Changeset 4624 for Tutorials/RigidBody


Ignore:
Timestamp:
Oct 26, 2020 9:40:05 PM (13 months ago)
Author:
toby
Message:

improve rigid body stuff; finish tutorial

Location:
Tutorials/RigidBody
Files:
6 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/RigidBody/RigidBodyRef.fld/filelist.xml

    r4574 r4624  
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  • Tutorials/RigidBody/RigidBodyRef.html

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     1328        mso-level-number-position:right;
     1329        text-indent:-9.0pt;}
     1330@list l3:level7
     1331        {mso-level-tab-stop:none;
     1332        mso-level-number-position:left;
     1333        text-indent:-.25in;}
     1334@list l3:level8
     1335        {mso-level-number-format:alpha-lower;
     1336        mso-level-tab-stop:none;
     1337        mso-level-number-position:left;
     1338        text-indent:-.25in;}
     1339@list l3:level9
     1340        {mso-level-number-format:roman-lower;
     1341        mso-level-tab-stop:none;
     1342        mso-level-number-position:right;
     1343        text-indent:-9.0pt;}
     1344@list l4
     1345        {mso-list-id:795608589;
     1346        mso-list-type:hybrid;
     1347        mso-list-template-ids:1385991440 67698711 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
     1348@list l4:level1
     1349        {mso-level-number-format:alpha-lower;
     1350        mso-level-text:"%1\)";
     1351        mso-level-tab-stop:none;
     1352        mso-level-number-position:left;
     1353        text-indent:-.25in;}
     1354@list l4:level2
     1355        {mso-level-number-format:alpha-lower;
     1356        mso-level-tab-stop:none;
     1357        mso-level-number-position:left;
     1358        text-indent:-.25in;}
     1359@list l4:level3
     1360        {mso-level-number-format:roman-lower;
     1361        mso-level-tab-stop:none;
     1362        mso-level-number-position:right;
     1363        text-indent:-9.0pt;}
     1364@list l4:level4
     1365        {mso-level-tab-stop:none;
     1366        mso-level-number-position:left;
     1367        text-indent:-.25in;}
     1368@list l4:level5
     1369        {mso-level-number-format:alpha-lower;
     1370        mso-level-tab-stop:none;
     1371        mso-level-number-position:left;
     1372        text-indent:-.25in;}
     1373@list l4:level6
     1374        {mso-level-number-format:roman-lower;
     1375        mso-level-tab-stop:none;
     1376        mso-level-number-position:right;
     1377        text-indent:-9.0pt;}
     1378@list l4:level7
     1379        {mso-level-tab-stop:none;
     1380        mso-level-number-position:left;
     1381        text-indent:-.25in;}
     1382@list l4:level8
     1383        {mso-level-number-format:alpha-lower;
     1384        mso-level-tab-stop:none;
     1385        mso-level-number-position:left;
     1386        text-indent:-.25in;}
     1387@list l4:level9
     1388        {mso-level-number-format:roman-lower;
     1389        mso-level-tab-stop:none;
     1390        mso-level-number-position:right;
     1391        text-indent:-9.0pt;}
     1392@list l5
     1393        {mso-list-id:1304966373;
     1394        mso-list-type:hybrid;
     1395        mso-list-template-ids:131908204 67698689 67698691 67698693 67698689 67698691 67698693 67698689 67698691 67698693;}
     1396@list l5:level1
     1397        {mso-level-number-format:bullet;
     1398        mso-level-text:;
     1399        mso-level-tab-stop:none;
     1400        mso-level-number-position:left;
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     1402        text-indent:-.25in;
     1403        font-family:Symbol;}
     1404@list l5:level2
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     1406        mso-level-text:o;
     1407        mso-level-tab-stop:none;
     1408        mso-level-number-position:left;
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     1411        font-family:"Courier New";}
     1412@list l5:level3
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     1414        mso-level-text:;
     1415        mso-level-tab-stop:none;
     1416        mso-level-number-position:left;
     1417        margin-left:2.0in;
     1418        text-indent:-.25in;
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     1431        mso-level-tab-stop:none;
     1432        mso-level-number-position:left;
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     1436@list l5:level6
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     1438        mso-level-text:;
     1439        mso-level-tab-stop:none;
     1440        mso-level-number-position:left;
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     1446        mso-level-text:;
     1447        mso-level-tab-stop:none;
     1448        mso-level-number-position:left;
     1449        margin-left:4.0in;
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     1452@list l5:level8
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     1454        mso-level-text:o;
     1455        mso-level-tab-stop:none;
     1456        mso-level-number-position:left;
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     1460@list l5:level9
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     1462        mso-level-text:;
     1463        mso-level-tab-stop:none;
     1464        mso-level-number-position:left;
     1465        margin-left:5.0in;
     1466        text-indent:-.25in;
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     1468@list l6
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     1471@list l6:level1
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     1488@list l6:level3
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     1498        mso-level-text:;
     1499        mso-level-tab-stop:2.0in;
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     1527        font-family:Wingdings;}
     1528@list l6:level8
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     1530        mso-level-text:;
     1531        mso-level-tab-stop:4.0in;
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     1536@list l6:level9
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     1544@list l7
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     1548@list l7:level1
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     1550        mso-level-number-position:left;
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     1552        mso-ansi-language:EN-US;}
     1553@list l7:level2
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     1555        mso-level-tab-stop:none;
     1556        mso-level-number-position:left;
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     1558@list l7:level3
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     1560        mso-level-tab-stop:none;
     1561        mso-level-number-position:right;
     1562        text-indent:-9.0pt;}
     1563@list l7:level4
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     1565        mso-level-number-position:left;
     1566        text-indent:-.25in;}
     1567@list l7:level5
     1568        {mso-level-number-format:alpha-lower;
     1569        mso-level-tab-stop:none;
     1570        mso-level-number-position:left;
     1571        text-indent:-.25in;}
     1572@list l7:level6
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     1574        mso-level-tab-stop:none;
     1575        mso-level-number-position:right;
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     1577@list l7:level7
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     1579        mso-level-number-position:left;
     1580        text-indent:-.25in;}
     1581@list l7:level8
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     1583        mso-level-tab-stop:none;
     1584        mso-level-number-position:left;
     1585        text-indent:-.25in;}
     1586@list l7:level9
     1587        {mso-level-number-format:roman-lower;
     1588        mso-level-tab-stop:none;
     1589        mso-level-number-position:right;
     1590        text-indent:-9.0pt;}
     1591@list l8
     1592        {mso-list-id:2145268393;
     1593        mso-list-type:hybrid;
     1594        mso-list-template-ids:-1754648594 758274268 67698691 67698693 67698689 67698691 67698693 67698689 67698691 67698693;}
     1595@list l8:level1
     1596        {mso-level-start-at:0;
     1597        mso-level-number-format:bullet;
     1598        mso-level-text:;
     1599        mso-level-tab-stop:none;
     1600        mso-level-number-position:left;
     1601        margin-left:.75in;
     1602        text-indent:-.25in;
     1603        font-family:Symbol;
     1604        mso-fareast-font-family:Calibri;
     1605        mso-fareast-theme-font:minor-latin;
     1606        mso-bidi-font-family:"Times New Roman";
     1607        mso-bidi-theme-font:minor-bidi;}
     1608@list l8:level2
     1609        {mso-level-number-format:bullet;
     1610        mso-level-text:o;
     1611        mso-level-tab-stop:none;
     1612        mso-level-number-position:left;
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     1615@list l8:level3
     1616        {mso-level-number-format:bullet;
     1617        mso-level-text:;
     1618        mso-level-tab-stop:none;
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     1622@list l8:level4
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     1625        mso-level-tab-stop:none;
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     1629@list l8:level5
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     1633        mso-level-number-position:left;
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     1636@list l8:level6
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     1639        mso-level-tab-stop:none;
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     1643@list l8:level7
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     1646        mso-level-tab-stop:none;
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     1650@list l8:level8
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     1657@list l8:level9
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    12331687        mso-ascii-theme-font:minor-latin;
    12341688        mso-hansi-font-family:Calibri;
    1235         mso-hansi-theme-font:minor-latin;
    1236         mso-bidi-font-family:"Times New Roman";
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     1689        mso-hansi-theme-font:minor-latin;}
    12381690</style>
    12391691<![endif]--><!--[if gte mso 9]><xml>
     
    12531705<u1:p></u1:p>
    12541706
    1255 <UL>
    1256   <LI><span style='mso-bidi-font-size:14.0pt'>Note: Exercise files are
    1257 found <a href="./data" target="_blank">here</a></span></LI>
    1258 </UL>
    1259 
    1260 <p class=MsoNormal><b><o:p>&nbsp;</o:p></b></p>
    1261 
    1262 <h2 align=left style='text-align:left;direction:ltr;unicode-bidi:embed'>Introduction</h2>
    1263 
    1264 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1265 
    1266 <p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>It is common that
    1267 powder diffraction does not provide enough observations to allow refinement of
    1268 all atoms independently. This is not only a problem for powder diffraction; it
    1269 is usually the case in protein refinement as well, as few datasets can be
    1270 collected to atomic resolution. When the number of parameters is not sufficient
    1271 to discern individual atomic positions, it is necessary to simplify the
    1272 crystallographic model to require fewer parameters through use of constraints
    1273 or to apply restraints, which effectively allow assumptions about the model to
     1707<p class=MsoNormal><span style='font-size:12.0pt;mso-bidi-font-size:14.0pt;
     1708font-family:"Times New Roman",serif'>Note: Exercise files are found <a
     1709href="data" target="_blank">here</a></span><span style='font-size:12.0pt;
     1710font-family:"Times New Roman",serif'><o:p></o:p></span></p>
     1711
     1712<h2>Introduction</h2>
     1713
     1714<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>It is a common situation
     1715that a powder diffraction dataset will not provide enough observations to allow
     1716refinement of all atoms independently. This is not only a problem for powder
     1717diffraction; it is usually the case in single-crystal protein refinement as
     1718well, as few datasets for that can be collected to atomic resolution. When the
     1719number of parameters is not sufficient to discern individual atomic positions,
     1720it is necessary to simplify the crystallographic model to require fewer
     1721parameters through use of constraints. A common constraint is to group <span
     1722class=SpellE>U<sub>iso</sub></span> values so that a single value is used for
     1723all atoms of a particular type or in a common bonding environment. Also common
     1724is to apply restraints, which effectively allows assumptions about the model to
    12741725be used as if they were experimental observations. Examples of restraints
    12751726include providing target values for bond distances and angles, or penalizing a
    1276 refinement if atoms diverge from a plane. A common constraint is to group <span
    1277 class=SpellE>Uiso</span> values so that a single value is used for all atoms of
    1278 a particular type or in a common bonding environment. <o:p></o:p></span></p>
     1727refinement if atoms diverge from a plane. <o:p></o:p></span></p>
    12791728
    12801729<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     
    12831732powerful types of constraints in GSAS-II is to constrain a group of atoms so
    12841733that their relative positions are fixed. Such a group of atoms is known as a
    1285 rigid body. The core concept in a rigid body refinement is that (at most) 3
    1286 position parameters and 3 orientation parameters are needed to locate a simple
    1287 rigid body. Sometimes symmetry can reduce the number of refinable parameters.
    1288 In contrast, 3 position parameters are needed for every atom in a structure on
    1289 a general position. Thus, a four-atom group requires 12 positional parameters
    1290 and a 6-atom group requires 18 positional parameters, if modeled with
    1291 individual atoms, but as rigid-bodies &lt;=6 parameters will be needed. <o:p></o:p></span></p>
     1734rigid body. The core concept in a rigid body refinement is that 3 parameters for
     1735an origin and 3 orientation parameters are needed to locate a rigid body,
     1736though in some cases symmetry can reduce the number of refinable parameters
     1737below 6. In contrast, 3 position parameters are needed for every atom in a
     1738structure on a general position. Thus, a four-atom group requires 12 positional
     1739parameters and a 6-atom group requires 18 positional parameters, when modeled
     1740with individual atoms, but as rigid-bodies only 6 parameters will be needed.
     1741Also, a more chemically reasonable result will be obtained. <o:p></o:p></span></p>
    12921742
    12931743<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     
    12951745<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>GSAS-II offers two
    12961746types of rigid bodies. This tutorial will demonstrate use of one type, residue
    1297 rigid bodies, which allow incorporation of optional torsional parameters, while
    1298 the second type, vector rigid bodies, offer one or more refinable size parameters,
    1299 which can allow for refinement of selected bond distances or geometrical
    1300 factors. <o:p></o:p></span></p>
     1747rigid bodies, which allow incorporation of optional torsional parameters. The second
     1748type, vector rigid bodies, offer one or more refinable size parameters, which
     1749can allow for refinement of selected bond distances or geometrical factors, but
     1750this is less commonly needed compared to torsions. <o:p></o:p></span></p>
    13011751
    13021752<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    13031753
    13041754<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>In the supplied
    1305 example GSAS-II project file, a set of diffraction data is supplied for a
    1306 crystal with two copies of the chiral <a
     1755example GSAS-II project file, a powder diffraction dataset is supplied for a sample
     1756where there are two independent copies of the chiral <a
    13071757href="https://pubchem.ncbi.nlm.nih.gov/compound/676113">R-(+)-Carbidopa
    1308 molecule</a> (shown below) and two water molecules in the asymmetric unit. <o:p></o:p></span></p>
    1309 
    1310 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1311 embed'><a href="https://pubchem.ncbi.nlm.nih.gov/compound/676113"><span
    1312 dir=LTR style='mso-bidi-font-size:14.0pt;color:windowtext;mso-no-proof:yes;
    1313 text-decoration:none;text-underline:none'><!--[if gte vml 1]><v:shapetype id="_x0000_t75"
    1314  coordsize="21600,21600" o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe"
    1315  filled="f" stroked="f">
     1758molecule</a> (shown below) as well as two water molecules in the asymmetric
     1759unit. <o:p></o:p></span></p>
     1760
     1761<p class=MsoNormal align=right style='text-align:right'><a
     1762href="https://pubchem.ncbi.nlm.nih.gov/compound/676113"><span style='color:
     1763windowtext;mso-no-proof:yes;text-decoration:none;text-underline:none'><!--[if gte vml 1]><v:shapetype
     1764 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
     1765 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
    13161766 <v:stroke joinstyle="miter"/>
    13171767 <v:formulas>
     
    13311781 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    13321782 <o:lock v:ext="edit" aspectratio="t"/>
    1333 </v:shapetype><v:shape id="Picture_x0020_6" o:spid="_x0000_i1064" type="#_x0000_t75"
     1783</v:shapetype><v:shape id="Picture_x0020_6" o:spid="_x0000_i1067" type="#_x0000_t75"
    13341784 href="https://pubchem.ncbi.nlm.nih.gov/compound/676113" style='width:174pt;
    13351785 height:215pt;visibility:visible;mso-wrap-style:square' o:button="t">
     
    13371787 <v:imagedata src="RigidBodyRef.fld/image001.png" o:title=""/>
    13381788</v:shape><![endif]--><![if !vml]><span style='mso-ignore:vglayout'><img
    1339 border=0 width=174 height=215 src="RigidBodyRef.fld/image001.png" v:shapes="Picture_x0020_6"></span><![endif]></span></a><span
    1340 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    1341 
    1342 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1343 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>
    1344 Since the phenyl ring defines a plane for the 6 atoms in the ring, as well as the 3 atoms directly bonded to the ring, and
    1345 since bond distances and angles are well known, the relative
    1346 positions of these atoms are fixed. The positions for the
    1347 remaining non-H atom can be determined with only 4 additional
    1348 parameters, because rotation is possible around the four bonds
    1349 circled below. </span><span lang=HE style='mso-bidi-font-size:14.0pt;
     1789border=0 width=174 height=215 src="RigidBodyRef.fld/image001.png" v:shapes="Picture_x0020_6"></span><![endif]></span></a></p>
     1790
     1791<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Since chemical
     1792knowledge dictates that the 6 atoms in the phenyl ring, as well as the 6 atoms
     1793bonded to them, will lie in a plane, and since bond distances and angles are
     1794well known for those atoms, there is no reason to give these atoms any degrees
     1795of freedom in the model used to fit the diffraction data, beyond the orientation
     1796and position of the group. The positions for the remaining non-H atom can be
     1797determined with only 4 additional parameters, noting that rotation is possible
     1798around the four bonds circled below. <o:p></o:p></span></p>
     1799
     1800<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     180114.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_7"
     1802 o:spid="_x0000_i1066" type="#_x0000_t75" style='width:170pt;height:210pt;
     1803 visibility:visible;mso-wrap-style:square'>
     1804 <v:imagedata src="RigidBodyRef.fld/image002.png" o:title=""/>
     1805</v:shape><![endif]--><![if !vml]><img border=0 width=170 height=210
     1806src="RigidBodyRef.fld/image002.png" v:shapes="Picture_x0020_7"><![endif]></span><span
     1807lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1808mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1809Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1810
     1811<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Thus, all 16
     1812non-hydrogen atoms can be positioned with 10 parameters: 3 coordinates, 3
     1813orientation parameters and 4 torsions. Compare this to the 48 positional
     1814parameters needed for 16 unconstrained atoms. If we had neutron data that would
     1815allow location of hydrogen atoms, adding 5 more torsions would allow for the
     1816hydrogen atoms to be positioned as well, where a total of 30 atoms would be
     1817located from 15 parameters.</span><span lang=HE dir=RTL style='mso-bidi-font-size:
     181814.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
     1819mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
     1820minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1821
     1822<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     1823font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     1824minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     1825mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     1826
     1827<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>In this example, the
     1828fit in the supplied GSAS-II project file appears quite good with respect to the
     1829agreement to the observed data, but closer examination shows that the bond
     1830distances and angles of the two molecular groups are quite irregular. Since
     1831this distorted structure is not physically reasonable, this model is not acceptable.
