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1011
1012	<body lang=EN-US link=blue vlink="#954F72" style='tab-interval:.5in;word-wrap:
1013	break-word'>
1014
1015	<div class=WordSection1>
1016
1017	<h1 align=center style='text-align:center'><a name="_GoBack"></a><span
1018	style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Tutorial:
1019	Preparing a Full CIF<o:p></o:p></span></h1>
1020
1021	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><BL><![if !supportLists]><span
1022	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1023	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1024	</span></span></span><![endif]><span dir=LTR></span>Exercise files are found <a
1025	href="data" target="_blank">here</a>. The data files are taken from the
1026	conclusion of the “<a href="../CWCombined/Combined%20refinement.htm">Combined
1027	X-ray/neutron refinement – PbSO<sub>4</sub></a>” tutorial. <o:p></o:p></p>
1028
1029	</BL>
1030
1031	<h1><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Background
1032	<o:p></o:p></span></h1>
1033
1034	<p class=MsoNormal>Crystallography has had a long tradition where experimental
1035	data as well as results were reported numerically, so that results could be
1036	verified independently as well as utilized. In the past two decades the field
1037	has set the standard for data science compared to almost all other areas of
1038	physical and biological science through the development of the Crystallographic
1039	Information Framework (CIF) which defines a universal format for the reporting
1040	of nearly all aspects of a crystallographic fit. This is particularly true for
1041	Rietveld fits, where the <span class=SpellE>pdCIF</span> subset of CIF has been
1042	developed to capture the observed and computed patterns as well as reflection
1043	tables and coordinates as well as interatomic distances and angles. </p>
1044
1045	<p class=MsoNormal><o:p> </o:p></p>
1046
1047	<p class=MsoNormal>Within GSAS-II, a CIF for a phase <span class=GramE>are</span>
1048	available as “quick” coordinate-only file, which provides atom coordinates and
1049	displacement parameters, but no uncertainties or other supporting information
1050	from the refinement. This is indeed easy with a single menu command. Likewise,
1051	a CIF containing only a dataset without phase information can be easily created
1052	from the Export menu, but the real power of CIF comes after a project has been
1053	completed. Using the “Entire project as…” a “Full CIF” menu command in the
1054	Export menu, all results can be reported in a machine and human readable. There
1055	are a few steps in generating a full project CIF. This tutorial goes through
1056	them and explains what is being done and why. </p>
1057
1058	<p class=MsoNormal><o:p> </o:p></p>
1059
1060	<p class=MsoNormal>A bit of background on CIF: The format allows a label (a CIF
1061	data item, such as _cell_length_a or _publ_author_name) to be associated with
1062	either a single value or a column in a table. A collection of data items is
1063	placed in a block. For a single-crystal structure, a block will usually contain
1064	the coordinates for a phase and the structure factors (experimental data and
1065	the matching simulated values) as well as supporting information and derived
1066	results. With multiple temperatures, a block would be needed for each setting
1067	because, for example, only one set of unit cell dimensions and coordinates can
1068	be defined in a block. With powder diffraction, if a single dataset (histogram)
1069	is used and only one phase is present, a single block can be used. If either
1070	more than one phase is present, or more than one histogram is used, multiple
1071	blocks are required. GSAS-II will create single-block CIFs when possible, but
1072	otherwise will create a block for the overall refinement plus a block for each
1073	histogram and a block for each phase. Referencing information between different
1074	blocks requires that each block be labeled with a unique name. These block
1075	labels are assembled from a number of fields supplied by the user and a
1076	timestamp when the file is created. </p>
1077
1078	<p class=MsoNormal><o:p> </o:p></p>
1079
1080	<p class=MsoNormal>A tremendous amount of information can be placed into a CIF
1081	file. No one is likely to specify all of the field in the IUCr-supplied
1082	template, which itself does not include all data items defined in CIF. Some
1083	information can be supplied by GSAS-II from what is defined inside a project,
1084	data such as symmetry and lattice parameters, but other information, for
1085	example synthesis conditions or sample color, must be supplied by the user.
1086	This could be done with a simple text editor once the file is created, but the
1087	problem that arises from that approach is that it is common that after one has
1088	produced the “final” refinement, another idea occurs for a slightly better fit.
