angles around the Pb and O atoms,
    1796 the values in the right-hand column and/or the angle search factor range must also
    1797 be extended. </p>
     1698the values in the right-hand column and/or the angle search factor range must
     1699also be extended. </p>
    17981700
    17991701<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    18051707crystallographic notation). Also note that in the CIF each distance has an
    18061708associated _<span class=SpellE>geom_bond_publ_flag</span> value (for angles, _<span
    1807 class=SpellE>geom_angle_publ_flag</span>). The value for this can be “yes”&nbsp;or
    1808 â€œno” and a “yes” value indicates that the value should be placed in a table of
    1809 bond distances/angles, if generated from the CIF. By default, this flag
    1810 defaults to “yes<span class=GramE>”</span> but this can be changed by clicking
    1811 on the distance or angle button. </p>
    1812 
    1813 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1814 
    1815 <h2>Part 8. Create a Customized Template File. <o:p></o:p></h2>
    1816 
    1817 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1818 
    1819 <p class=MsoNormal>For this particular project, since these were data distributed
    1820 from a round-robin study many years ago, relatively little is documented on the
    1821 instruments, but as a useful exercise, I recommend opening documenting an
    1822 instrument that you use frequently (or twist the arm of the instrument
    1823 scientist at your favorite facility to do so.) <span
    1824 style='mso-spacerun:yes'> </span></p>
    1825 
    1826 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1827 
    1828 <p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1829 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1830 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    1831 </span></span></span><![endif]><span dir=LTR></span>Press the “Edit Template”
     1709class=SpellE>geom_angle_publ_flag</span>). The value for this can be
     1710“yes”&nbsp;or “no” and a “yes” value indicates that the value should be placed
     1711in a table of bond distances/angles, if generated from the CIF. By default,
     1712this flag defaults to “yes<span class=GramE>”</span> but this can be changed by
     1713clicking on the distance or angle button. </p>
     1714
     1715<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1716
     1717<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
     17189. Create a Customized Template File. <o:p></o:p></span></h2>
     1719
     1720<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1721
     1722<p class=MsoNormal>For this particular project, since these were data
     1723distributed from a round-robin study many years ago, relatively little is
     1724documented on the instruments, but as a useful exercise, I recommend opening
     1725documenting an instrument that you use frequently (or twist the arm of the
     1726instrument scientist at your favorite facility to do so.)<span
     1727style='mso-spacerun:yes'>  </span></p>
     1728
     1729<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1730
     1731<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1732style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1733Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1734</span></span></span><![endif]><span dir=LTR></span>Press the “Edit Template”
    18321735button for either histogram <span class=GramE>and</span> define as many of the
    18331736appropriate fields as are appropriate. </p>
     
    18441747v:shapes="Picture_x0020_19"><![endif]></span></p>
    18451748
    1846 <p class=MsoListParagraphCxSpFirst style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1847 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1848 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    1849 </span></span></span><![endif]><span dir=LTR></span>Press the “Save as template”
    1850 button and save the file with a name and location that will make this readily
    1851 available for future use.</p>
     1749<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1750style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1751Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1752</span></span></span><![endif]><span dir=LTR></span>Press the “Save as
     1753template” button and save the file with a name and location that will make this
     1754readily available for future use.</p>
    18521755
    18531756<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
    18541757
    1855 <p class=MsoNormal>Note that the next time that “Export
 project
 to CIF” is
    1856 used, this template can be used by pressing the “Select Template File” button
    1857 for that histogram and by doing this all of the information specified previously
    1858 can be used without additional data entry effort. <span
    1859 style='mso-spacerun:yes'> </span></p>
    1860 
    1861 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1862 
    1863 <h2>Part 9. Create the CIF</h2>
    1864 
    1865 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1866 
    1867 <p class=MsoListParagraphCxSpFirst style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
    1868 style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1869 Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
    1870 </span></span></span><![endif]><span dir=LTR></span>Pressing the “Create CIF”
     1758<p class=MsoNormal>Note that the next time that “Export… project… to CIF” is
     1759used, this template can be used by pressing the “Select Template File” button
     1760for that histogram and by doing this all of the information specified
     1761previously can be used without additional data entry effort.<span
     1762style='mso-spacerun:yes'>  </span></p>
     1763
     1764<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1765
     1766<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
     176710. Create the CIF<o:p></o:p></span></h2>
     1768
     1769<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1770
     1771<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
     1772style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
     1773Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
     1774</span></span></span><![endif]><span dir=LTR></span>Pressing the “Create CIF”
    18711775button will cause the CIF to be written. </p>
    18721776
     
    18751779<p class=MsoNormal>Depending on the number and size of histograms, this can be
    18761780a fairly large file as it contains observed and computed patterns for each, as
    1877 well as a reflection table, plus unit cell parameters, symmetry information, coordinates
    1878 and bond distances and angles for each phase. <o:p></o:p></p>
     1781well as a reflection table, plus unit cell parameters, symmetry information,
     1782coordinates and bond distances and angles for each phase. </p>
    18791783
    18801784<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    18831787example by introducing a new variable, changing the background model etc. all
    18841788that need be done to create a CIF with updated information will be to select
    1885 the “Entire project as” menu item and the “Full CIF” submenu option from the
    1886 Export menu and then press the “Create CIF” button again. All information generated
    1887 by GSAS-II will be updated and previously entered will be retained and placed
    1888 in the new file. </p>
     1789the “Entire project as” menu item and the “Full CIF” submenu option from the
     1790Export menu and then press the “Create CIF” button again. All information
     1791generated by GSAS-II will be updated and previously entered will be retained
     1792and placed in the new file. </p>
    18891793
    18901794<p class=MsoNormal><o:p>&nbsp;</o:p></p>
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