     1832This well-fitting but poor-quality model arises because too many parameters
     1833were introduced, which is sometimes called overfitting. In this tutorial, a
     1834better model will be developed using rigid bodies for the two molecules,
     1835providing a more chemically reasonable representation with fewer parameters -- simply
     1836a better fit. </span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    13501837font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    13511838minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    13521839mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    13531840
    1354 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1355 embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1356  id="Picture_x0020_7" o:spid="_x0000_i1063" type="#_x0000_t75" style='width:170pt;
    1357  height:210pt;visibility:visible;mso-wrap-style:square'>
    1358  <v:imagedata src="RigidBodyRef.fld/image002.png" o:title=""/>
    1359 </v:shape><![endif]--><![if !vml]><img border=0 width=170 height=210
    1360 src="RigidBodyRef.fld/image002.png" v:shapes="Picture_x0020_7"><![endif]></span><span
    1361 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    1362 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    1363 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    1364 
    1365 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1366 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Thus, all
    1367 16 non-hydrogen atoms can be positioned with 3 coordinates, 3 orientation
    1368 parameters and 4 torsions. Compare these 10 parameters to the 48 positional
    1369 parameters for 16 unconstrained atoms. (Adding 5 more torsions would allow for
    1370 the hydrogen atoms to be positioned as well, for a total of 30 atoms from 15
    1371 parameters.) </span><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1372 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     1841<h2>Step 1. Export Cartesian coordinates for R<span class=GramE>-(</span>+)-Carbidopa
     1842from a crystal structure<span lang=HE dir=RTL style='font-size:13.0pt;
     1843mso-ansi-font-size:16.0pt'><o:p></o:p></span></h2>
     1844
     1845<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>There are two steps
     1846to working with rigid bodies in GSAS-II. The first is to obtain an accurate set
     1847of coordinates for the molecule, molecular fragment, or ionic moiety, which can
     1848be done in a number of ways. One way is to locate an accurate crystal structure
     1849from a database or paper. A second method is to use a computational tool to
     1850determine an approximate structure regularized for reasonable bond lengths.
     1851This can be done with low-accuracy forcefield computations or varying levels of
     1852improved theory. A good tool for simple forcefield minimization is the free
     1853cross-platform <a href="https://avogadro.cc/">Avogadro program</a>. <o:p></o:p></span></p>
     1854
     1855<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     1856
     1857<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Note that we could
     1858generate the R-(+)-Carbidopa fairly simply from inside Avogadro by drawing the
     1859molecule (process <a href="https://avogadro.cc/docs/tools/draw-tool">described
     1860here</a>), or even quicker, since the <a
     1861href="https://pubchem.ncbi.nlm.nih.gov/compound/676113">PubChem entry</a> lists
     1862<a
     1863href="https://pubchem.ncbi.nlm.nih.gov/compound/676113#section=Canonical-SMILES">a
     1864SMILES description</a> of the atomic bonding [C[C@@](CC1=CC(=C(C=C1)O)O)(C(=O)O)NN],
     1865that description could also be used using the Avogadro Build/Insert/SMILES…
     1866menu command, but in this step we will use a more general method to input a
     1867molecular fragment to Avogadro, so that it can be regularized. <o:p></o:p></span></p>
     1868
     1869<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     1870
     1871<p class=MsoNormal><span class=MsoIntenseReference>1A)</span> <i><span
     1872style='mso-bidi-font-size:14.0pt'>For this tutorial, we will export coordinates
     1873from GSAS-II in a form to be read Avogadro. They will be regularized in the
     1874next step. </span></i><i><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     1875font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    13731876minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1374 mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    1375 
    1376 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1377 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1378 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    1379 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1380 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    1381 
    1382 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1383 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>In this
    1384 example, the fit in the supplied GSAS-II project file appears quite good with
    1385 respect to the agreement to the observed data, but closer examination shows
    1386 that the bond distances and angles of the two molecular groups are quite
    1387 irregular. Since this distorted structure is not physically reasonable, this
    1388 model is far from optimal. This well-fitting but <span class=GramE>poor quality</span>
    1389 model arises because too many parameters were introduced,
    1390 which is sometimes called
    1391 overfitting. In this tutorial, a better model will be developed using rigid
    1392 bodies for the two molecules, providing a more chemically reasonable
    1393 representation with fewer parameters -- and a better fit.
    1394 <o:p></o:p></span></p>
    1395 
    1396 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1397 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1398 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    1399 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1400 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    1401 
    1402 <h2 dir=RTL><span dir=LTR>Step 1. Export Cartesian coordinates for R<span
    1403 class=GramE>-(</span>+)-Carbidopa from crystal structure</span></h2>
    1404 
    1405 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1406 embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    1407 
    1408 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1409 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>There are
    1410 two steps to working with rigid bodies in GSAS-II. The first is to obtain an
    1411 accurate set of coordinates for the molecule, molecular fragment, or ionic
    1412 moiety, which can be done in a number of ways. One way is to locate an accurate
    1413 crystal structure from a database or paper. A second method is to use a
    1414 computational tool to determine an approximate structure regularized for
    1415 reasonable bond lengths. This can be done with low-accuracy forcefield
    1416 computations or varying levels of theory. A good tool for force field
    1417 minimization is the free cross-platform <a href="https://avogadro.cc/">Avogadro
    1418 program</a>. The R-(+)-Carbidopa can be generated inside Avogadro by drawing
    1419 the molecule (<a href="https://avogadro.cc/docs/tools/draw-tool">described here</a>),
    1420 or since the <a href="https://pubchem.ncbi.nlm.nih.gov/compound/676113">PubChem
    1421 entry</a> lists <a
    1422 href="https://pubchem.ncbi.nlm.nih.gov/compound/676113#section=Canonical-SMILES">a
    1423 SMILES description</a> of the atomic bonding
    1424 [C[C@@](CC1=CC(=C(C=C1)O)O)(C(=O)O)NN], this can also be used using the
    1425 Build/Insert/SMILES… menu command in that program, but in the next step we will
    1426 use a more general method to regularize a structure. <o:p></o:p></span></p>
    1427 
    1428 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1429 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    1430 
    1431 <h3 dir=RTL><span dir=LTR>1A) </span></h3>
    1432 
    1433 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1434 unicode-bidi:embed'><i><span dir=LTR style='mso-bidi-font-size:14.0pt'>For this
    1435 tutorial, we will export the coordinates from GSAS-II into a form to be read Avogadro.
    1436 They will be regularized in the next step. <o:p></o:p></span></i></p>
    1437 
    1438 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1439 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    1440 
    1441 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1442 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Begin by <u>starting
     1877mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></i></p>
     1878
     1879<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     1880
     1881<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Begin by <u>starting
    14431882GSAS-II</u>. Any .<span class=SpellE>gpx</span> file (GSAS-II project) may be
    1444 used. If a new project is used, select the <u>Data<span class=GramE>/“</span>Add
     1883used. If a new, empty, project is used, select the <u>Data<span class=GramE>/“</span>Add
    14451884new phase”</u> menu item first. Select the <u>Rigid Bodies tab</u> in the data
    14461885tree. <o:p></o:p></span></p>
    14471886
    1448 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1449 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1450 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    1451 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1452 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    1453 
    1454 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>1B)</span></h3>
    1455 
    1456 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1457 unicode-bidi:embed'><span dir=LTR>Use the </span><u><span dir=LTR
     1887<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     1888
     1889<p class=MsoNormal><span class=MsoIntenseReference>1B)</span> Use the <u><span
    14581890style='mso-bidi-font-size:14.0pt'>“Edit Vector Body”<span class=GramE>/“</span>Extract
    1459 from file”</span></u><span dir=LTR style='mso-bidi-font-size:14.0pt'> menu item
    1460 select the GSAS-II <span class=SpellE>gpx</span> format a</span><span dir=LTR
     1891from file”</span></u><span style='mso-bidi-font-size:14.0pt'> menu item select
     1892the GSAS-II <span class=SpellE>gpx</span> format a</span><span
    14611893style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    14621894minor-latin'>nd <u>read in the distort1.gpx</u> file included </span><span
    1463 dir=LTR style='mso-bidi-font-size:14.0pt'>in the sample input. This will read
    1464 in the coordinates for 34 atoms (two carbidopa molecules and two O atoms), from
    1465 this we want to select only one carbidopa molecule. <o:p></o:p></span></p>
    1466 
    1467 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1468 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1469 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_1"
    1470  o:spid="_x0000_i1062" type="#_x0000_t75" style='width:380pt;height:245pt;
    1471  visibility:visible;mso-wrap-style:square'>
     1895style='mso-bidi-font-size:14.0pt'>in the sample input. This will read in the
     1896coordinates for 34 atoms (two carbidopa molecules and two O atoms), from this
     1897we want to select only one carbidopa molecule. </span><span lang=HE dir=RTL
     1898style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1899mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1900Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1901
     1902<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     1903style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     1904HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_1" o:spid="_x0000_i1065"
     1905 type="#_x0000_t75" style='width:380pt;height:245pt;visibility:visible;
     1906 mso-wrap-style:square'>
    14721907 <v:imagedata src="RigidBodyRef.fld/image003.png" o:title=""/>
    14731908</v:shape><![endif]--><![if !vml]><img border=0 width=380 height=245
    14741909src="RigidBodyRef.fld/image003.png" v:shapes="Picture_x0020_1"><![endif]></span><span
    1475 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    1476 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    1477 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    1478 
    1479 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1480 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1481 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     1910style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     1911
     1912<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     1913font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    14821914minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    14831915mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    14841916
    1485 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>1C)</span><span
    1486 class=MsoIntenseEmphasis><span dir=LTR style='font-size:16.0pt;mso-bidi-font-size:
    1487 15.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> <o:p></o:p></span></span></h3>
    1488 
    1489 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1490 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Unselect
     1917<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     1918dir=LTR></span>1C)</span><span class=MsoIntenseEmphasis><span style='font-size:
     191916.0pt;mso-bidi-font-size:12.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1920minor-latin'> </span></span><span style='mso-bidi-font-size:14.0pt'>Unselect
    14911921all atoms by pressing the <u>Toggle All</u> button and then <u>select the first
    14921922sixteen atoms</u> using the “Set Range” button and selecting the first [“0) C”]
    1493 and the sixteenth atom [“15) O3”]. Note that the selected atoms appear
    1494 differently from unselected atoms in the plot of the structure. <o:p></o:p></span></p>
    1495 
    1496 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1497 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1498 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_3"
    1499  o:spid="_x0000_i1061" type="#_x0000_t75" style='width:383pt;height:246pt;
    1500  visibility:visible;mso-wrap-style:square'>
     1923and the sixteenth atom [“15) O3”]. Note that in the plot of the structure, unselected
     1924atoms appear partially “greyed out” compared to selected atoms. <o:p></o:p></span></p>
     1925
     1926<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     1927style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     1928HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_3" o:spid="_x0000_i1064"
     1929 type="#_x0000_t75" style='width:383pt;height:246pt;visibility:visible;
     1930 mso-wrap-style:square'>
    15011931 <v:imagedata src="RigidBodyRef.fld/image004.png" o:title=""/>
    15021932</v:shape><![endif]--><![if !vml]><img border=0 width=383 height=246
    15031933src="RigidBodyRef.fld/image004.png" v:shapes="Picture_x0020_3"><![endif]></span><span
    1504 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1934style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     1935
     1936<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Once the 16 atoms
     1937are selected, <u>press “Continue”</u>. The rigid body then appears in the plot
     1938window. Note how distorted the molecule appears.</span><span lang=HE dir=RTL
     1939style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    15051940mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    15061941Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    15071942
    1508 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1509 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Then <u>press
    1510 “Continue”</u>. The rigid body then appears in the plot window. Note how
    1511 distorted the molecule appears.</span><span lang=HE style='mso-bidi-font-size:
    1512 14.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    1513 mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
    1514 minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    1515 
    1516 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1517 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1518 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4"
    1519  o:spid="_x0000_i1060" type="#_x0000_t75" style='width:221pt;height:127pt;
    1520  visibility:visible;mso-wrap-style:square'>
     1943<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     1944style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     1945HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4" o:spid="_x0000_i1063"
     1946 type="#_x0000_t75" style='width:221pt;height:127pt;visibility:visible;
     1947 mso-wrap-style:square'>
    15211948 <v:imagedata src="RigidBodyRef.fld/image005.png" o:title=""/>
    15221949</v:shape><![endif]--><![if !vml]><img border=0 width=221 height=127
    15231950src="RigidBodyRef.fld/image005.png" v:shapes="Picture_x0020_4"><![endif]></span><span
    1524 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1951lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    15251952mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    15261953Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    15271954
    1528 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1529 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    1530 
    1531 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1532 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1533 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     1955<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     1956font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    15341957minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    15351958mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    15361959
    1537 <h3 dir=RTL><span dir=LTR></span><span class=MsoIntenseEmphasis><span dir=LTR
    1538 style='font-size:16.0pt;mso-bidi-font-size:15.0pt;mso-bidi-font-family:Calibri;
    1539 mso-bidi-theme-font:minor-latin;font-style:normal'><span dir=LTR></span>1D)</span></span><span
    1540 dir=LTR style='font-size:14.0pt;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
    1541 minor-latin;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
    1542 color:black;mso-style-textfill-fill-color:black;mso-style-textfill-fill-alpha:
    1543 100.0%;font-weight:normal'><span style='color:black;mso-style-textfill-fill-color:
    1544 black;mso-style-textfill-fill-alpha:100.0%'> </span></span><span dir=LTR
    1545 style='font-size:14.0pt;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
    1546 minor-latin;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
    1547 color:black;mso-style-textfill-fill-color:black;mso-style-textfill-fill-alpha:
    1548 100.0%;font-weight:normal'><o:p></o:p></span></h3>
    1549 
    1550 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1551 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Export the
    1552 coordinates by pressing the <u>“export as <span class=SpellE>xyz</span>”</u>
    1553 button on the GSAS-II window.<o:p></o:p></span></p>
    1554 
    1555 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1556 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1557 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5"
    1558  o:spid="_x0000_i1059" type="#_x0000_t75" style='width:351pt;height:225pt;
    1559  visibility:visible;mso-wrap-style:square'>
     1960<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     1961
     1962<p class=MsoNormal><span class=MsoIntenseReference>1D)</span><b><span
     1963style='mso-bidi-font-size:14.0pt;color:black'> </span></b><span
     1964style='mso-bidi-font-size:14.0pt'>If these coordinates were satisfactory, the
     1965rigid body could be created at this point, but since these coordinates are
     1966distorted, we will regularize them in Avogadro first. Export the coordinates by
     1967pressing the <u>“export as <span class=SpellE>xyz</span>”</u> button on the
     1968GSAS-II window.<o:p></o:p></span></p>
     1969
     1970<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     1971style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     1972HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5" o:spid="_x0000_i1062"
     1973 type="#_x0000_t75" style='width:352pt;height:225pt;visibility:visible;
     1974 mso-wrap-style:square'>
    15601975 <v:imagedata src="RigidBodyRef.fld/image006.png" o:title=""/>
    1561 </v:shape><![endif]--><![if !vml]><img border=0 width=351 height=225
     1976</v:shape><![endif]--><![if !vml]><img border=0 width=352 height=225
    15621977src="RigidBodyRef.fld/image006.png" v:shapes="Picture_x0020_5"><![endif]></span><span
    1563 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1978style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     1979
     1980<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Make a note of the
     1981file name, as it will be needed in the next step. Press <u>Cancel</u> to close
     1982this window. It is fine to close GSAS-II, but it can also remain open. </span><span
     1983lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    15641984mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    15651985Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    15661986
    1567 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1568 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Make a note
    1569 of the file name, as it will be needed in the next step. If these coordinates
    1570 were satisfactory, the rigid body could be created at this point, but since
    1571 these coordinates are distorted, we will regularize them first. Press <u>Cancel</u>
    1572 to close this window. It is fine to close GSAS-II, but it can remain open. </span><span
    1573 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1987<h2>Step 2: Regularize coordinates in Avogadro<span lang=HE dir=RTL
     1988style='font-size:13.0pt;mso-ansi-font-size:16.0pt'><o:p></o:p></span></h2>
     1989
     1990<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt'>For this step, it
     1991is assumed that the cross-platform software <a href="https://avogadro.cc/">Avogadro
     1992program</a> has been installed. If you do not want to install this program,