1089	The approach used in GSAS-II is that as the CIF is generated, copies of
1090	template files are made that contain all the user-supplied information. Thus,
1091	the CIF can be recreated from the updated project without having to repeat all
1092	the work in supplying that information. Also, by saving template files that
1093	have setting information that will be common amongst multiple projects (for
1094	example, diffraction instrumentation descriptions) these files can be reused,
1095	avoiding 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>
1099
1100	<p class=MsoNormal>Before beginning this tutorial, either complete the
1101	refinement in the “<a href="../../../CWCombined/Combined%20refinement.htm">Combined
1102	X-ray/neutron refinement – PbSO<sub>4</sub></a>” tutorial or download the
1103	GSAS-II project file provided <a href="../../../Scratch/data" target="_blank">here</a>,
1104	which provides a two histogram, one phase refinement. </p>
1105
1106	<p class=MsoNormal><o:p> </o:p></p>
1107
1108	<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
1109	1. Enter a name for the author of the CIF file. <o:p></o:p></span></h2>
1110
1111	<p class=MsoNormal><o:p> </o:p></p>
1112
1113	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1114	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1115	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1116	</span></span></span><![endif]><span dir=LTR></span>Select the Controls entry
1117	on the data tree and enter the name for the main author for the project and
1118	CIF.</p>
1119
1120	<p class=MsoNormal><o:p> </o:p></p>
1121
1122	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
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1151
1152	<p class=MsoNormal><o:p> </o:p></p>
1153
1154	<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
1155	2: Start the export process<o:p></o:p></span></h2>
1156
1157	<p class=MsoNormal><o:p> </o:p></p>
1158
1159	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
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1161	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1162	</span></span></span><![endif]><span dir=LTR></span>Using the Export menu,
1163	select the “Entire project as” menu item and the “Full CIF” submenu option. </p>
1164
1165	<p class=MsoNormal><o:p> </o:p></p>
1166
1167	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1174
1175	<p class=MsoNormal><o:p> </o:p></p>
1176
1177	<p class=MsoNormal>This opens a dialog (exact appearance will depend on the
1178	operating system you are using) where you can select a name for the file to be
1179	created. </p>
1180
1181	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1190
1191	<p class=MsoNormal><o:p> </o:p></p>
1192
1193	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1194	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1195	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1196	</span></span></span><![endif]><span dir=LTR></span>Enter a name for the file
1197	if you wish to override the default name and press Save. If that file exists, you
1198	will need to agree to overwrite it or to select a new name. </p>
1199
1200	<p class=MsoNormal><o:p> </o:p></p>
1201
1202	<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
1203	3: Select instrument name(s)<o:p></o:p></span></h2>
1204
1205	<p class=MsoNormal><o:p> </o:p></p>
1206
1207	<p class=MsoNormal>Before a CIF can be created, each histogram must have
1208	associated with it an instrument name. Note that the instrument name appears in
1209	the Sample Parameters tree entry for each histogram. If any instrument does not
1210	have a name, the dialog below is displayed. </p>
1211
1212	<p class=MsoNormal><o:p> </o:p></p>
1213
1214	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1219	src="CIFtutorial.fld/image024.png"
1220	alt="Graphical user interface, application Description automatically generated"
1221	v:shapes="Picture_x0020_20"><![endif]></span></p>
1222
1223	<p class=MsoNormal><o:p> </o:p></p>
1224
1225	<p class=MsoNormal><o:p> </o:p></p>
1226
1227	<p class=MsoNormal>Ideally the instrument name will be unique, so the
1228	combination of the name and a timestamp will create an identifier that is
1229	unlikely to be repeated. The instrument name should also allow the data source
1230	to be identified should there be several similar instruments within an
1231	institution, but the details for naming are left as a local decision. Inclusion
1232	of an institution name is a good idea, so an ideal name might be “Univ. of
1233	Mars, Curiosity II”. While in this case the two histograms are from different
1234	instruments, 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;
1236	mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
1237	Symbol'>Ú</span></span>) button will copy the entered name to all fields below,
1238	simplifying the data entry task, when appropriate. </p>
1239
1240	<p class=MsoNormal><o:p> </o:p></p>
1241