     1993this step can be skipped, as described at the <a href="#step3">beginning of Step
     19943</a>.</span></i><span style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     1995
     1996<p class=MsoNormal><b><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></b></p>
     1997
     1998<p class=MsoNormal><span class=MsoIntenseReference>2A)</span> <span
     1999style='mso-bidi-font-size:14.0pt'>Read the coordinates into Avogadro by
     2000starting the program and using the <u>Avogadro File/Open command</u>; select
     2001the <u>XYZ file type</u> option and <u>read</u> the file produced in step 1D.</span><span
     2002lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    15742003mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    15752004Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    15762005
    1577 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1578 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1579 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    1580 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1581 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    1582 
    1583 <h2 dir=RTL><span dir=LTR>Step 2: Regularize coordinates in Avogadro</span></h2>
    1584 
    1585 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1586 unicode-bidi:embed'><b><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></b></p>
    1587 
    1588 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1589 unicode-bidi:embed'><i><span dir=LTR style='mso-bidi-font-size:14.0pt'>For this
    1590 step, it is assumed that the cross-platform software <a
    1591 href="https://avogadro.cc/">Avogadro program</a> has been installed. If you do
    1592 not want to install this program, this step can be skipped.<span
    1593 style='mso-spacerun:yes'>  </span></span></i><span dir=LTR style='mso-bidi-font-size:
    1594 14.0pt'><o:p></o:p></span></p>
    1595 
    1596 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1597 unicode-bidi:embed'><b><span lang=HE style='mso-bidi-font-size:14.0pt;
    1598 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    1599 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1600 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></b></p>
    1601 
    1602 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>2A) </span></h3>
    1603 
    1604 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1605 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Read the
    1606 coordinates into Avogadro by starting the program and using the <u>Avogadro
    1607 File/Open command</u>; select the <u>XYZ file type</u> option and <u>read</u>
    1608 the file produced in step 1D.<o:p></o:p></span></p>
    1609 
    1610 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1611 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1612 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_8"
    1613  o:spid="_x0000_i1058" type="#_x0000_t75" style='width:391pt;height:383pt;
    1614  visibility:visible;mso-wrap-style:square'>
     2006<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2007style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     2008HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_8" o:spid="_x0000_i1061"
     2009 type="#_x0000_t75" style='width:391pt;height:383pt;visibility:visible;
     2010 mso-wrap-style:square'>
    16152011 <v:imagedata src="RigidBodyRef.fld/image007.png" o:title=""/>
    16162012</v:shape><![endif]--><![if !vml]><img border=0 width=391 height=383
    16172013src="RigidBodyRef.fld/image007.png" v:shapes="Picture_x0020_8"><![endif]></span><span
    1618 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    1619 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    1620 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    1621 
    1622 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1623 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1624 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2014style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2015
     2016<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2017font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    16252018minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    16262019mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    16272020
    1628 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1629 unicode-bidi:embed'><span dir=LTR></span><span class=Heading3Char><span
    1630 dir=LTR style='font-size:15.0pt;font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1631 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'><span
    1632 dir=LTR></span>2B) <o:p></o:p></span></span></p>
    1633 
    1634 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1635 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Note that
     2021<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2022dir=LTR></span>2B)</span><span class=Heading3Char><span style='font-size:15.0pt;
     2023font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2024minor-latin'> </span></span><span style='mso-bidi-font-size:14.0pt'>Note that
    16362025the program noted the correct bonding of the carboxylic acid group, where one
    16372026of the C-O bonds is noted as a double bond, but the phenyl group does not have
     
    16412030symbol</u> to bring up the “Ball and Sticks Settings” dialog, below.<o:p></o:p></span></p>
    16422031
    1643 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1644 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1645 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_9"
    1646  o:spid="_x0000_i1057" type="#_x0000_t75" style='width:281pt;height:193pt;
    1647  visibility:visible;mso-wrap-style:square'>
     2032<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2033style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     2034HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_9" o:spid="_x0000_i1060"
     2035 type="#_x0000_t75" style='width:281pt;height:193pt;visibility:visible;
     2036 mso-wrap-style:square'>
    16482037 <v:imagedata src="RigidBodyRef.fld/image008.png" o:title=""/>
    16492038</v:shape><![endif]--><![if !vml]><img border=0 width=281 height=193
    16502039src="RigidBodyRef.fld/image008.png" v:shapes="Picture_x0020_9"><![endif]></span><span
    1651 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2040style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2041
     2042<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>When the “balls” are
     2043<u>made smaller</u>, it becomes possible to click on bonds. </span><span
     2044lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    16522045mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    16532046Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    16542047
    1655 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1656 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>When the
    1657 “balls” are <u>smaller</u>, it becomes possible to click on every other bond in
    1658 the phenyl ring. </span><span lang=HE style='mso-bidi-font-size:14.0pt;
     2048<p class=MsoNormal><b><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    16592049font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    16602050minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1661 mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    1662 
    1663 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1664 unicode-bidi:embed'><b><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></b></p>
    1665 
    1666 <h3 dir=RTL><span dir=LTR>2C)</span></h3>
    1667 
    1668 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1669 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Switch to
    1670 the <u>pencil</u> in the toolbar </span><span lang=HE style='mso-bidi-font-size:
     2051mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></b></p>
     2052
     2053<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2054dir=LTR></span>2C)</span> <span style='mso-bidi-font-size:14.0pt'>Switch to the
     2055<u>pencil</u> in the toolbar </span><span lang=HE dir=RTL style='mso-bidi-font-size:
    1671205614.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    16722057mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
    16732058minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    16742059
    1675 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1676 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1677 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_11"
    1678  o:spid="_x0000_i1056" type="#_x0000_t75" style='width:112pt;height:90pt;
    1679  visibility:visible;mso-wrap-style:square'>
     2060<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2061style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     2062HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_11" o:spid="_x0000_i1059"
     2063 type="#_x0000_t75" style='width:112pt;height:90pt;visibility:visible;
     2064 mso-wrap-style:square'>
    16802065 <v:imagedata src="RigidBodyRef.fld/image009.png" o:title=""/>
    16812066</v:shape><![endif]--><![if !vml]><img border=0 width=112 height=90
    16822067src="RigidBodyRef.fld/image009.png" v:shapes="Picture_x0020_11"><![endif]></span><span
    1683 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2068lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    16842069mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    16852070Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    16862071
    1687 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1688 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1689 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2072<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2073font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    16902074minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    16912075mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    16922076
    1693 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1694 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Click on
    1695 directly on every other C-C bond in the ring to <u>change the bonds</u> from
    1696 single to double. (Use care to avoid clicking elsewhere or additional atoms
    1697 will be created; use a right click to delete them.)<o:p></o:p></span></p>
    1698 
    1699 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1700 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1701 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_12"
    1702  o:spid="_x0000_i1055" type="#_x0000_t75" style='width:162pt;height:164pt;
    1703  visibility:visible;mso-wrap-style:square'>
     2077<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Click on directly on
     2078every other C-C bond in the phenyl ring to <u>change the bonds</u> from single
     2079to double. Note that when a C-C bond is clicked on, the order changes successively
     2080from single to double and to triple and then back to single again. (Use care to
     2081avoid clicking elsewhere than on a bond or additional atoms will be created;
     2082use a right click to delete unneeded atoms.)</span><span lang=HE dir=RTL
     2083style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2084mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2085Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2086
     2087<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2088style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     2089HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_12" o:spid="_x0000_i1058"
     2090 type="#_x0000_t75" style='width:162pt;height:164pt;visibility:visible;
     2091 mso-wrap-style:square'>
    17042092 <v:imagedata src="RigidBodyRef.fld/image010.png" o:title=""/>
    17052093</v:shape><![endif]--><![if !vml]><img border=0 width=162 height=164
    17062094src="RigidBodyRef.fld/image010.png" v:shapes="Picture_x0020_12"><![endif]></span><span
    1707 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    1708 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    1709 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    1710 
    1711 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1712 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1713 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2095style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2096
     2097<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2098font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    17142099minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    17152100mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    17162101
    1717 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>2D)</span></h3>
    1718 
    1719 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1720 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Use the <u>Build<span
     2102<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2103dir=LTR></span>2D)</span> <span style='mso-bidi-font-size:14.0pt'>Use the <u>Build<span
    17212104class=GramE>/“</span>Add Hydrogens”</u> menu item to add the remaining H atoms
    1722 to the other end of the molecule. <o:p></o:p></span></p>
    1723 
    1724 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1725 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1726 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_13"
    1727  o:spid="_x0000_i1054" type="#_x0000_t75" style='width:169pt;height:244pt;
    1728  visibility:visible;mso-wrap-style:square'>
    1729  <v:imagedata src="RigidBodyRef.fld/image011.png" o:title=""/>
     2105to the other end of the molecule. </span><span lang=HE dir=RTL
     2106style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2107mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2108Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2109
     2110<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2111style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     2112HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_13" o:spid="_x0000_i1057"
     2113 type="#_x0000_t75" style='width:169pt;height:244pt;visibility:visible;
     2114 mso-wrap-style:square'>
     2115 <v:imagedata src="RigidBodyRef.fld/image020.png" o:title=""/>
    17302116</v:shape><![endif]--><![if !vml]><img border=0 width=169 height=244
    1731 src="RigidBodyRef.fld/image011.png" v:shapes="Picture_x0020_13"><![endif]></span><span
    1732 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    1733 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    1734 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    1735 
    1736 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1737 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1738 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2117src="RigidBodyRef.fld/image020.png" v:shapes="Picture_x0020_13"><![endif]></span><span
     2118style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2119
     2120<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2121font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    17392122minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    17402123mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    17412124
    1742 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>2E)</span></h3>
    1743 
    1744 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1745 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Optimize
    1746 the bond distances and angles using <u>Extensions<span class=GramE>/“</span>Optimize
     2125<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2126dir=LTR></span>2E)</span> <span style='mso-bidi-font-size:14.0pt'>Optimize the
     2127bond distances and angles using <u>Extensions<span class=GramE>/“</span>Optimize
    17472128Geometry”</u>. Use it a few times until no further changes are visible. The
    1748 molecule should appear as below. <o:p></o:p></span></p>
    1749 
    1750 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1751 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1752 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_14"
    1753  o:spid="_x0000_i1053" type="#_x0000_t75" style='width:172pt;height:202pt;
    1754  visibility:visible;mso-wrap-style:square'>
    1755  <v:imagedata src="RigidBodyRef.fld/image012.png" o:title=""/>
     2129molecule should appear as below. </span><span lang=HE dir=RTL style='mso-bidi-font-size:
     213014.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
     2131mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
     2132minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2133
     2134<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2135style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     2136HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_14" o:spid="_x0000_i1056"
     2137 type="#_x0000_t75" style='width:172pt;height:202pt;visibility:visible;
     2138 mso-wrap-style:square'>
     2139 <v:imagedata src="RigidBodyRef.fld/image022.png" o:title=""/>
    17562140</v:shape><![endif]--><![if !vml]><img border=0 width=172 height=202
    1757 src="RigidBodyRef.fld/image012.png" v:shapes="Picture_x0020_14"><![endif]></span><span
    1758 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    1759 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    1760 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    1761 
    1762 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1763 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1764 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2141src="RigidBodyRef.fld/image022.png" v:shapes="Picture_x0020_14"><![endif]></span><span
     2142style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2143
     2144<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2145font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    17652146minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    17662147mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    17672148
    1768 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>2F) </span></h3>
    1769 
    1770 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1771 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Use <u>“Save
     2149<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2150dir=LTR></span>2F)</span> <span style='mso-bidi-font-size:14.0pt'>Use <u>“Save
    17722151as”</u> to write the newly generated coordinates out. Be sure to select the
    1773 file type as “<u>XYZ</u>”. I used </span><span dir=LTR style='mso-bidi-font-size:
    1774 14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>name <span
     2152file type as “<u>XYZ</u>”. I used </span><span style='mso-bidi-font-size:14.0pt;
     2153mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>name <span
    17752154class=SpellE>regularized.xyz</span> for the file. <u>Exit</u> Avogadro. </span><span
    1776 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    1777 
    1778 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1779 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1780 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    1781 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1782 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    1783 
    1784 <h2 dir=RTL><span dir=LTR>Step 3: Create the rigid body in GSAS-II</span></h2>
    1785 
    1786 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1787 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    1788 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    1789 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1790 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    1791 
    1792 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1793 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1794 Calibri;mso-bidi-theme-font:minor-latin'>If you skipped step 2, you can
    1795 download the Avogadro output file, supplied as <span class=SpellE>regularized.xyz</span><o:p></o:p></span></p>
    1796 
    1797 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1798 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2155lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2156mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2157Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2158
     2159<h2>Step 3: Create the rigid body in GSAS-II<span lang=HE dir=RTL
     2160style='font-size:13.0pt;mso-ansi-font-size:16.0pt'><o:p></o:p></span></h2>
     2161
     2162<p class=MsoNormal><a name=step3><span style='mso-bidi-font-size:14.0pt;
     2163mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>If you skipped
     2164step 2, you can use the file I created with Avogadro, supplied as </span></a><span
     2165class=SpellE><span style='mso-bookmark:step3'><span style='mso-bidi-font-size:
     216614.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>regularized.xyz</span></span></span><span
     2167style='mso-bookmark:step3'><span lang=HE dir=RTL style='mso-bidi-font-size:
     216814.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></span></p>
     2169
     2170<span style='mso-bookmark:step3'></span>
     2171
     2172<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    17992173Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    18002174
    1801 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>3A)</span></h3>
    1802 
    1803 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1804 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1805 Calibri;mso-bidi-theme-font:minor-latin'>To start, <u>open</u> the distort1.gpx
    1806 file in GSAS-II. Click on the <u>“Rigid bodies”</u> tree item. Click on the <u>“Edit
    1807 Residue Body”<span class=GramE>/“</span>Extract from file”</u> menu item,
    1808 select the format as <u>XYZ</u> and then select the file written in step 2F (<span
    1809 class=SpellE>regularized.xyz</span>).<o:p></o:p></span></p>
    1810 
    1811 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1812 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2175<p class=MsoNormal><span class=MsoIntenseReference>3A)</span> <span
     2176style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2177minor-latin'>To start, <u>open</u> the supplied <u>distort1.gpx file</u> in
     2178GSAS-II. Then we will create a rigid body for this project by clicking on the <u>“Rigid
     2179bodies”</u> tree item. Click on the <u>“Edit Residue Body”<span class=GramE>/“</span>Extract
     2180from file”</u> menu item, select the format as <u>XYZ</u> and then select the
     2181file written in step 2F (<span class=SpellE>regularized.xyz</span>).<span
     2182lang=HE dir=RTL><o:p></o:p></span></span></p>
     2183
     2184<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    18132185Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    18142186
    1815 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1816 unicode-bidi:embed'><i><span dir=LTR style='mso-bidi-font-size:14.0pt;
    1817 mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Note that if
    1818 “Import XYZ” were used, the coordinates would be used exactly as in created by
    1819 Avogadro, but Extract from file allows atoms to be selected, recomputes the
    1820 origin as the midpoint between atoms and allows rigid body axes and the origin
    1821 to be defined by user preferences.<o:p></o:p></span></i></p>
    1822 
    1823 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1824 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2187<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2188Calibri;mso-bidi-theme-font:minor-latin'>Note that the “</span></i><span
     2189style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2190minor-latin'>Import XYZ<i>” menu command could also be used, but “</i>Extract
     2191from file<i>” allows atoms to be selected, recomputes the origin as the
     2192midpoint between atoms and allows rigid body axes and the origin to be defined based
     2193on user preferences. With “</i>Import XYZ<i>” the coordinates would be used
     2194exactly as in created by Avogadro.<span lang=HE dir=RTL><o:p></o:p></span></i></span></p>
     2195
     2196<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    18252197Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    18262198
    1827 <h3 dir=RTL><span dir=LTR style='mso-bidi-font-size:14.0pt'>3B)<o:p></o:p></span></h3>
    1828 
    1829 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1830 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1831 Calibri;mso-bidi-theme-font:minor-latin'>Once the file is opened and read; by <span
    1832 class=GramE>default</span> all atoms are selected. Note that H atoms are not
    1833 moved when torsional groups are moved, so we do not want to include any of the
    1834 non-phenyl H atoms. It is easier to remove all of the H atoms (they can be
    1835 regenerated later as riders if desired). After <u>selecting only atoms #0-#15</u>
    1836 (as below), press <u>Continue</u>.<o:p></o:p></span></p>
    1837 
    1838 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1839 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1840 Calibri;mso-bidi-theme-font:minor-latin;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1841  id="Picture_x0020_20" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:326pt;
     2199<p class=MsoNormal><span class=MsoIntenseReference>3B)</span><span
     2200style='mso-bidi-font-size:14.0pt'> </span><span style='mso-bidi-font-size:14.0pt;
     2201mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>After the <span
     2202class=SpellE>regularized.xyz</span> file is opened and read; all atoms are selected
     2203by default. Note that H atoms are not moved when torsional groups are rotated,
     2204so we do not want to include any of the non-phenyl H atoms. For simplicity <span
     2205class=GramE>here</span> we will remove all of the H atoms. (They could be
     2206regenerated later, if desired). <u>Select only atoms #0-#15</u> (as below) and
     2207press <u>Continue</u>.<o:p></o:p></span></p>
     2208
     2209<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2210style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2211minor-latin;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2212 id="Picture_x0020_20" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:326pt;
    18422213 height:303pt;visibility:visible;mso-wrap-style:square'>
    1843  <v:imagedata src="RigidBodyRef.fld/image013.png" o:title=""/>
     2214 <v:imagedata src="RigidBodyRef.fld/image042.png" o:title=""/>
    18442215</v:shape><![endif]--><![if !vml]><img border=0 width=326 height=303
    1845 src="RigidBodyRef.fld/image013.png" v:shapes="Picture_x0020_20"><![endif]></span><span
    1846 dir=RTL></span><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1847 Calibri;mso-bidi-theme-font:minor-latin'><span dir=RTL></span><span
    1848 style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
    1849 
    1850 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1851 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2216src="RigidBodyRef.fld/image042.png" v:shapes="Picture_x0020_20"><![endif]></span><span
     2217dir=RTL></span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2218mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span dir=RTL></span><span
     2219style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:14.0pt;
     2220mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     2221
     2222<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2223mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     2224
     2225<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2226dir=LTR></span>3C)</span> <i><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2227Calibri;mso-bidi-theme-font:minor-latin'>Note that there are several other
     2228things that can be done on the window that is now created. These include:
     2229defining axes and reordering the atoms by dragging rows in the list. As an
     2230example, selecting the atoms in the phenyl ring and pressing “Place in plane”, where
     2231the adjacent button has “<span class=SpellE>xy</span>” selected, will orient
     2232the z axis as normal to the plane of the ring. Selecting a single atom and
     2233pressing “Set origin” will place that atom as the origin, or if two atoms are
     2234selected the origin will be the midpoint between the two atoms. None of this is
     2235needed here, but such actions will likely be needed for bodies that will be
     2236placed at high-symmetry locations in a unit cell. <span lang=HE dir=RTL><o:p></o:p></span></span></i></p>
     2237
     2238<p class=MsoNormal><span lang=HE dir=RTL style='font-size:15.0pt;mso-ansi-font-size:
     223914.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     2240
     2241<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2242Calibri;mso-bidi-theme-font:minor-latin'>For this exercise all that is needed
     2243to select all atoms (done by default) and then use the selected atoms to create
     2244a rigid body by pressing the <u>“a Residue Body” button</u> near the bottom of
     2245the list of buttons. <span lang=HE dir=RTL><o:p></o:p></span></span></p>
     2246
     2247<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2248style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2249minor-latin;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2250 id="Picture_x0020_21" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:429pt;
     2251 height:215pt;visibility:visible;mso-wrap-style:square'>
     2252 <v:imagedata src="RigidBodyRef.fld/image046.png" o:title=""/>
     2253</v:shape><![endif]--><![if !vml]><img border=0 width=429 height=215
     2254src="RigidBodyRef.fld/image046.png" v:shapes="Picture_x0020_21"><![endif]></span><span
     2255dir=RTL></span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2256mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span dir=RTL></span><span
     2257style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:14.0pt;
     2258mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     2259
     2260<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2261mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     2262
     2263<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2264Calibri;mso-bidi-theme-font:minor-latin'>The rigid body is then created as
     2265shown below.<span lang=HE dir=RTL><o:p></o:p></span></span></p>
     2266
     2267<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2268style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2269minor-latin;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2270 id="Picture_x0020_22" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:438pt;
     2271 height:220pt;visibility:visible;mso-wrap-style:square'>
     2272 <v:imagedata src="RigidBodyRef.fld/image047.png" o:title=""/>
     2273</v:shape><![endif]--><![if !vml]><img border=0 width=438 height=220
     2274src="RigidBodyRef.fld/image047.png" v:shapes="Picture_x0020_22"><![endif]></span><span
     2275style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2276minor-latin'><o:p></o:p></span></p>
     2277
     2278<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2279mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     2280
     2281<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    18522282Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    18532283
    1854 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>3C)</span></h3>
    1855 
    1856 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1857 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1858 Calibri;mso-bidi-theme-font:minor-latin'>Here all that is needed to select all
    1859 atoms (done by default) and then use the selected atoms to create a rigid body
    1860 by pressing the <u>“a Residue Body” button</u> near the bottom of the list of buttons.
    1861 <o:p></o:p></span></p>
    1862 
    1863 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1864 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1865 Calibri;mso-bidi-theme-font:minor-latin;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1866  id="Picture_x0020_21" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:429pt;
    1867  height:215pt;visibility:visible;mso-wrap-style:square'>
    1868  <v:imagedata src="RigidBodyRef.fld/image014.png" o:title=""/>
    1869 </v:shape><![endif]--><![if !vml]><img border=0 width=429 height=215
    1870 src="RigidBodyRef.fld/image014.png" v:shapes="Picture_x0020_21"><![endif]></span><span
    1871 dir=RTL></span><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1872 Calibri;mso-bidi-theme-font:minor-latin'><span dir=RTL></span><span
    1873 style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
    1874 
    1875 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1876 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2284<p class=MsoNormal><span class=MsoIntenseReference>3D) Find atoms in torsions<o:p></o:p></span></p>
     2285
     2286<p class=MsoNormal><u><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2287Calibri;mso-bidi-theme-font:minor-latin'>Press the Plot button</span></u><span
     2288style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2289minor-latin'> to see the rigid body. Note that dragging with the left mouse
     2290button held down is needed to see all the atom labels, as below.<span lang=HE
     2291dir=RTL><o:p></o:p></span></span></p>
     2292
     2293<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2294style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2295minor-latin;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2296 id="Picture_x0020_23" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:341pt;
     2297 height:231pt;visibility:visible;mso-wrap-style:square'>
     2298 <v:imagedata src="RigidBodyRef.fld/image048.png" o:title=""/>
     2299</v:shape><![endif]--><![if !vml]><img border=0 width=341 height=231
     2300src="RigidBodyRef.fld/image048.png" v:shapes="Picture_x0020_23"><![endif]></span><span
     2301dir=RTL></span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2302mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span dir=RTL></span><span
     2303style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:14.0pt;
     2304mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     2305
     2306<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2307mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     2308
     2309<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2310Calibri;mso-bidi-theme-font:minor-latin'>From this it can be seen that the four
     2311bonds with possible torsional rotations are:<o:p></o:p></span></p>
     2312
     2313<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l4 level1 lfo9'><![if !supportLists]><span
     2314style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2315minor-latin'><span style='mso-list:Ignore'>a)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     2316</span></span></span><![endif]><span dir=LTR></span><span style='mso-bidi-font-size:
     231714.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>C3-C5, <o:p></o:p></span></p>
     2318
     2319<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo9'><![if !supportLists]><span
     2320style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2321minor-latin'><span style='mso-list:Ignore'>b)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
     2322</span></span></span><![endif]><span dir=LTR></span><span style='mso-bidi-font-size:
     232314.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>C5-C7, <o:p></o:p></span></p>
     2324
     2325<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo9'><![if !supportLists]><span
     2326style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2327minor-latin'><span style='mso-list:Ignore'>c)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     2328</span></span></span><![endif]><span dir=LTR></span><span style='mso-bidi-font-size:
     232914.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>C7-N2 and <o:p></o:p></span></p>
     2330
     2331<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l4 level1 lfo9'><![if !supportLists]><span
     2332style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2333minor-latin'><span style='mso-list:Ignore'>d)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
     2334</span></span></span><![endif]><span dir=LTR></span><span style='mso-bidi-font-size:
     233514.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>C7-C9. <span
     2336lang=HE dir=RTL><o:p></o:p></span></span></p>
     2337
     2338<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    18772339Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    18782340
    1879 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1880 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1881 Calibri;mso-bidi-theme-font:minor-latin'>The rigid body is then created. <o:p></o:p></span></p>
    1882 
    1883 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1884 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1885 Calibri;mso-bidi-theme-font:minor-latin;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1886  id="Picture_x0020_22" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:438pt;
    1887  height:220pt;visibility:visible;mso-wrap-style:square'>
    1888  <v:imagedata src="RigidBodyRef.fld/image015.png" o:title=""/>
    1889 </v:shape><![endif]--><![if !vml]><img border=0 width=438 height=220
    1890 src="RigidBodyRef.fld/image015.png" v:shapes="Picture_x0020_22"><![endif]></span><span
    1891 lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;
     2341<p class=MsoNormal><span class=MsoIntenseReference>3E) Define the torsions</span><span
     2342class=MsoIntenseReference><span lang=HE dir=RTL style='font-size:12.0pt;
     2343mso-ansi-font-size:14.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:
     2344Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;
     2345mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></span></p>
     2346
     2347<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2348Calibri;mso-bidi-theme-font:minor-latin'>Press the <u>“Edit Residue Body”<span
     2349class=GramE>/”Define</span> torsion”</u> menu item. This opens a window to select
     2350an origin atom. Once that is selected, you are offered a choice of atoms that
     2351are bonded to the selected atom. <o:p></o:p></span></p>
     2352
     2353<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2354Calibri;mso-bidi-theme-font:minor-latin'>Thus, for the C3-C5 bond, if <u>C3 is
     2355selected first</u> as the origin atom, the options in the second menu for pivot
     2356atom are: C1, C5 or C8. <u>Select C5</u>. (Note that if C5 had been selected
     2357first as origin, then the pivot choices would be C3 and C7.)<o:p></o:p></span></p>
     2358
     2359<p class=MsoNormal align=right style='text-align:right'><span style='mso-no-proof:
     2360yes'><span style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:
     236114.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;mso-no-proof:
     2362yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_42" o:spid="_x0000_i1051"
     2363 type="#_x0000_t75" style='width:133pt;height:140pt;visibility:visible;
     2364 mso-wrap-style:square'>
     2365 <v:imagedata src="RigidBodyRef.fld/image049.png" o:title=""/>
     2366</v:shape><![endif]--><![if !vml]><img border=0 width=133 height=140
     2367src="RigidBodyRef.fld/image049.png" v:shapes="Picture_x0020_42"><![endif]></span><span
     2368style='mso-no-proof:yes'><span style='mso-spacerun:yes'> </span><!--[if gte vml 1]><v:shape
     2369 id="Picture_x0020_44" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:121pt;
     2370 height:90pt;visibility:visible;mso-wrap-style:square'>
     2371 <v:imagedata src="RigidBodyRef.fld/image050.png" o:title=""/>
     2372</v:shape><![endif]--><![if !vml]><img border=0 width=121 height=90
     2373src="RigidBodyRef.fld/image050.png" v:shapes="Picture_x0020_44"><![endif]></span><span
     2374lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;
    18922375mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
    18932376
    1894 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1895 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2377<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    18962378Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    18972379
    1898 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1899 unicode-bidi:embed'><i><span dir=LTR style='mso-bidi-font-size:14.0pt;
    1900 mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Other things that
    1901 can be done on the previous <span class=GramE>window <span
    1902 style='mso-spacerun:yes'> </span>include</span> defining axes and reordering
    1903 the atoms by dragging rows in the list. As an example, selecting the atoms in
    1904 the phenyl ring and pressing “Place in plane” “<span class=SpellE>xy</span>”
    1905 will orient the z axis as normal to the plane of the ring. Selecting a single
    1906 atom and pressing “Set origin” will place that atom as the origin, or if two
    1907 atoms are selected the origin will be the midpoint between the two atoms. None
    1908 of this is needed here, but such actions can be needed for bodies that will be
    1909 placed relative to special positions in a unit cell. <o:p></o:p></span></i></p>
    1910 
    1911 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1912 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1913 Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    1914 
    1915 <h3 dir=RTL><span dir=LTR>3D) Find atoms in torsions</span><span lang=HE
    1916 style='font-size:14.0pt'><o:p></o:p></span></h3>
    1917 
    1918 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1919 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1920 Calibri;mso-bidi-theme-font:minor-latin'>Press the Plot button to see the rigid
    1921 body. Note that dragging with the left mouse button held down is needed to see
    1922 all the atom labels, as below.<o:p></o:p></span></p>
    1923 
    1924 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1925 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1926 Calibri;mso-bidi-theme-font:minor-latin;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1927  id="Picture_x0020_23" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:341pt;
    1928  height:231pt;visibility:visible;mso-wrap-style:square'>
    1929  <v:imagedata src="RigidBodyRef.fld/image016.png" o:title=""/>
    1930 </v:shape><![endif]--><![if !vml]><img border=0 width=341 height=231
    1931 src="RigidBodyRef.fld/image016.png" v:shapes="Picture_x0020_23"><![endif]></span><span
    1932 dir=RTL></span><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1933 Calibri;mso-bidi-theme-font:minor-latin'><span dir=RTL></span><span
    1934 style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
    1935 
    1936 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1937 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1938 Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    1939 
    1940 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1941 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1942 Calibri;mso-bidi-theme-font:minor-latin'>From this it can be seen that the
    1943 bonds with possible torsional rotations are C3-C5, C5-C7, C7-N2 and C7-C9. <o:p></o:p></span></p>
    1944 
    1945 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1946 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1947 Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    1948 
    1949 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>3E) Define
    1950 the torsions</span><span lang=HE><o:p></o:p></span></h3>
    1951 
    1952 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1953 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1954 Calibri;mso-bidi-theme-font:minor-latin'>Press the <u>“Edit Residue Body”<span
    1955 class=GramE>/”Define</span> torsion.”</u> This requires selecting an origin
    1956 atom. Once that is selected, you are offered a choice of atoms that are bonded
    1957 to the selected atom. <span class=GramE>Thus</span> for the C3-C5 bond, if <u>C3
    1958 is selected first</u>, the options in the second menu are C1, C5 or C8 and <u>C5
    1959 is selected</u>. If C5 is selected first, then the choices are C3 and C7. <o:p></o:p></span></p>
    1960 
    1961 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1962 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1963 Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    1964 
    1965 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1966 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1967 Calibri;mso-bidi-theme-font:minor-latin'>Then <u>repeat</u> this to define a
    1968 total of <u>4 torsions</u>, by then adding <u>C5-C7</u>, <u>C7-N2</u> and <u>C7-C9</u>.