1242	<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1243	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1244	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1245	</span></span></span><![endif]><span dir=LTR></span>Enter names for each
1246	instrument and then press OK.</p>
1247
1248	<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p> </o:p></p>
1249
1250	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1258
1259	<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
1260	4: Bond distance/Angle criteria<o:p></o:p></span></h2>
1261
1262	<p class=MsoNormal><o:p> </o:p></p>
1263
1264	<p class=MsoNormal>One significant part of a CIF is the computation of bond
1265	distances and angles. For this there is a set of atomic radii for each phase
1266	along with a tolerance factor. When the CIF creation is initially invoked, the
1267	dialog below is shown for each phase:</p>
1268
1269	<p class=MsoNormal><o:p> </o:p></p>
1270
1271	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1272	id="Picture_x0020_5" o:spid="_x0000_i1040" type="#_x0000_t75" alt="Graphical user interface Description automatically generated"
1273	style='width:180pt;height:164pt;visibility:visible;mso-wrap-style:square'>
1274	<v:imagedata src="CIFtutorial.fld/image007.png" o:title="Graphical user interface Description automatically generated"/>
1275	</v:shape><![endif]--><![if !vml]><img border=0 width=180 height=164
1276	src="CIFtutorial.fld/image007.png"
1277	alt="Graphical user interface Description automatically generated"
1278	v:shapes="Picture_x0020_5"><![endif]></span></p>
1279
1280	<p class=MsoNormal><o:p> </o:p></p>
1281
1282	<p class=MsoNormal>This dialog will not be shown again, unless invoked
1283	manually. To explain what these numbers mean, distances between Pb and O atoms
1284	will 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
1286	the Pb-O distance is less than or equal to (1.75+0.89)*0.85 Å (=2.244 Å) <i>and</i>
1287	the O-X or Pb-X is within the requirement for that pair of atoms as well (in
1288	this case X could be O, Pb or S). </p>
1289
1290	<p class=MsoNormal><o:p> </o:p></p>
1291
1292	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1293	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1294	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1295	</span></span></span><![endif]><span dir=LTR></span>At this point no changes
1296	are needed, so simply press OK.</p>
1297
1298	<p class=MsoNormal><o:p> </o:p></p>
1299
1300	<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
1301	5. <span class=GramE>Conditions</span> warning<o:p></o:p></span></h2>
1302
1303	<p class=MsoNormal><o:p> </o:p></p>
1304
1305	<p class=MsoNormal>Note that when a histogram is created in GSAS-II, unless
1306	pressure and temperature values are reported in the metadata in a standardized
1307	fashion (this is uncommon), the sample temperature defaults to 300 K and the
1308	ambient pressure to 0.1 MPa. It is likely that these values do not describe the
1309	actual data collection conditions. Since they will be included in the CIF, they
1310	should be updated with more appropriate values.</p>
1311
1312	<p class=MsoNormal><o:p> </o:p></p>
1313
1314	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1315	id="Picture_x0020_23" o:spid="_x0000_i1039" type="#_x0000_t75" alt="Graphical user interface, text, application, email 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 Description automatically generated"/>
1318	</v:shape><![endif]--><![if !vml]><img border=0 width=220 height=87
1319	src="CIFtutorial.fld/image026.png"
1320	alt="Graphical user interface, text, application, email Description automatically generated"
1321	v:shapes="Picture_x0020_23"><![endif]></span></p>
1322
1323	<p class=MsoNormal><o:p> </o:p></p>
1324
1325	<p class=MsoNormal>The warning above will be shown every time the code for CIF
1326	generation code is initiated, unless the sample temperature has been set to a
1327	value other than 300 K for each histogram. If indeed the histogram temperature/pressure
1328	values are correct, this warning may be ignored. Note that the Command<span
1329	class=GramE>/“</span>Copy Selected” menu command may be useful to change a
1330	value in multiple histograms in one operation. <o:p></o:p></p>
1331
1332	<p class=MsoNormal><o:p> </o:p></p>
1333
1334	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1335	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1336	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1337	</span></span></span><![endif]><span dir=LTR></span>Press Cancel to stop the
1338	export</p>
1339
1340	<p class=MsoNormal><o:p> </o:p></p>
1341
1342	<p class=MsoNormal>In this case it is of particular importance to note the data
1343	collection temperatures. The neutron dataset was collected at cryogenic
1344	temperatures, 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> </o:p></p>
1347
1348	<p class=MsoListParagraphCxSpLast style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1349	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1350	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1351	</span></span></span><![endif]><span dir=LTR></span>Change the temperature
1352	values in each histogram, as shown below. Note that ideally, temperature and
1353	pressure values will be available to GSAS-II in a data file’s metadata and will
1354	be set in the Sample Parameters automatically, but this is seldom the case.</p>
1355
1356	<p class=MsoNormal style='margin-left:0in'><o:p> </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 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 Description automatically generated"/>
1362	</v:shape><![endif]--><![if !vml]><img border=0 width=292 height=279
1363	src="CIFtutorial.fld/image027.png"
1364	alt="Graphical user interface Description automatically generated"
1365	v:shapes="Picture_x0020_24"><![endif]></span></p>
1366
1367	<p class=MsoNormal style='margin-left:0in'><o:p> </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 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 Description automatically generated"/>
1373	</v:shape><![endif]--><![if !vml]><img border=0 width=291 height=280
1374	src="CIFtutorial.fld/image028.png"
1375	alt="Graphical user interface, table Description automatically generated"
1376	v:shapes="Picture_x0020_25"><![endif]></span></p>
1377
1378	<p class=MsoNormal style='margin-left:0in'><o:p> </o:p></p>
1379
1380	<p class=MsoNormal><o:p> </o:p></p>
1381
1382	<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
1383	6. 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> </o:p></span></h2>
1386
1387	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1388	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1389	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1390	</span></span></span><![endif]><span dir=LTR></span>As before, use the Export
1391	menu and select the “Entire project as” menu item and the “Full CIF” submenu
1392	option. If you use the same file name as in Part 2, you will likely need to say
1393	yes to overwrite the file. </p>
1394
1395	<p class=MsoNormal><o:p> </o:p></p>
1396
1397	<p class=MsoNormal>Note that the windows opened previously in steps 3-5 will
1398	not occur again, since the requested information has been provided. <o:p></o:p></p>
1399
1400	<p class=MsoNormal><o:p> </o:p></p>
1401
1402	<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
1403	7. Specifying CIF Contents. <o:p></o:p></span></h2>
1404
1405	<p class=MsoNormal><o:p> </o:p></p>
1406
1407	<p class=MsoNormal>Once the previous steps have been performed, a window such
1408	as the one below is shown. Note that the “Edit CIF Author” button opens a
1409	dialog 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>
1411
1412	<p class=MsoNormal><o:p> </o:p></p>
1413
1414	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1415	id="Picture_x0020_7" o:spid="_x0000_i1036" type="#_x0000_t75" alt="Graphical user interface, text, application Description automatically generated"
1416	style='width:194pt;height:298pt;visibility:visible;mso-wrap-style:square'>
1417	<v:imagedata src="CIFtutorial.fld/image009.png" o:title="Graphical user interface, text, application Description automatically generated"/>
1418	</v:shape><![endif]--><![if !vml]><img border=0 width=194 height=298
1419	src="CIFtutorial.fld/image009.png"
1420	alt="Graphical user interface, text, application Description automatically generated"
1421	v:shapes="Picture_x0020_7"><![endif]></span></p>
1422
1423	<p class=MsoNormal><o:p> </o:p></p>
1424
1425	<p class=MsoNormal>Note that for every other section of the window, there is
1426	are a pair of buttons labeled “Select Template File” and “Edit Template.” A
1427	default template file is selected initially, and information can be included in
1428	that template with the “Edit Template” button, as will be shown below. Note
1429	that there are four types of template files for (1) overall information; (2)
1430	phase information; (3) powder diffraction data and instrumentation details; and
1431	(4) single-crystal diffraction data and instrumentation details. Note that data
1432	items that are set by GSAS-II directly (for example, lattice parameters and
1433	space group information for a phase) are not included in the template. </p>
1434
1435	<p class=MsoNormal><o:p> </o:p></p>
1436
1437	<p class=MsoNormal>The information you specify to place in a template is
1438	included in the GSAS-II project (.<span class=SpellE>gpx</span>) file so that
1439	if you perform a new refinement, all of the template edits you have made are
1440	used automatically when a new CIF is created. </p>
1441
1442	<p class=MsoNormal><o:p> </o:p></p>
1443
1444	<p class=MsoNormal>As you are editing each template, you can save that
1445	information in a file. There are two reasons for doing this. One is that by
1446	saving the information as a file you potentially create a customized template