    1969 The torsions are displayed at the bottom of the window, as shown below:<o:p></o:p></span></p>
    1970 
    1971 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    1972 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    1973 Calibri;mso-bidi-theme-font:minor-latin;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1974  id="Picture_x0020_24" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:493pt;
     2380<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2381Calibri;mso-bidi-theme-font:minor-latin'>After defining C3 and C5 for a
     2382torsion, then <u>repeat</u> this to define a total of <u>4 torsions</u>, by adding
     2383<u>C5-C7</u>, <u>C7-N2</u> and <u>C7-C9</u>. The torsions are displayed at the
     2384bottom of the window, as shown below:<span lang=HE dir=RTL><o:p></o:p></span></span></p>
     2385
     2386<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2387style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2388minor-latin;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2389 id="Picture_x0020_24" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:493pt;
    19752390 height:251pt;visibility:visible;mso-wrap-style:square'>
    1976  <v:imagedata src="RigidBodyRef.fld/image017.png" o:title=""/>
     2391 <v:imagedata src="RigidBodyRef.fld/image051.png" o:title=""/>
    19772392</v:shape><![endif]--><![if !vml]><img border=0 width=493 height=251
    1978 src="RigidBodyRef.fld/image017.png" v:shapes="Picture_x0020_24"><![endif]></span><span
    1979 lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;
    1980 mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
    1981 
    1982 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1983 unicode-bidi:embed'><i><span lang=HE style='mso-bidi-font-size:14.0pt;
     2393src="RigidBodyRef.fld/image051.png" v:shapes="Picture_x0020_24"><![endif]></span><span
     2394style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2395minor-latin'><o:p></o:p></span></p>
     2396
     2397<p class=MsoNormal><i><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    19842398mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></i></p>
    19852399
    1986 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1987 unicode-bidi:embed'><i><span dir=LTR style='mso-bidi-font-size:14.0pt;
    1988 mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>It can be
    1989 instructive to select each torsional mode in turn and move the slider to see
    1990 how the mode rotates the riding atoms.</span></i><i><span dir=LTR
    1991 style='mso-bidi-font-size:14.0pt'> <o:p></o:p></span></i></p>
    1992 
    1993 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1994 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    1995 
    1996 <h2 dir=RTL><span dir=LTR>Introduction to Steps 4 &amp; 5</span></h2>
    1997 
    1998 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    1999 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    2000 
    2001 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2002 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Now that
    2003 the rigid body has been defined, the next step is to insert it into the crystal
    2004 structure model. This means defining where the rigid body is located, oriented
    2005 and how it is mapped to atoms in the asymmetric unit. The origin of the rigid
    2006 body Cartesian system is placed at a specified location (in fractional coordinates)
     2400<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2401Calibri;mso-bidi-theme-font:minor-latin'>It can be instructive to select each
     2402torsional mode in turn and move the slider to see how the mode rotates the
     2403riding atoms.</span></i><i><span style='mso-bidi-font-size:14.0pt'> </span></i><i><span
     2404lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2405mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2406Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></i></p>
     2407
     2408<h2>Introduction to Steps 4 &amp; 5</h2>
     2409
     2410<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Now that the rigid
     2411body has been defined, the next step is to insert it into the crystal structure
     2412model. This means defining where the rigid body is located, oriented and how it
     2413is mapped to atoms in the asymmetric unit. The origin of the rigid body
     2414Cartesian system is placed at a specified location (in fractional coordinates)
    20072415and a quaternion defines the rigid body orientation. The same rigid body may be
    20082416used multiple times in the asymmetric unit. There will need to be a set of
     
    20102418be a set of torsion values angle values associated with each body use. <o:p></o:p></span></p>
    20112419
    2012 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2013 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2014 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2015 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2016 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2017 
    2018 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2019 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Note that
     2420<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2421
     2422<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Note that
    20202423understanding GSAS-II’s 3D visualization can be key to managing rigid bodies.
    20212424It is valuable to move and rotate the representation, so that distances along
    20222425all axes can be visualized. For this it is valuable to understand that as the
    20232426structure is viewed, movement of the mouse while holding down a button (also
    2024 called dragging) changes the view of the crystal structure, as described here):<o:p></o:p></span></p>
    2025 
    2026 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2027 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2028 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2427called dragging) changes the view of the crystal structure, as described here):</span><span
     2428lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2429mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2430Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2431
     2432<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2433
     2434<p class=MsoListParagraphCxSpFirst style='margin-left:.75in;mso-add-space:auto;
     2435text-indent:-.25in;mso-list:l1 level1 lfo3'><![if !supportLists]><span
     2436style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
     2437Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
     2438style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     2439dir=LTR></span><span style='mso-bidi-font-size:14.0pt'>Dragging with the right
     2440button down: moves the viewpoint, which is kept at the center of the screen
     2441(effectively translating the structure)</span><span lang=HE dir=RTL
     2442style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2443mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2444Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2445
     2446<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
     2447auto;text-indent:-.25in;mso-list:l1 level1 lfo3'><![if !supportLists]><span
     2448style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
     2449Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
     2450style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     2451dir=LTR></span><span style='mso-bidi-font-size:14.0pt'>Dragging with the left
     2452button down: rotates axes around screen x &amp; y. Rotation is around the
     2453viewpoint<o:p></o:p></span></p>
     2454
     2455<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
     2456auto;text-indent:-.25in;mso-list:l1 level1 lfo3'><![if !supportLists]><span
     2457style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
     2458Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
     2459style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     2460dir=LTR></span><span style='mso-bidi-font-size:14.0pt'>Dragging with the center
     2461button down: rotates axes around screen z</span><span lang=HE dir=RTL
     2462style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2463mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2464Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2465
     2466<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto;
     2467text-indent:-.25in;mso-list:l1 level1 lfo3'><![if !supportLists]><span
     2468style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
     2469Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
     2470style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     2471dir=LTR></span><span style='mso-bidi-font-size:14.0pt'>Rotating the scroll
     2472wheel: changes “camera position” (zoom in/out)</span><span lang=HE dir=RTL
     2473style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2474mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2475Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2476
     2477<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2478
     2479<p class=MsoNormal style='margin-left:.5in'><span style='mso-bidi-font-size:
     248014.0pt'>Note that the screen axes are x: horizontal, y: vertical and z: out of
     2481screen. Also, additional plot controls are available by pressing on the “Draw
     2482Options” tab. </span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2483font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2484minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     2485mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2486
     2487<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2488font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    20292489minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    20302490mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    20312491
    2032 <p class=MsoNormal align=right dir=RTL style='margin-right:.55in;text-align:
    2033 left;text-indent:-.3in;direction:rtl;unicode-bidi:embed'><span dir=LTR></span><span
    2034 dir=LTR style='mso-bidi-font-size:14.0pt'><span dir=LTR></span>* Dragging with
    2035 the right button down: moves the viewpoint, which is kept at the center of the
    2036 screen (effectively translating the structure)<o:p></o:p></span></p>
    2037 
    2038 <p class=MsoNormal align=right dir=RTL style='margin-right:.55in;text-align:
    2039 left;text-indent:-.3in;direction:rtl;unicode-bidi:embed'><span dir=LTR
    2040 style='mso-bidi-font-size:14.0pt'>* Dragging with the left <span class=GramE>button
    2041 down</span> H: rotates axes around screen x &amp; y. Rotation is around the
    2042 viewpoint</span><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2043 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2492<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>When inserting a
     2493rigid body into a unit cell, as described in the next section, the rigid body can
     2494be is being located into the unit cell, a second set of actions can be accessed
     2495with the mouse that affect the rigid body only. This is done by holding the Alt
     2496keyboard key down while “dragging” the mouse. <o:p></o:p></span></p>
     2497
     2498<p class=MsoListParagraphCxSpFirst style='margin-left:.75in;mso-add-space:auto;
     2499text-indent:-.25in;mso-list:l8 level1 lfo4'><![if !supportLists]><span
     2500style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
     2501Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
     2502style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     2503dir=LTR></span><span class=SpellE><span style='mso-bidi-font-size:14.0pt'>Alt+right</span></span><span
     2504style='mso-bidi-font-size:14.0pt'> mouse dragging changes the rigid body
     2505origin, <o:p></o:p></span></p>
     2506
     2507<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
     2508auto;text-indent:-.25in;mso-list:l8 level1 lfo4'><![if !supportLists]><span
     2509style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
     2510Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
     2511style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     2512dir=LTR></span><span class=SpellE><span style='mso-bidi-font-size:14.0pt'>Alt+middle</span></span><span
     2513style='mso-bidi-font-size:14.0pt'> button dragging rotates the rigid body
     2514around the screen z axis.<o:p></o:p></span></p>
     2515
     2516<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
     2517auto;text-indent:-.25in;mso-list:l8 level1 lfo4'><![if !supportLists]><span
     2518style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
     2519Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
     2520style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     2521dir=LTR></span><span class=SpellE><span style='mso-bidi-font-size:14.0pt'>Alt+left</span></span><span
     2522style='mso-bidi-font-size:14.0pt'> button dragging rotates the body around the x
     2523&amp; y screen axes. <o:p></o:p></span></p>
     2524
     2525<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto'><span
     2526style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2527
     2528<p class=MsoNormal style='margin-left:.5in'><span style='mso-bidi-font-size:
     252914.0pt'>Visually, the rigid body motions are analogous to what appears when the
     2530view of the structure is changed.<o:p></o:p></span></p>
     2531
     2532<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></i></p>
     2533
     2534<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt'>In this tutorial,
     2535we want to place the rigid bodies into the approximate locations where those
     2536molecules are already found. There are two ways to do this. One is that if
     2537specified atoms in the rigid body are paired to atoms in the crystal, the
     2538origin and/or quaternion can be optimized to best collocate the pairs of atoms.
     2539This will be shown in Step 4. Another choice is to visually move the rigid body
     2540to the desired location, which will be shown in Step 5. That process might be
     2541needed to insert a molecule into a region of a Fourier map.</span></i><span
     2542style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2543
     2544<h2>Step 4: Insert the first rigid body into the model</h2>
     2545
     2546<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt'>In this step we
     2547will assign pairs of atoms that match between the rigid body and the crystal asymmetric
     2548unit and have the best rigid body location be computed. </span></i><i><span
     2549lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2550mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2551Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></i></p>
     2552
     2553<p class=MsoNormal><b><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2554font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    20442555minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2045 mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2046 
    2047 <p class=MsoNormal align=right dir=RTL style='margin-right:.55in;text-align:
    2048 left;text-indent:-.3in;direction:rtl;unicode-bidi:embed'><span dir=LTR></span><span
    2049 dir=LTR style='mso-bidi-font-size:14.0pt'><span dir=LTR></span>* Dragging with
    2050 the center button down: rotates axes around screen z</span><span lang=HE
    2051 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2556mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></b></p>
     2557
     2558<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2559dir=LTR></span>4A) </span><span style='mso-bidi-font-size:14.0pt'>To insert a
     2560rigid body into a structure, select the desired phase in the data tree (here
     2561there is only one choice) and then select the <u>“Edit Body”<span class=GramE>/“</span>Locate
     2562&amp; Insert Rigid Body”</u> menu item. If more than one body were defined, a window
     2563to select which body would be offered. A window is displayed with options to
     2564define where the rigid body will be placed, as below. </span><span lang=HE
     2565dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    20522566mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    20532567Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    20542568
    2055 <p class=MsoNormal align=right dir=RTL style='margin-right:.55in;text-align:
    2056 left;text-indent:-.3in;direction:rtl;unicode-bidi:embed'><span dir=LTR></span><span
    2057 dir=LTR style='mso-bidi-font-size:14.0pt'><span dir=LTR></span>* Rotating the
    2058 scroll wheel: changes “camera position” (zoom in/out)</span><span lang=HE
    2059 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2569<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     257014.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_46"
     2571 o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;height:313pt;
     2572 visibility:visible;mso-wrap-style:square'>
     2573 <v:imagedata src="RigidBodyRef.fld/image052.png" o:title=""/>
     2574</v:shape><![endif]--><![if !vml]><img border=0 width=468 height=313
     2575src="RigidBodyRef.fld/image052.png" v:shapes="Picture_x0020_46"><![endif]></span><span
     2576style='mso-bidi-font-size:14.0pt'><span style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
     2577
     2578<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2579
     2580<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Also shown in the
     2581GSAS-II graphics window is a plot of the structure, along with the rigid body
     2582location. Note that by default the asymmetric unit is shown with van der Waals
     2583spheres. The rigid body is displayed as a ball-and-stick model with green
     2584bonds. Note that the origin of the rigid body is shown with a triplet of red,
     2585green and blue lines (for x, y, &amp; z, respectively) as well as a white line
     2586that shows the orientation vector. <o:p></o:p></span></p>
     2587
     2588<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2589font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2590minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     2591mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     2592
     2593<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     259414.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_47"
     2595 o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt;height:220pt;
     2596 visibility:visible;mso-wrap-style:square'>
     2597 <v:imagedata src="RigidBodyRef.fld/image053.png" o:title=""/>
     2598</v:shape><![endif]--><![if !vml]><img border=0 width=468 height=220
     2599src="RigidBodyRef.fld/image053.png" v:shapes="Picture_x0020_47"><![endif]></span><span
     2600lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    20602601mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    20612602Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    20622603
    2063 <p class=MsoNormal align=right dir=RTL style='margin-right:.55in;text-align:
    2064 left;text-indent:-.3in;direction:rtl;unicode-bidi:embed'><span dir=LTR
    2065 style='mso-bidi-font-size:14.0pt'>Note that the screen axes are x: horizontal,
    2066 y: vertical and z: out of screen. Also, additional plot controls are available
    2067 by pressing on the “Draw Options” tab. </span><span lang=HE style='mso-bidi-font-size:
     2604<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Change the crystal
     2605structure display mode to either <u>Ball &amp; Sticks</u> or <u>Sticks </u>(your
     2606preference) using the buttons on the upper right. This is needed because with
     2607van der Waals spheres, it is hard to see when the rigid body is close to the
     2608location where it will be docked.</span><span lang=HE dir=RTL style='mso-bidi-font-size:
    2068260914.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    20692610mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
    20702611minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    20712612
    2072 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2073 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2074 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2613<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2614
     2615<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt'>Note that the
     2616table at the lower part of the window shows each atom in the rigid body and the
     2617closest atom in the crystal structure and the distance to that atom. In the
     2618column labeled as “Assign as atom” to the extreme right of the table, we can assign
     2619specific pairing between atoms in the rigid body and atoms in the crystal
     2620structure that will override the closest atom pairing. Scrolling or expanding
     2621the window so the entire table is visible will make subsequent steps easier (as
     2622seen below). As the rigid body is moved, the distances will be updated. The
     2623closest atom may also change if an assignment has not been made. <o:p></o:p></span></i></p>
     2624
     2625<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2626
     2627<p class=MsoNormal><span class=MsoIntenseReference>4B) </span><span
     2628style='mso-bidi-font-size:14.0pt'>We will align the rigid body to the molecule
     2629in the cell closest to the upper right corner by assigning rigid body atoms to
     2630the matching atoms in the unit cell. </span><span lang=HE dir=RTL
     2631style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2632mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2633Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2634
     2635<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2636
     2637<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>If we <u>click on
     2638the 2<sup>nd</sup> row</u> in the table (with row label “C2”), the row is
     2639highlighted </span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2640font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2641minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     2642mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2643
     2644<p class=MsoNormal align=right style='text-align:right'><span dir=LTR></span><span
     2645lang=HE style='mso-no-proof:yes'><span dir=LTR></span><span
     2646style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:14.0pt;
     2647mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1046" type="#_x0000_t75"
     2648 style='width:468pt;height:261pt;visibility:visible;mso-wrap-style:square'>
     2649 <v:imagedata src="RigidBodyRef.fld/image054.png" o:title=""/>
     2650</v:shape><![endif]--><![if !vml]><img border=0 width=468 height=261
     2651src="RigidBodyRef.fld/image054.png" v:shapes="_x0000_i1046"><![endif]></span><span
     2652style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2653
     2654<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2655font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    20752656minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    20762657mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    20772658
    2078 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2079 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>When, as
    2080 described in the next section, a rigid body is being located into the unit
    2081 cell, a second set of actions can be accessed with the mouse. This is done by
    2082 holding the Alt keyboard key down while dragging the mouse. <span class=SpellE>Alt+right</span>
    2083 mouse dragging changes the rigid body origin, while <span class=SpellE>Alt+middle</span>
    2084 button and <span class=SpellE>Alt+left</span> button actions rotate the body by
    2085 changing the quaternion. Visually, the rigid body motions are analogous to what
    2086 appears when the view of the structure is changed. <o:p></o:p></span></p>
    2087 
    2088 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2089 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2090 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2659<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Note that atom C2 in
     2660the rigid body is highlighted by the ball color changing to green, as well as
     2661its matching atom in the crystal structure (C6), as shown below. </span><span
     2662lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2663mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2664Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2665
     2666<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2667style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     2668HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_29" o:spid="_x0000_i1045"
     2669 type="#_x0000_t75" style='width:391pt;height:154pt;visibility:visible;
     2670 mso-wrap-style:square'>
     2671 <v:imagedata src="RigidBodyRef.fld/image055.png" o:title=""/>
     2672</v:shape><![endif]--><![if !vml]><img border=0 width=391 height=154
     2673src="RigidBodyRef.fld/image055.png" v:shapes="Picture_x0020_29"><![endif]></span><span
     2674style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2675
     2676<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2677font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    20912678minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    20922679mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    20932680
    2094 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2095 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>In this
    2096 example, we want to place the rigid bodies into the approximate locations where
    2097 those molecules are already found. There are two ways to do this. One is that
    2098 if specified atoms in the rigid body are paired to atoms in the crystal, the
    2099 origin and/or quaternion can be optimized to best collocate the pairs of atoms.