1447	file. Use of this file in the future for a different project can save you
1448	considerable time, as an example, when documenting a diffractometer. Also, if a
1449	file is saved, instead of keeping all of the template contents in the .<span
1450	class=SpellE>gpx</span> file, only the name of the template file is saved,
1451	reducing the project file size slightly. (The default template files range from
1452	1K to 4K bytes in size, so this not usually very significant savings.) Once a
1453	customized template file has been created, use the “Select Template File”
1454	button to select it in place of the default. </p>
1455
1456	<p class=MsoNormal><o:p> </o:p></p>
1457
1458	<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1459	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1460	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1461	</span></span></span><![endif]><span dir=LTR></span>Edit the Publication
1462	template by pressing the “Edit Template” button closest to the top of the
1463	window [just below the “Publication (overall) template” heading] a window
1464	similar to the one below is created. </p>
1465
1466	<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p> </o:p></p>
1467
1468	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1469	id="Picture_x0020_9" o:spid="_x0000_i1035" type="#_x0000_t75" alt="Graphical user interface Description automatically generated"
1470	style='width:169pt;height:225pt;visibility:visible;mso-wrap-style:square'>
1471	<v:imagedata src="CIFtutorial.fld/image010.png" o:title="Graphical user interface Description automatically generated"/>
1472	</v:shape><![endif]--><![if !vml]><img border=0 width=169 height=225
1473	src="CIFtutorial.fld/image010.png"
1474	alt="Graphical user interface Description automatically generated"
1475	v:shapes="Picture_x0020_9"><![endif]></span></p>
1476
1477	<p class=MsoNormal><o:p> </o:p></p>
1478
1479	<p class=MsoNormal>A few notes on the arrangement of this window, which is a
1480	bit easier to use if manually resized, as below. </p>
1481
1482	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1483	id="Picture_x0020_10" o:spid="_x0000_i1034" type="#_x0000_t75" alt="Graphical user interface Description automatically generated"
1484	style='width:269pt;height:200pt;visibility:visible;mso-wrap-style:square'>
1485	<v:imagedata src="CIFtutorial.fld/image011.png" o:title="Graphical user interface Description automatically generated"/>
1486	</v:shape><![endif]--><![if !vml]><img border=0 width=269 height=200
1487	src="CIFtutorial.fld/image011.png"
1488	alt="Graphical user interface Description automatically generated"
1489	v:shapes="Picture_x0020_10"><![endif]></span><span
1490	style='mso-spacerun:yes'> </span></p>
1491
1492	<p class=MsoNormal>Note that this contains three CIF items, _<span
1493	class=SpellE>publ_author_name</span>, _<span class=SpellE>publ_author_footnote</span>
1494	and _<span class=SpellE>publ_author_address</span>, in a table (loop_). Note
1495	the “Add row” button to the upper left which allows additional rows to be added
1496	to the table. The remainder of this template is a series of CIF items that
1497	accept a single value. Most CIF items are tagged with a help button, marked
1498	with a question mark. That indicates that that CIF item is defined in a CIF
1499	dictionary. The definition can be looked up by pressing that help button or by
1500	allowing the mouse to stay stationary on a CIF item name for a few seconds
1501	which causes the definition text to appear as a tool tip, as below,</p>
1502
1503	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1504	id="Picture_x0020_11" o:spid="_x0000_i1033" type="#_x0000_t75" alt="A picture containing graphical user interface Description automatically generated"
1505	style='width:205pt;height:96pt;visibility:visible;mso-wrap-style:square'>
1506	<v:imagedata src="CIFtutorial.fld/image012.png" o:title="A picture containing graphical user interface Description automatically generated"/>
1507	</v:shape><![endif]--><![if !vml]><img border=0 width=205 height=96
1508	src="CIFtutorial.fld/image012.png"
1509	alt="A picture containing graphical user interface Description automatically generated"
1510	v:shapes="Picture_x0020_11"><![endif]></span></p>
1511
1512	<p class=MsoNormal><o:p> </o:p></p>
1513
1514	<p class=MsoNormal>or clicking on the button displays the same information at
1515	the bottom of the window, as below.</p>
1516
1517	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1518	id="Picture_x0020_12" o:spid="_x0000_i1032" type="#_x0000_t75" alt="Graphical user interface Description automatically generated with medium confidence"
1519	style='width:257pt;height:165pt;visibility:visible;mso-wrap-style:square'>
1520	<v:imagedata src="CIFtutorial.fld/image013.png" o:title="Graphical user interface Description automatically generated with medium confidence"/>
1521	</v:shape><![endif]--><![if !vml]><img border=0 width=257 height=165
1522	src="CIFtutorial.fld/image013.png"
1523	alt="Graphical user interface Description automatically generated with medium confidence"
1524	v:shapes="Picture_x0020_12"><![endif]></span></p>
1525
1526	<p class=MsoNormal><o:p> </o:p></p>
1527
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
1530	to resize the text entry box to allow viewing a longer line of text and/or
1531	several lines of text. </p>
1532
1533	<p class=MsoNormal><o:p> </o:p></p>
1534
1535	<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1536	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1537	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1538	</span></span></span><![endif]><span dir=LTR></span>Press the “Add row” button to
1539	create entries for a second author. </p>
1540
1541	<p class=MsoListParagraphCxSpMiddle style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1542	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1543	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1544	</span></span></span><![endif]><span dir=LTR></span>Enlarge the width of either
1545	of the _<span class=SpellE>publ_author_name</span> entry boxes as well as the
1546	height and width of the _<span class=SpellE>publ_author_address</span> item to
1547	accommodate more text. </p>
1548
1549	<p class=MsoListParagraphCxSpLast style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1550	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1551	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1552	</span></span></span><![endif]><span dir=LTR></span>Add text to describe
1553	authorship, such as what has been done below (authorship of the original
1554	Anglesite, aka PbSO<sub>4</sub>, crystal structure). Note that as is described
1555	in the CIF definition, author names are supplied as last name, first name. </p>
1556
1557	<p class=MsoNormal><o:p> </o:p></p>
1558
1559	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1560	id="Picture_x0020_13" o:spid="_x0000_i1031" type="#_x0000_t75" alt="Graphical user interface Description automatically generated"
1561	style='width:331pt;height:277pt;visibility:visible;mso-wrap-style:square'>
1562	<v:imagedata src="CIFtutorial.fld/image014.png" o:title="Graphical user interface Description automatically generated"/>
1563	</v:shape><![endif]--><![if !vml]><img border=0 width=331 height=277
1564	src="CIFtutorial.fld/image014.png"
1565	alt="Graphical user interface Description automatically generated"
1566	v:shapes="Picture_x0020_13"><![endif]></span></p>
1567
1568	<p class=MsoNormal><o:p> </o:p></p>
1569
1570	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1571	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1572	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1573	</span></span></span><![endif]><span dir=LTR></span>After completing all
1574	appropriate CIF items that would be appropriate for this work, press the “Use”
1575	button to close the window, saving the entries into the project file. </p>
1576
1577	<p class=MsoNormal><o:p> </o:p></p>
1578
1579	<p class=MsoNormal>Note that the window contents changes to indicate that the
1580	template information is no longer from a file. </p>
1581
1582	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1583	id="Picture_x0020_14" o:spid="_x0000_i1030" type="#_x0000_t75" alt="Graphical user interface, text, application, email Description automatically generated"
1584	style='width:148pt;height:86pt;visibility:visible;mso-wrap-style:square'>
1585	<v:imagedata src="CIFtutorial.fld/image015.png" o:title="Graphical user interface, text, application, email Description automatically generated"
1586	croptop="910f" cropbottom="38375f"/>
1587	</v:shape><![endif]--><![if !vml]><img border=0 width=148 height=86
1588	src="CIFtutorial.fld/image006.png"
1589	alt="Graphical user interface, text, application, email Description automatically generated"
1590	v:shapes="Picture_x0020_14"><![endif]></span></p>
1591
1592	<p class=MsoNormal><o:p> </o:p></p>
1593
1594	<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
1595	8. Edit Phase Information including Distances and Angles. <o:p></o:p></span></h2>
1596
1597	<p class=MsoNormal>The phase template contains a relatively small number of
1598	items that can document information about a phase, as shown below. If one
1599	produced several projects all using the same sample, it might make sense to
1600	produce a template file that might be used for that sample in all projects. </p>
1601
1602	<p class=MsoNormal><o:p> </o:p></p>
1603
1604	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1605	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1606	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1607	</span></span></span><![endif]><span dir=LTR></span>Press the “Edit Template”
1608	button in the Phase section of the “Edit CIF settings” window and the window
1609	below appears. Enter any information desired. Press “Use” when done.<o:p></o:p></p>