    2100 This will be shown in Step 4. The other choice is to visually “dock” the rigid
    2101 body to the location already found, which will be shown in Step 5.<i> <o:p></o:p></i></span></p>
    2102 
    2103 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2104 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    2105 
    2106 <h2 dir=RTL><span dir=LTR>Step 4: Insert the first rigid body into the model</span></h2>
    2107 
    2108 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2109 unicode-bidi:embed'><b><span lang=HE style='mso-bidi-font-size:14.0pt;
    2110 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2111 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2112 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></b></p>
    2113 
    2114 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>4A)</span></h3>
    2115 
    2116 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2117 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>To insert a
    2118 rigid body into a structure, select the desired phase in the data tree (here
    2119 there is only one choice) and then select the <u>“Edit Body”<span class=GramE>/“</span>Locate
    2120 &amp; Insert Rigid Body”</u> menu item. A window is displayed with options to
    2121 define where the rigid body will be placed<o:p></o:p></span></p>
    2122 
    2123 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2124 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2125 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_25"
    2126  o:spid="_x0000_i1047" type="#_x0000_t75" style='width:478pt;height:239pt;
     2681<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>The crystal
     2682structure atom is not the correct one to match to C2. To find the right one, we
     2683can highlight different atoms in the crystal structure by pressing the <u>Tab</u>
     2684keyboard key until the correct atom is displayed; alternately, select different
     2685atoms in the “Crystal Highlight” pull down. After cycling through, one can see
     2686that C11 in the crystal structure should be paired to C2 in the rigid body. </span><span
     2687lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2688mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2689Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2690
     2691<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2692
     2693<p class=MsoNormal><span class=MsoIntenseReference>4C)</span> Assign <span
     2694style='mso-bidi-font-size:14.0pt'>C11 in the crystal structure to be paired to
     2695C2 by clicking in the <u>right-most box </u>in the C2 row of the table and <u>selecting
     2696atom C11</u> from the dropdown list. <o:p></o:p></span></p>
     2697
     2698<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     269914.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_50"
     2700 o:spid="_x0000_i1044" type="#_x0000_t75" style='width:329pt;height:166pt;
    21272701 visibility:visible;mso-wrap-style:square'>
    2128  <v:imagedata src="RigidBodyRef.fld/image018.png" o:title=""/>
    2129 </v:shape><![endif]--><![if !vml]><img border=0 width=478 height=239
    2130 src="RigidBodyRef.fld/image018.png" v:shapes="Picture_x0020_25"><![endif]></span><span
    2131 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    2132 
    2133 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2134 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2135 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2136 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2137 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2138 
    2139 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2140 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>and a plot
    2141 of the structure along with the rigid body location are shown in the plot
    2142 window<o:p></o:p></span></p>
    2143 
    2144 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2145 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>where the
    2146 asymmetric unit is shown initially with van der Waals spheres and the rigid
    2147 body is displayed as a ball-and-stick model with green bonds. </span><span
    2148 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2149 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2150 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2151 
    2152 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2153 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2154 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_26"
    2155  o:spid="_x0000_i1046" type="#_x0000_t75" style='width:460pt;height:208pt;
    2156  visibility:visible;mso-wrap-style:square'>
    2157  <v:imagedata src="RigidBodyRef.fld/image019.png" o:title=""/>
    2158 </v:shape><![endif]--><![if !vml]><img border=0 width=460 height=208
    2159 src="RigidBodyRef.fld/image019.png" v:shapes="Picture_x0020_26"><![endif]></span><span
    2160 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2161 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2162 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2163 
    2164 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2165 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2166 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2167 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2168 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2169 
    2170 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2171 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Change the
    2172 crystal structure display to either <u>Ball &amp; Sticks or Sticks </u>(your
    2173 preference) using the buttons on the upper right. This is needed because with
    2174 van der Waals spheres it is hard to see when the rigid body is close to the
    2175 location where it will be docked.<o:p></o:p></span></p>
    2176 
    2177 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2178 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2179 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2180 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2181 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2182 
    2183 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2184 unicode-bidi:embed'><i><span dir=LTR style='mso-bidi-font-size:14.0pt'>Note
    2185 that the table at the lower part of the window shows each atom in the rigid
    2186 body and the closest atom in the crystal structure and the distance to that
    2187 atom. In the column labeled as “Assign as atom” to the extreme right of the
    2188 table, we can specify specific pairing between atoms in the rigid body and
    2189 atoms in the crystal structure. Scrolling or expanding the window so the entire
    2190 table is visible will make subsequent steps easier (as seen below). As the
    2191 rigid body is moved, the distances, and if not paired explicitly, possibly the
    2192 closest atom will be updated. <o:p></o:p></span></i></p>
    2193 
    2194 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2195 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    2196 
    2197 <h3 dir=RTL><span dir=LTR>4B)</span></h3>
    2198 
    2199 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2200 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>We will
    2201 align the rigid body to the molecule in the cell closest to the upper right
    2202 corner by matching the atoms to the corresponding atoms. <o:p></o:p></span></p>
    2203 
    2204 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2205 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2206 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2207 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2208 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2209 
    2210 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2211 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>If we <u>click
    2212 on the 2<sup>nd</sup> row</u> in the table (with row label “C1”), the row is
    2213 highlighted <o:p></o:p></span></p>
    2214 
    2215 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2216 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2217 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_28"
    2218  o:spid="_x0000_i1045" type="#_x0000_t75" style='width:457pt;height:267pt;
    2219  visibility:visible;mso-wrap-style:square'>
    2220  <v:imagedata src="RigidBodyRef.fld/image020.png" o:title=""/>
    2221 </v:shape><![endif]--><![if !vml]><img border=0 width=457 height=267
    2222 src="RigidBodyRef.fld/image020.png" v:shapes="Picture_x0020_28"><![endif]></span><span
    2223 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2224 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2225 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2226 
    2227 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2228 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2229 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2230 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2231 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2232 
    2233 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2234 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Note that
    2235 atom C1 in the rigid body is highlighted by the ball color changing to green,
    2236 as well as its matching atom in the crystal structure (C6), as shown below. <o:p></o:p></span></p>
    2237 
    2238 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2239 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2240 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_29"
    2241  o:spid="_x0000_i1044" type="#_x0000_t75" style='width:391pt;height:154pt;
    2242  visibility:visible;mso-wrap-style:square'>
    2243  <v:imagedata src="RigidBodyRef.fld/image021.png" o:title=""/>
    2244 </v:shape><![endif]--><![if !vml]><img border=0 width=391 height=154
    2245 src="RigidBodyRef.fld/image021.png" v:shapes="Picture_x0020_29"><![endif]></span><span
    2246 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2247 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2248 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2249 
    2250 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2251 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2252 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2253 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2254 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2255 
    2256 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2257 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>The crystal
    2258 structure atom is not the correct atom to match to C1. We can highlight
    2259 different atoms (of the same type) in the crystal structure by pressing the <u>Tab</u>
    2260 keyboard key until the correct atom is displayed or by selecting different
    2261 atoms in the “Crystal Highlight” pull down. This shows that C11 in the crystal
    2262 structure should be paired to C1 in the rigid body. <o:p></o:p></span></p>
    2263 
    2264 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2265 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2266 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2267 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2268 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2269 
    2270 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>4C)</span></h3>
    2271 
    2272 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2273 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Force C11
    2274 in the crystal structure should be paired to C1 by clicking in the <u>right-most
    2275 box </u>in the C2 row of the table and <u>selecting atom C11</u> from the list.
    2276 Optional: press “Process Assignments” and the distance between C1 (RB) and C11
    2277 (C) will be shown in the table. Likewise, pressing “Set Origin” will translate
    2278 the rigid body to best match the assigned atoms. Since there is only one, the
    2279 distance will be zero. <o:p></o:p></span></p>
    2280 
    2281 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2282 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2283 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_30"
    2284  o:spid="_x0000_i1043" type="#_x0000_t75" style='width:437pt;height:233pt;
    2285  visibility:visible;mso-wrap-style:square'>
    2286  <v:imagedata src="RigidBodyRef.fld/image022.png" o:title=""/>
    2287 </v:shape><![endif]--><![if !vml]><img border=0 width=437 height=233
    2288 src="RigidBodyRef.fld/image022.png" v:shapes="Picture_x0020_30"><![endif]></span><span
    2289 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2290 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2291 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2292 
    2293 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2294 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2295 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2296 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2297 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2298 
    2299 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>4D)</span></h3>
    2300 
    2301 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2302 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Setting the
    2303 orientation requires assignment of at least one more atom and preferably a few.
    2304 Select an easy to identify an atom in the rigid body by <u>click</u>ing on the <u>C4
    2305 row</u> in the table. (Alternately, press Alt-Tab to highlight different rigid
    2306 body atoms.) Using Tab, it can be seen that crystal structure atom C13 should
    2307 be paired. <u>Select atom C13</u> in the “Assign as atom” cell for C4.<o:p></o:p></span></p>
    2308 
    2309 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2310 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2311 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2312 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2313 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2314 
    2315 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2316 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Likewise,
    2317 rigid body atom C5 should be matched to crystal structure atom C14 by <u>selecting
    2318 atom C14</u> in the “Assign as atom” cell for C5.<o:p></o:p></span></p>
    2319 
    2320 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2321 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2322 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2323 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2324 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2325 
    2326 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>4E)</span></h3>
    2327 
    2328 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2329 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Then <u>press</u>
    2330 the <u>“Set Both”</u> button and the phenyl ring positions are approximately
    2331 matched, as below. <o:p></o:p></span></p>
    2332 
    2333 <p class=MsoNormal align=center dir=RTL style='text-align:center;direction:
    2334 rtl;unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;
    2335 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32" o:spid="_x0000_i1042"
    2336  type="#_x0000_t75" style='width:468pt;height:189pt;visibility:visible;
    2337  mso-wrap-style:square'>
    2338  <v:imagedata src="RigidBodyRef.fld/image023.png" o:title=""/>
    2339 </v:shape><![endif]--><![if !vml]><img border=0 width=468 height=189
    2340 src="RigidBodyRef.fld/image023.png" v:shapes="Picture_x0020_32"><![endif]></span><span
    2341 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2342 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2343 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2344 
    2345 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2346 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2347 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2348 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2349 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2350 
    2351 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>4F)</span></h3>
    2352 
    2353 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2354 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>The
    2355 agreement in atom positions at the other end of the molecule is still not very
    2356 good, but this can be improved by <b>repositioning the view</b> (dragging with
    2357 the left mouse button) to look approximately along the plane of the ring. When
    2358 this is done, it becomes clear that the agreement can be improved significantly
    2359 by rotating around the <u>first torsion</u> angle by <u>moving the slider</u>.
    2360 An angle of 22-23 degrees is much brings the atoms much closer, but there are
    2361 still atoms as much as 1 Å in disagreement, since the crystal structure
    2362 molecule is rather distorted. <o:p></o:p></span></p>
    2363 
    2364 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2365 embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><span
    2366 style='mso-spacerun:yes'>  </span><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2367  id="Picture_x0020_33" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:225pt;
    2368  height:181pt;visibility:visible;mso-wrap-style:square'>
    2369  <v:imagedata src="RigidBodyRef.fld/image024.png" o:title="" croptop="7159f"
    2370   cropright="6357f"/>
    2371 </v:shape><![endif]--><![if !vml]><img border=0 width=225 height=181
    2372 src="RigidBodyRef.fld/image042.png" v:shapes="Picture_x0020_33"><![endif]></span><span
    2373 style='mso-spacerun:yes'>    </span><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2374  id="Picture_x0020_34" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:212pt;
    2375  height:181pt;visibility:visible;mso-wrap-style:square'>
    2376  <v:imagedata src="RigidBodyRef.fld/image026.png" o:title=""/>
    2377 </v:shape><![endif]--><![if !vml]><img border=0 width=212 height=181
    2378 src="RigidBodyRef.fld/image026.png" v:shapes="Picture_x0020_34"><![endif]></span></span><span
    2379 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2380 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2381 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2382 
    2383 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2384 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2385 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_36"
    2386  o:spid="_x0000_i1039" type="#_x0000_t75" style='width:230pt;height:215pt;
    2387  visibility:visible;mso-wrap-style:square'>
    2388  <v:imagedata src="RigidBodyRef.fld/image027.png" o:title=""/>
    2389 </v:shape><![endif]--><![if !vml]><img border=0 width=230 height=215
    2390 src="RigidBodyRef.fld/image027.png" v:shapes="Picture_x0020_36"><![endif]></span><span
    2391 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2392 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2393 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2394 
    2395 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2396 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2397 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2398 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2399 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2400 
    2401 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>4G)</span></h3>
    2402 
    2403 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2404 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Note that
    2405 the table now shows that the rigid body has crystal structure atoms 16-31
    2406 linked consecutively, which is to be expected since the atom order was never
    2407 changed.<span style='mso-spacerun:yes'>  </span><u>Press Add</u> to define
    2408 these atoms from the rigid body parameters shown in the window. A warning is
    2409 displayed, since some of the distances are larger than 0.5 Å, but <u>press Yes</u>
    2410 since this is about as good as we can do.<o:p></o:p></span></p>
    2411 
    2412 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2413 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2414 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_37"
    2415  o:spid="_x0000_i1038" type="#_x0000_t75" style='width:262pt;height:95pt;
    2416  visibility:visible;mso-wrap-style:square'>
    2417  <v:imagedata src="RigidBodyRef.fld/image028.png" o:title=""/>
    2418 </v:shape><![endif]--><![if !vml]><img border=0 width=262 height=95
    2419 src="RigidBodyRef.fld/image028.png" v:shapes="Picture_x0020_37"><![endif]></span><span
    2420 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    2421 
    2422 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2423 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>The
    2424 rigid-body constrained molecule is now shown in orange, unless “Show Rigid Bodies”
    2425 is unchecked on the “Draw Options” tab. Press the c key (with the graphics
    2426 window active) to see the view below.</span><span lang=HE style='mso-bidi-font-size:
     2702 <v:imagedata src="RigidBodyRef.fld/image056.png" o:title=""/>
     2703</v:shape><![endif]--><![if !vml]><img border=0 width=329 height=166
     2704src="RigidBodyRef.fld/image056.png" v:shapes="Picture_x0020_50"><![endif]></span><span
     2705style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2706
     2707<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Optional: press
     2708“Process Assignments” and the distance between RB C2 and unit cell C11 will be
     2709shown in the table. Likewise, pressing “Set Origin” will translate the rigid
     2710body to best match the assigned atoms. Since there is only one assigned atom,
     2711the distance will be zero. </span><span lang=HE dir=RTL style='mso-bidi-font-size:
    2427271214.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    24282713mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
    24292714minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    24302715
    2431 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2432 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2433 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_38"
    2434  o:spid="_x0000_i1037" type="#_x0000_t75" style='width:322pt;height:113pt;
    2435  visibility:visible;mso-wrap-style:square'>
    2436  <v:imagedata src="RigidBodyRef.fld/image029.png" o:title=""/>
    2437 </v:shape><![endif]--><![if !vml]><img border=0 width=322 height=113
    2438 src="RigidBodyRef.fld/image029.png" v:shapes="Picture_x0020_38"><![endif]></span><span
    2439 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    2440 
    2441 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2442 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2443 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2716<p class=MsoNormal><span dir=LTR></span><span lang=HE style='mso-no-proof:yes'><span
     2717dir=LTR></span><span style='mso-spacerun:yes'> </span></span><span
     2718style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2719
     2720<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2721font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    24442722minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    24452723mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    24462724
    2447 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2448 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2449 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2725<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2726dir=LTR></span>4D)</span> <span style='mso-bidi-font-size:14.0pt'>Setting the
     2727orientation and origin requires assignment of at least two more atoms and
     2728preferably more. Select another easy to identify an atom in the rigid body by <u>click</u>ing
     2729on the <u>C4 row</u> in the table. (Alternately, press Alt-Tab to highlight
     2730different rigid body atoms.) Using Tab, it can be seen that crystal structure
     2731atom C13 should be paired. <u>Select atom C13</u> in the “Assign as atom” cell
     2732for C4.</span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2733font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2734minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     2735mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2736
     2737<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2738
     2739<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Likewise, rigid body
     2740atom C5 should be assigned to crystal structure atom C14 by <u>selecting atom
     2741C14</u> in the “Assign as atom” cell for C5.</span><span lang=HE dir=RTL
     2742style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2743mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2744Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2745
     2746<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2747
     2748<p class=MsoNormal><span class=MsoIntenseReference>4E)</span> <span
     2749style='mso-bidi-font-size:14.0pt'>Then <u>press</u> the <u>“Set Both”</u>
     2750button and the phenyl ring positions are approximately matched, as below. </span><span
     2751lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2752mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2753Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2754
     2755<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     275614.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
     2757 o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;height:189pt;
     2758 visibility:visible;mso-wrap-style:square'>
     2759 <v:imagedata src="RigidBodyRef.fld/image057.png" o:title=""/>
     2760</v:shape><![endif]--><![if !vml]><img border=0 width=468 height=189
     2761src="RigidBodyRef.fld/image057.png" v:shapes="Picture_x0020_32"><![endif]></span><span
     2762style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2763
     2764<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2765font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    24502766minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    24512767mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    24522768
    2453 <h2 dir=RTL><span dir=LTR>Step 5: Insert the second rigid body into the model</span></h2>
    2454 
    2455 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2456 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2457 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2769<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2770dir=LTR></span>4F)</span> <span style='mso-bidi-font-size:14.0pt'>The agreement
     2771in atom positions at the other end of the molecule is still not very good, but
     2772this can be improved by <b>repositioning the view</b> (dragging with the left
     2773mouse button) to look approximately along the plane of the ring. When this is
     2774done, it becomes clear that the agreement can be improved significantly by
     2775rotating around the <u>first torsion</u> angle by <u>moving the slider</u>. An
     2776angle of ~23 degrees brings the atoms much closer, but there are still atoms as
     2777much as 1 Å in disagreement, since the crystal structure molecule is rather
     2778distorted. </span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2779font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2780minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     2781mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2782
     2783<p class=MsoNormal align=right style='text-align:right'><span dir=LTR></span><span
     2784style='mso-bidi-font-size:14.0pt'><span dir=LTR></span><span
     2785style='mso-spacerun:yes'>  </span><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2786 id="Picture_x0020_33" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:225pt;
     2787 height:181pt;visibility:visible;mso-wrap-style:square'>
     2788 <v:imagedata src="RigidBodyRef.fld/image058.png" o:title="" croptop="7159f"
     2789  cropright="6357f"/>
     2790</v:shape><![endif]--><![if !vml]><img border=0 width=225 height=181
     2791src="RigidBodyRef.fld/image012.png" v:shapes="Picture_x0020_33"><![endif]></span><span
     2792style='mso-spacerun:yes'>    </span><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2793 id="Picture_x0020_34" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:212pt;
     2794 height:181pt;visibility:visible;mso-wrap-style:square'>
     2795 <v:imagedata src="RigidBodyRef.fld/image060.png" o:title=""/>
     2796</v:shape><![endif]--><![if !vml]><img border=0 width=212 height=181
     2797src="RigidBodyRef.fld/image060.png" v:shapes="Picture_x0020_34"><![endif]></span><o:p></o:p></span></p>
     2798
     2799<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2800style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     2801HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_36" o:spid="_x0000_i1040"
     2802 type="#_x0000_t75" style='width:230pt;height:215pt;visibility:visible;
     2803 mso-wrap-style:square'>
     2804 <v:imagedata src="RigidBodyRef.fld/image061.png" o:title=""/>
     2805</v:shape><![endif]--><![if !vml]><img border=0 width=230 height=215
     2806src="RigidBodyRef.fld/image061.png" v:shapes="Picture_x0020_36"><![endif]></span><span
     2807lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2808mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2809Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2810
     2811<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2812font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    24582813minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    24592814mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    24602815
    2461 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2462 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>As
    2463 mentioned in the introduction to steps 4 &amp; 5, above, mouse holding a mouse
    2464 button down (mouse dragging) changes the view of the crystal while holding Alt
    2465 down while dragging the mouse, moves the rigid body within the cell. We will
    2466 use this to c<o:p></o:p></span></p>
    2467 
    2468 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2469 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2470 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2471 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2472 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2473 
    2474 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>5A)</span></h3>
    2475 
    2476 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2477 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>To insert a
    2478 second copy of the rigid body into the structure, again select the <u>“Edit
    2479 Body”<span class=GramE>/“</span>Locate &amp; Insert Rigid Body”</u> menu item.
    2480 A window is displayed with options to define where the rigid body will be
    2481 placed<b> <o:p></o:p></b></span></p>
    2482 
    2483 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2484 unicode-bidi:embed'><b><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></b></p>
    2485 
    2486 <h3 dir=RTL><span dir=LTR>5B)</span></h3>
    2487 
    2488 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2489 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Hold the <u>Alt
    2490 key down</u> and <u>drag</u> with the <u>middle mouse</u> button to rotate the
    2491 rigid body by 180 degrees, as shown below.<o:p></o:p></span></p>
    2492 
    2493 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2494 embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2495  id="Picture_x0020_40" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:332pt;
    2496  height:135pt;visibility:visible;mso-wrap-style:square'>
    2497  <v:imagedata src="RigidBodyRef.fld/image030.png" o:title=""/>
    2498 </v:shape><![endif]--><![if !vml]><img border=0 width=332 height=135
    2499 src="RigidBodyRef.fld/image030.png" v:shapes="Picture_x0020_40"><![endif]></span><span
    2500 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2501 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2502 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2503 
    2504 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2505 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2506 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2507 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2508 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2509 
    2510 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>5C)</span></h3>
    2511 
    2512 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2513 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>With the <u>Alt
    2514 key down</u> and <u>drag</u> with the <u>right mouse</u> button and move the
    2515 rigid body so that the phenyl rings are aligned.<o:p></o:p></span></p>
    2516 
    2517 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2518 embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><span
    2519 style='mso-spacerun:yes'> </span><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2520  id="Picture_x0020_41" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:354pt;
    2521  height:150pt;visibility:visible;mso-wrap-style:square'>
    2522  <v:imagedata src="RigidBodyRef.fld/image031.png" o:title=""/>
    2523 </v:shape><![endif]--><![if !vml]><img border=0 width=354 height=150
    2524 src="RigidBodyRef.fld/image031.png" v:shapes="Picture_x0020_41"><![endif]></span><o:p></o:p></span></p>
    2525 
    2526 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2527 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2528 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2529 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2530 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2531 
    2532 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>5D)</span></h3>
    2533 
    2534 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2535 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>To see how
    2536 far the rings are separated in the screen z direction, we must rotate the view.
    2537 (Without pressing Alt) <u>drag</u> the mouse <u>upwards</u> with the <u>left
    2538 button</u> down to obtain a view similar to the one below.<o:p></o:p></span></p>
    2539 
    2540 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2541 embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2542  id="Picture_x0020_43" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:358pt;
    2543  height:202pt;visibility:visible;mso-wrap-style:square'>
    2544  <v:imagedata src="RigidBodyRef.fld/image032.png" o:title=""/>
    2545 </v:shape><![endif]--><![if !vml]><img border=0 width=358 height=202
    2546 src="RigidBodyRef.fld/image032.png" v:shapes="Picture_x0020_43"><![endif]></span><span
    2547 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2548 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2549 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2550 
    2551 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2552 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2553 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2554 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2555 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2556 
    2557 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2558 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>From this
    2559 view it is clear that a small rotation is needed and a small translation. First
    2560 with the <u>Alt</u> and the <u>middle mouse</u> button both pressed, drag
    2561 upwards until the <span class=GramE>rings</span> molecules are more parallel.
    2562 Then with the <span class=SpellE>the</span> <u>Alt</u> and the <u>right mouse</u>
    2563 button both pressed, drag upwards until the molecules are better overlapped. <o:p></o:p></span></p>
    2564 
    2565 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2566 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2567 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2568 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2569 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2570 
    2571 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>5E)</span></h3>
    2572 
    2573 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2574 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>At the
    2575 point the rigid body is pretty close to the initial position, with distances in
    2576 the table ranging from 0.1 to nearly 2 Å, but better agreement can be obtained
    2577 by making small adjustments with the Alt down and successively pressing each of
    2578 the three mouse buttons alternated with changing the view to see the molecules
    2579 from a different perspective. Another choice is to assign several atoms and
    2580 optimize, as was done in steps 4D and 4E. Choices of atoms to optimize are
    2581 clear since the atoms are properly paired in the table. Updating the C3-C5
    2582 torsion to ~30 degrees will also improve the agreement. <o:p></o:p></span></p>
    2583 
    2584 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2585 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2586 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2587 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2588 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2589 
    2590 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>5F)</span></h3>
    2591 
    2592 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2593 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>When the agreement
    2594 is sufficient, press Add, accept the warning and this molecule is also now
    2595 constrained by the rigid body. <o:p></o:p></span></p>
    2596 
    2597 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2598 unicode-bidi:embed'><b><span lang=HE style='mso-bidi-font-size:14.0pt;
    2599 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2600 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2601 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></b></p>
    2602 
    2603 <h2 dir=RTL><span dir=LTR>Step 6: Optimize the model</span></h2>
    2604 
    2605 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2606 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    2607 
    2608 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2609 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>If the
    2610 number of cycles is set to zero (in the Controls tree item), the fit will be
    2611 seen to have gotten significantly worse, with the profile <span class=SpellE>wR</span>
    2612 jumping from 2.2% with the distorted model to 5.8%. This is not surprising, but
    2613 a few refinement steps will provide a more realistic model with comparable
    2614 agreement but far fewer parameters. <o:p></o:p></span></p>
    2615 
    2616 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2617 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2618 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2619 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2620 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2621 
    2622 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>6A)</span><span
    2623 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></h3>
    2624 
    2625 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2626 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Initially, <u>set
    2627 all atoms to be refined as U only</u>. (Select the <u>Atoms tab</u>,
    2628 double-click on the refine column label and then <u>select U</u>.<span
    2629 style='mso-spacerun:yes'>  </span>In fact, this change is cosmetic, as the X
    2630 flag for the atoms in rigid bodies is ignored. <o:p></o:p></span></p>
    2631 
    2632 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2633 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2634 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_45"
    2635  o:spid="_x0000_i1033" type="#_x0000_t75" style='width:442pt;height:183pt;
    2636  visibility:visible;mso-wrap-style:square'>
    2637  <v:imagedata src="RigidBodyRef.fld/image033.png" o:title=""/>
    2638 </v:shape><![endif]--><![if !vml]><img border=0 width=442 height=183
    2639 src="RigidBodyRef.fld/image033.png" v:shapes="Picture_x0020_45"><![endif]></span><span
    2640 lang=HE dir=LTR style='mso-bidi-font-size:14.0pt'><span
    2641 style='mso-spacerun:yes'> </span></span><span lang=HE style='mso-bidi-font-size:
     2816<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2817dir=LTR></span>4G)</span> <span style='mso-bidi-font-size:14.0pt'>Note that the
     2818table now shows that the rigid body has crystal structure atoms 16-31 paired consecutively,
     2819which is to be expected since the atom order was never changed.<span
     2820style='mso-spacerun:yes'>  </span><u>Press Add</u> to define these atoms from
     2821the rigid body parameters shown in the window. A warning is displayed, since
     2822some of the distances are larger than 0.5 Å, but <u>press Yes</u> since this is
     2823about as good as we can do.</span><span lang=HE dir=RTL style='mso-bidi-font-size:
    2642282414.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    26432825mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
    26442826minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    26452827
    2646 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2647 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2648 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2828<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2829style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     2830HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_37" o:spid="_x0000_i1039"
     2831 type="#_x0000_t75" style='width:262pt;height:95pt;visibility:visible;
     2832 mso-wrap-style:square'>
     2833 <v:imagedata src="RigidBodyRef.fld/image062.png" o:title=""/>
     2834</v:shape><![endif]--><![if !vml]><img border=0 width=262 height=95
     2835src="RigidBodyRef.fld/image062.png" v:shapes="Picture_x0020_37"><![endif]></span><span
     2836style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2837
     2838<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>This causes any
     2839unpaired (shown as “create new”) to be added to the Atoms list and then every
     2840atom in the rigid body is linked to an atom in the asymmetric unit. <span
     2841style='mso-spacerun:yes'> </span>The rigid-body constrained atoms are now shown
     2842with bonds in orange (unless “Show Rigid Bodies” is unchecked on the “Draw
     2843Options” tab.) The atom coordinates are shown with a grey background on the
     2844Atoms tab. Press the c key (with the graphics window active) to see the view
     2845below.<o:p></o:p></span></p>
     2846
     2847<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     2848style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     2849HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_38" o:spid="_x0000_i1038"
     2850 type="#_x0000_t75" style='width:322pt;height:113pt;visibility:visible;
     2851 mso-wrap-style:square'>
     2852 <v:imagedata src="RigidBodyRef.fld/image063.png" o:title=""/>
     2853</v:shape><![endif]--><![if !vml]><img border=0 width=322 height=113
     2854src="RigidBodyRef.fld/image063.png" v:shapes="Picture_x0020_38"><![endif]></span><span
     2855lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2856mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2857Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2858
     2859<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2860font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    26492861minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    26502862mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    26512863
    2652 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2653 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Then select
    2654 the <u>RB Models</u> tab. The first rigid body is automatically selected.