1610
1611	<p class=MsoNormal><o:p> </o:p></p>
1612
1613	<p class=MsoNormal><o:p> </o:p></p>
1614
1615	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1616	id="Picture_x0020_26" o:spid="_x0000_i1029" type="#_x0000_t75" alt="Diagram 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 Description automatically generated with medium confidence"/>
1619	</v:shape><![endif]--><![if !vml]><img border=0 width=214 height=316
1620	src="CIFtutorial.fld/image008.png"
1621	alt="Diagram Description automatically generated with medium confidence"
1622	v:shapes="Picture_x0020_26"><![endif]></span></p>
1623
1624	<p class=MsoNormal><o:p> </o:p></p>
1625
1626	<p class=MsoNormal><o:p> </o:p></p>
1627
1628	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1629	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1630	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1631	</span></span></span><![endif]><span dir=LTR></span>Press the “Set
1632	distance/angle publication flag” and the window below appears. </p>
1633
1634	<p class=MsoNormal><o:p> </o:p></p>
1635
1636	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1637	id="Picture_x0020_16" o:spid="_x0000_i1028" type="#_x0000_t75" alt="Table Description automatically generated"
1638	style='width:257pt;height:325pt;visibility:visible;mso-wrap-style:square'>
1639	<v:imagedata src="CIFtutorial.fld/image018.png" o:title="Table Description automatically generated"/>
1640	</v:shape><![endif]--><![if !vml]><img border=0 width=257 height=325
1641	src="CIFtutorial.fld/image018.png"
1642	alt="Table Description automatically generated" v:shapes="Picture_x0020_16"><![endif]></span></p>
1643
1644	<p class=MsoNormal><o:p> </o:p></p>
1645
1646	<p class=MsoNormal>This shows the interatomic distances and angles that that
1647	occur within the radii specified above. Note that the Pb radius is too small to
1648	pick up the coordination of that atom, so we should change that:</p>
1649
1650	<p class=MsoNormal><o:p> </o:p></p>
1651
1652	<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1653	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1654	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1655	</span></span></span><![endif]><span dir=LTR></span>Press the “Done” button to
1656	close this window</p>
1657
1658	<p class=MsoListParagraphCxSpMiddle style='mso-list:l0 level1 lfo2'><![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"'>
1661	</span></span></span><![endif]><span dir=LTR></span>Press the “Edit
1662	distance/angle ranges” button to bring up the screen below. Change the bond
1663	search factor from 0.85 to 0.9 to increase the search range, as below.</p>
1664
1665	<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p> </o:p></p>
1666
1667	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1668	id="Picture_x0020_17" o:spid="_x0000_i1027" type="#_x0000_t75" alt="Graphical user interface, application Description automatically generated"
1669	style='width:150pt;height:137pt;visibility:visible;mso-wrap-style:square'>
1670	<v:imagedata src="CIFtutorial.fld/image019.png" o:title="Graphical user interface, application Description automatically generated"/>
1671	</v:shape><![endif]--><![if !vml]><img border=0 width=150 height=137
1672	src="CIFtutorial.fld/image019.png"
1673	alt="Graphical user interface, application Description automatically generated"
1674	v:shapes="Picture_x0020_17"><![endif]></span></p>
1675
1676	<p class=MsoNormal><o:p> </o:p></p>
1677
1678	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1679	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1680	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1681	</span></span></span><![endif]><span dir=LTR></span>Press the “Set
1682	distance/angle publication flag” and note the additional distances (but not
1683	angles) in the window below. </p>
1684
1685	<p class=MsoNormal><o:p> </o:p></p>
1686
1687	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1688	id="Picture_x0020_18" o:spid="_x0000_i1026" type="#_x0000_t75" alt="Table Description automatically generated"
1689	style='width:262pt;height:337pt;visibility:visible;mso-wrap-style:square'>
1690	<v:imagedata src="CIFtutorial.fld/image020.png" o:title="Table Description automatically generated"/>
1691	</v:shape><![endif]--><![if !vml]><img border=0 width=262 height=337
1692	src="CIFtutorial.fld/image020.png"
1693	alt="Table Description automatically generated" v:shapes="Picture_x0020_18"><![endif]></span></p>
1694
1695	<p class=MsoNormal><o:p> </o:p></p>
1696
1697	<p class=MsoNormal>Note that to obtain the angles around the Pb and O atoms,
1698	the values in the right-hand column and/or the angle search factor range must
1699	also be extended. </p>
1700
1701	<p class=MsoNormal><o:p> </o:p></p>
1702
1703	<p class=MsoNormal>Every bond and angle that is listed on the window will be
1704	placed in the CIF when written. Note that while distances and angles are shown
1705	in the window without uncertainties, if the atom positions have been varied,
1706	the values with their uncertainties will be placed in the CIF (in standard
1707	crystallographic notation). Also note that in the CIF each distance has an
1708	associated _<span class=SpellE>geom_bond_publ_flag</span> value (for angles, _<span
1709	class=SpellE>geom_angle_publ_flag</span>). The value for this can be
1710	“yes” or “no” and a “yes” value indicates that the value should be placed
1711	in a table of bond distances/angles, if generated from the CIF. By default,
1712	this flag defaults to “yes<span class=GramE>”</span> but this can be changed by
1713	clicking on the distance or angle button. </p>
1714
1715	<p class=MsoNormal><o:p> </o:p></p>
1716
1717	<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
1718	9. Create a Customized Template File. <o:p></o:p></span></h2>
1719
1720	<p class=MsoNormal><o:p> </o:p></p>
1721
1722	<p class=MsoNormal>For this particular project, since these were data
1723	distributed from a round-robin study many years ago, relatively little is
1724	documented on the instruments, but as a useful exercise, I recommend opening
1725	documenting an instrument that you use frequently (or twist the arm of the
1726	instrument scientist at your favorite facility to do so.)<span
1727	style='mso-spacerun:yes'> </span></p>
1728
1729	<p class=MsoNormal><o:p> </o:p></p>
1730
1731	<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1732	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1733	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1734	</span></span></span><![endif]><span dir=LTR></span>Press the “Edit Template”
1735	button for either histogram <span class=GramE>and</span> define as many of the
1736	appropriate fields as are appropriate. </p>
1737
1738	<p class=MsoNormal><o:p> </o:p></p>
1739
1740	<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1741	id="Picture_x0020_19" o:spid="_x0000_i1025" type="#_x0000_t75" alt="Graphical user interface Description automatically generated"
1742	style='width:233pt;height:243pt;visibility:visible;mso-wrap-style:square'>
1743	<v:imagedata src="CIFtutorial.fld/image021.png" o:title="Graphical user interface Description automatically generated"/>
1744	</v:shape><![endif]--><![if !vml]><img border=0 width=233 height=243
1745	src="CIFtutorial.fld/image021.png"
1746	alt="Graphical user interface Description automatically generated"
1747	v:shapes="Picture_x0020_19"><![endif]></span></p>
1748
1749	<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1750	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1751	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1752	</span></span></span><![endif]><span dir=LTR></span>Press the “Save as
1753	template” button and save the file with a name and location that will make this
1754	readily available for future use.</p>
1755
1756	<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p> </o:p></p>
1757
1758	<p class=MsoNormal>Note that the next time that “Export… project… to CIF” is
1759	used, this template can be used by pressing the “Select Template File” button
1760	for that histogram and by doing this all of the information specified
1761	previously can be used without additional data entry effort.<span
1762	style='mso-spacerun:yes'> </span></p>
1763
1764	<p class=MsoNormal><o:p> </o:p></p>
1765
1766	<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
1767	10. Create the CIF<o:p></o:p></span></h2>
1768
1769	<p class=MsoNormal><o:p> </o:p></p>
1770
1771	<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1772	style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1773	Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>
1774	</span></span></span><![endif]><span dir=LTR></span>Pressing the “Create CIF”
1775	button will cause the CIF to be written. </p>
1776
1777	<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p> </o:p></p>
1778
1779	<p class=MsoNormal>Depending on the number and size of histograms, this can be
1780	a fairly large file as it contains observed and computed patterns for each, as
1781	well as a reflection table, plus unit cell parameters, symmetry information,
1782	coordinates and bond distances and angles for each phase. </p>
1783
1784	<p class=MsoNormal><o:p> </o:p></p>
1785
1786	<p class=MsoNormal>Note that if the refinement information is changed, for
1787	example by introducing a new variable, changing the background model etc. all
1788	that need be done to create a CIF with updated information will be to select
1789	the “Entire project as” menu item and the “Full CIF” submenu option from the
1790	Export menu and then press the “Create CIF” button again. All information
1791	generated by GSAS-II will be updated and previously entered will be retained
1792	and placed in the new file. </p>
1793
1794	<p class=MsoNormal><o:p> </o:p></p>
1795
1796	</div>
1797
1798	</body>
1799
1800	</html>

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