    2655 Select to <u>refine</u> the <u>Origin</u> and the rotation angle/vector with
    2656 the <u>AV flag</u>. <o:p></o:p></span></p>
    2657 
    2658 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2659 embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2660  id="Picture_x0020_46" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:447pt;
    2661  height:222pt;visibility:visible;mso-wrap-style:square'>
    2662  <v:imagedata src="RigidBodyRef.fld/image034.png" o:title=""/>
    2663 </v:shape><![endif]--><![if !vml]><img border=0 width=447 height=222
    2664 src="RigidBodyRef.fld/image034.png" v:shapes="Picture_x0020_46"><![endif]></span><span
    2665 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    2666 
    2667 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2668 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2669 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2864<h2>Step 5: Insert the second rigid body into the model<span lang=HE dir=RTL
     2865style='font-size:13.0pt;mso-ansi-font-size:16.0pt'><o:p></o:p></span></h2>
     2866
     2867<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt'>As mentioned in
     2868the introduction to steps 4 &amp; 5, above, holding a mouse button down (mouse
     2869dragging) changes the view of the crystal while holding Alt down while dragging
     2870the mouse, moves the rigid body within the cell. In this step, to show how that
     2871works, we will use the mouse to place the rigid body. <o:p></o:p></span></i></p>
     2872
     2873<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2874
     2875<p class=MsoNormal><span class=MsoIntenseReference>5A)</span> <span
     2876style='mso-bidi-font-size:14.0pt'>To insert the rigid body into the structure
     2877again to match the second copy of the molecule, again select the <u>“Edit Body”<span
     2878class=GramE>/“</span>Locate &amp; Insert Rigid Body”</u> menu item. A window is
     2879displayed as before with options to define where the rigid body will be placed
     2880and the graphical display will look like this:<o:p></o:p></span></p>
     2881
     2882<p class=MsoNormal align=right style='text-align:right'><b><span
     2883style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2884 id="Picture_x0020_51" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:357pt;
     2885 height:154pt;visibility:visible;mso-wrap-style:square'>
     2886 <v:imagedata src="RigidBodyRef.fld/image064.png" o:title=""/>
     2887</v:shape><![endif]--><![if !vml]><img border=0 width=357 height=154
     2888src="RigidBodyRef.fld/image064.png" v:shapes="Picture_x0020_51"><![endif]></span></b><b><span
     2889lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2890mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2891Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></b></p>
     2892
     2893<p class=MsoNormal><b><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></b></p>
     2894
     2895<p class=MsoNormal><span class=MsoIntenseReference>5B)</span> <span
     2896style='mso-bidi-font-size:14.0pt'>Hold the <u>Alt key down</u> and <u>drag</u>
     2897with the <u>middle mouse</u> button to rotate the rigid body by 180 degrees, as
     2898shown below.<span style='mso-no-proof:yes'> <o:p></o:p></span></span></p>
     2899
     2900<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     290114.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1036" type="#_x0000_t75"
     2902 style='width:331pt;height:136pt;visibility:visible;mso-wrap-style:square'>
     2903 <v:imagedata src="RigidBodyRef.fld/image065.png" o:title=""/>
     2904</v:shape><![endif]--><![if !vml]><img border=0 width=331 height=136
     2905src="RigidBodyRef.fld/image065.png" v:shapes="_x0000_i1036"><![endif]><span
     2906style='mso-spacerun:yes'> </span></span><span lang=HE dir=RTL style='mso-bidi-font-size:
     290714.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
     2908mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
     2909minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2910
     2911<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     291214.0pt'><o:p>&nbsp;</o:p></span></p>
     2913
     2914<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2915font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    26702916minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    26712917mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    26722918
    2673 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>6B)</span></h3>
    2674 
    2675 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2676 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Then <u>select
    2677 the second rigid body</u> and repeat the previous actions (setting the <u>refine
    2678 checkbox</u> and selecting <u>AV</u> for the orientation refinement.)<o:p></o:p></span></p>
    2679 
    2680 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2681 embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2682  id="Picture_x0020_47" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:453pt;
    2683  height:226pt;visibility:visible;mso-wrap-style:square'>
    2684  <v:imagedata src="RigidBodyRef.fld/image035.png" o:title=""/>
    2685 </v:shape><![endif]--><![if !vml]><img border=0 width=453 height=226
    2686 src="RigidBodyRef.fld/image035.png" v:shapes="Picture_x0020_47"><![endif]></span><span
    2687 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    2688 
    2689 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2690 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2691 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2919<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2920dir=LTR></span>5C)</span> Again w<span style='mso-bidi-font-size:14.0pt'>ith
     2921the <u>Alt key down</u>, <u>drag</u> with the <u>right mouse</u> button and
     2922move the rigid body so that the phenyl rings are more or less aligned.</span><span
     2923lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2924mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2925Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2926
     2927<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     292814.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_53"
     2929 o:spid="_x0000_i1035" type="#_x0000_t75" style='width:354pt;height:155pt;
     2930 visibility:visible;mso-wrap-style:square'>
     2931 <v:imagedata src="RigidBodyRef.fld/image066.png" o:title=""/>
     2932</v:shape><![endif]--><![if !vml]><img border=0 width=354 height=155
     2933src="RigidBodyRef.fld/image066.png" v:shapes="Picture_x0020_53"><![endif]></span><span
     2934style='mso-bidi-font-size:14.0pt'><span style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
     2935
     2936<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2937
     2938<p class=MsoNormal><span class=MsoIntenseReference>5D)</span> <span
     2939style='mso-bidi-font-size:14.0pt'>To see how far the rings are separated in the
     2940screen z direction, we must rotate the view. <u>Drag</u> the mouse <u>upwards</u>
     2941with the <u>left button</u> down (without pressing Alt) to obtain a view
     2942similar to the one below.</span><span lang=HE dir=RTL style='mso-bidi-font-size:
     294314.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
     2944mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
     2945minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2946
     2947<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     294814.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1034" type="#_x0000_t75"
     2949 style='width:358pt;height:231pt;visibility:visible;mso-wrap-style:square'>
     2950 <v:imagedata src="RigidBodyRef.fld/image067.png" o:title=""/>
     2951</v:shape><![endif]--><![if !vml]><img border=0 width=358 height=231
     2952src="RigidBodyRef.fld/image067.png" v:shapes="_x0000_i1034"><![endif]></span><span
     2953style='mso-bidi-font-size:14.0pt'><span style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
     2954
     2955<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2956font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    26922957minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    26932958mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    26942959
    2695 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>6C)</span></h3>
    2696 
    2697 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2698 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Set the <u>number
    2699 of cycles back to 5</u> and <u>refine</u>. The fit will converge quickly to an <span
    2700 class=SpellE>wR</span> of 4.0%.<b><o:p></o:p></b></span></p>
    2701 
    2702 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2703 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    2704 
    2705 <h3 dir=RTL><span dir=LTR>6D)</span></h3>
    2706 
    2707 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2708 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Add
    2709 refinement of the <u>four torsion angles</u> for each of the <u>two rigid
    2710 bodies</u>. The <span class=SpellE>wR</span> quickly drops to 2.5%<o:p></o:p></span></p>
    2711 
    2712 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2713 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2714 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2960<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>From this view it is
     2961clear that a small rotation is needed and a small translation. First with the <u>Alt</u>
     2962and the <u>middle mouse</u> button both pressed, drag upwards until the two rings
     2963molecules are more parallel. Then, with the <u>Alt</u> and the <u>right mouse</u>
     2964buttons both pressed, drag upwards until the molecules are better overlapped. </span><span
     2965lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2966mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2967Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2968
     2969<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2970
     2971<p class=MsoNormal><span class=MsoIntenseReference>5E)</span> <span
     2972style='mso-bidi-font-size:14.0pt'>At the point the rigid body is pretty close
     2973to the position of the molecule in the unit cell, with distances in the table
     2974ranging from 0.1 to nearly 2 Å, but better agreement can be obtained by making
     2975small adjustments with the Alt down and successively pressing each of the three
     2976mouse buttons alternated with changing the view to see the molecules from a
     2977different perspective. Another choice is to assign several atoms and optimize,
     2978as was done in steps 4D and 4E. Choices of atoms to optimize are clear since
     2979the atoms are properly paired in the table. Updating the C3-C5 torsion to ~20
     2980degrees will also improve the agreement. </span><span lang=HE dir=RTL
     2981style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2982mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2983Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2984
     2985<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2986
     2987<p class=MsoNormal><span class=MsoIntenseReference>5F)</span> <span
     2988style='mso-bidi-font-size:14.0pt'>When the agreement is sufficient, press Add,
     2989accept the warning and this molecule is also now constrained by the rigid body.
     2990Now both molecules will appear as orange. </span><span lang=HE dir=RTL
     2991style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2992mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2993Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2994
     2995<h2>Step 6: Optimize the model<span lang=HE dir=RTL style='font-size:13.0pt;
     2996mso-ansi-font-size:16.0pt'><o:p></o:p></span></h2>
     2997
     2998<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>If the number of
     2999cycles is set to zero (in the Controls tree item), the fit will be seen to have
     3000gotten significantly worse, with the profile <span class=SpellE>wR</span>
     3001jumping from 2.2% with the distorted model to ~6%. This is not surprising and
     3002only a few refinement steps will provide a more realistic model with comparable
     3003agreement, but far fewer parameters.<o:p></o:p></span></p>
     3004
     3005<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3006
     3007<p class=MsoNormal><span class=MsoIntenseReference>6A)</span> <span
     3008style='mso-bidi-font-size:14.0pt'>Initially, <u>turn off refinement of all atoms</u>.
     3009(Select the <u>Atoms tab</u>, double-click on the refine column label and then leave
     3010all boxes unchecked and press OK). Note that the X flag for the atoms in the rigid
     3011bodies would be ignored anyway. <o:p></o:p></span></p>
     3012
     3013<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     301414.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1033" type="#_x0000_t75"
     3015 style='width:433pt;height:205pt;visibility:visible;mso-wrap-style:square'>
     3016 <v:imagedata src="RigidBodyRef.fld/image068.png" o:title=""/>
     3017</v:shape><![endif]--><![if !vml]><img border=0 width=433 height=205
     3018src="RigidBodyRef.fld/image068.png" v:shapes="_x0000_i1033"><![endif]></span><span
     3019style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     3020
     3021<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><span
     3022style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
     3023
     3024<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     3025font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    27153026minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    27163027mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    27173028
    2718 <h2 dir=RTL><span dir=LTR>Optional Step 7: Try rigid body TLS motion </span></h2>
    2719 
    2720 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2721 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    2722 
    2723 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2724 unicode-bidi:embed'><i><span dir=LTR style='mso-bidi-font-size:14.0pt'>The
    2725 motion of rigid bodies has been worked out (<span class=SpellE>Schomaker</span>
    2726 &amp; Trueblood, Acta <span class=SpellE>Cryst</span>, 1968) known as the TLS
    2727 description, which consists of three tensors: for translation (movement of all
    2728 atoms together, described with the T tensor), <span class=SpellE>libration</span>
    2729 (rotation of all atoms as a unit around the rigid body origin, described with
    2730 the L tensor) and correlated <span class=SpellE>librational</span>-translational
    2731 motion (screw-like motion, described with the S tensor). In the full expansion
    2732 there are 6 T and 6 L and 8 S terms. It is unlikely that all of these terms can
    2733 be used with powder data. The S terms can be readily omitted if the rigid body
    2734 origin is at the body center of mass. This is not exactly true here, but the
    2735 origin is close to the center of mass. <o:p></o:p></span></i></p>
    2736 
    2737 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2738 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2739 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     3029<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Then select the <u>RB
     3030Models</u> tab. The first rigid body is automatically selected. Make the following
     3031changes:<o:p></o:p></span></p>
     3032
     3033<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l3 level1 lfo5'><![if !supportLists]><span
     3034style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3035minor-latin'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     3036</span></span></span><![endif]><span dir=LTR></span><span style='mso-bidi-font-size:
     303714.0pt'>Select to <u>refine</u> the <u>Origin</u> <o:p></o:p></span></p>
     3038
     3039<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo5'><![if !supportLists]><span
     3040style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3041minor-latin'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     3042</span></span></span><![endif]><span dir=LTR></span><span style='mso-bidi-font-size:
     304314.0pt'>Refine both the orientation azimuth and vector by <u>setting</u> the <u>AV
     3044flag</u><o:p></o:p></span></p>
     3045
     3046<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo5'><![if !supportLists]><span
     3047style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3048minor-latin'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     3049</span></span></span><![endif]><span dir=LTR></span><span style='mso-bidi-font-size:
     305014.0pt'>Set the “thermal motion” <u>mode to <span class=SpellE>Uiso</span></u> <o:p></o:p></span></p>
     3051
     3052<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo5'><![if !supportLists]><span
     3053style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3054minor-latin'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     3055</span></span></span><![endif]><span dir=LTR></span><span style='mso-bidi-font-size:
     305614.0pt'>Set the initial <span class=SpellE><u>Uiso</u></span><u> value</u> to
     3057something reasonable, say <u>0.01</u><o:p></o:p></span></p>
     3058
     3059<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l3 level1 lfo5'><![if !supportLists]><span
     3060style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3061minor-latin'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     3062</span></span></span><![endif]><span dir=LTR></span><span style='mso-bidi-font-size:
     306314.0pt'>Set the <u>refinement flag</u> for thermal motion</span><span lang=HE
     3064dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3065mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3066Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     3067
     3068<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     306914.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1032" type="#_x0000_t75"
     3070 style='width:425pt;height:238pt;visibility:visible;mso-wrap-style:square'>
     3071 <v:imagedata src="RigidBodyRef.fld/image069.png" o:title=""/>
     3072</v:shape><![endif]--><![if !vml]><img border=0 width=425 height=238
     3073src="RigidBodyRef.fld/image069.png" v:shapes="_x0000_i1032"><![endif]></span><span
     3074style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     3075
     3076<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     307714.0pt'><o:p>&nbsp;</o:p></span></p>
     3078
     3079<p class=MsoNormal><span class=MsoIntenseReference>6B)</span> <span
     3080style='mso-bidi-font-size:14.0pt'>Then <u>select the second rigid body</u> and
     3081repeat the previous actions (setting the <u>refine checkbox</u>, selecting <u>AV</u>
     3082for the orientation refinement, setting <span class=SpellE><u>Uiso</u></span><u>
     3083mode</u>, set the <span class=SpellE><u>Uiso</u></span><u> value</u> to <u>0.01</u>
     3084and set the thermal motion <u>refinement flag</u>.)</span><span lang=HE
     3085dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3086mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3087Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     3088
     3089<p class=MsoNormal align=right style='text-align:right'><span lang=HE dir=RTL
     3090style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3091mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3092Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     3093
     3094<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     309514.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_58"
     3096 o:spid="_x0000_i1031" type="#_x0000_t75" style='width:451pt;height:256pt;
     3097 visibility:visible;mso-wrap-style:square'>
     3098 <v:imagedata src="RigidBodyRef.fld/image070.png" o:title=""/>
     3099</v:shape><![endif]--><![if !vml]><img border=0 width=451 height=256
     3100src="RigidBodyRef.fld/image070.png" v:shapes="Picture_x0020_58"><![endif]></span><span
     3101style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     3102
     3103<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3104
     3105<p class=MsoNormal><span class=MsoIntenseReference>6C)</span> <span
     3106style='mso-bidi-font-size:14.0pt'>Set the <u>number of cycles back to 5</u> and
     3107<u>refine</u>. The fit will converge quickly to an <span class=SpellE>wR</span>
     3108of ~4%.</span><b><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     3109font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     3110minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     3111mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></b></p>
     3112
     3113<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3114
     3115<p class=MsoNormal><span class=MsoIntenseReference>6D)</span> <span
     3116style='mso-bidi-font-size:14.0pt'>Add refinement of the <u>four torsion angles</u>
     3117for each of the <u>two rigid bodies</u>. Then refine again. The <span
     3118class=SpellE>wR</span> quickly drops to 2.5%<o:p></o:p></span></p>
     3119
     3120<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     312114.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_60"
     3122 o:spid="_x0000_i1030" type="#_x0000_t75" style='width:322pt;height:236pt;
     3123 visibility:visible;mso-wrap-style:square'>
     3124 <v:imagedata src="RigidBodyRef.fld/image071.png" o:title=""/>
     3125</v:shape><![endif]--><![if !vml]><img border=0 width=322 height=236
     3126src="RigidBodyRef.fld/image071.png" v:shapes="Picture_x0020_60"><![endif]></span><span
     3127lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3128mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3129Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     3130
     3131<h2>Optional Step 7: Try rigid body TLS motion <span lang=HE dir=RTL
     3132style='font-size:13.0pt;mso-ansi-font-size:16.0pt'><o:p></o:p></span></h2>
     3133
     3134<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt'>The motion of
     3135rigid bodies, known as the TLS description, has been worked out (<span
     3136class=SpellE>Schomaker</span> &amp; Trueblood, Acta <span class=SpellE>Cryst</span>.
     3137B<b>24</b>, 63-76, 1968) and consists of three tensors:<o:p></o:p></span></i></p>
     3138
     3139<p class=MsoListParagraphCxSpFirst style='margin-left:.75in;mso-add-space:auto;
     3140text-indent:-.25in;mso-list:l0 level1 lfo7'><![if !supportLists]><span
     3141style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
     3142Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span
     3143style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     3144</span></span></span><![endif]><span dir=LTR></span><i><span style='mso-bidi-font-size:
     314514.0pt'>the T tensor for translation movement of all atoms together<o:p></o:p></span></i></p>
     3146
     3147<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
     3148auto;text-indent:-.25in;mso-list:l0 level1 lfo7'><![if !supportLists]><span
     3149style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
     3150Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span
     3151style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     3152</span></span></span><![endif]><span dir=LTR></span><i><span style='mso-bidi-font-size:
     315314.0pt'>the L tensor for <span class=SpellE>libration</span>, rotation of all
     3154atoms as a unit around the rigid body origin, and <o:p></o:p></span></i></p>
     3155
     3156<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto;
     3157text-indent:-.25in;mso-list:l0 level1 lfo7'><![if !supportLists]><span
     3158style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
     3159Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span
     3160style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     3161</span></span></span><![endif]><span dir=LTR></span><i><span style='mso-bidi-font-size:
     316214.0pt'>the S tensor, to describe correlated <span class=SpellE>librational</span>-translational
     3163motion (screw-like motion). The S terms can be readily omitted if the rigid
     3164body origin is at the body center of mass.<o:p></o:p></span></i></p>
     3165
     3166<p class=MsoNormal style='margin-left:.5in'><i><span style='mso-bidi-font-size:
     316714.0pt'>In the full expansion there are 6 T and 6 L and 8 S terms. It is
     3168unlikely that all of these terms can ever be used with powder data. <o:p></o:p></span></i></p>
     3169
     3170<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3171
     3172<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt'>The simplest
     3173description that can be made with a rigid body is to assume that all motion is
     3174translational and isotropic. This is what we have done and would be equivalent
     3175to refining <span class=SpellE>Uiso</span> for each atom in the rigid body, but
     3176applying a constraint so that all atoms in the rigid body share that <span
     3177class=SpellE>Uiso</span> value. It makes sense to see if further expansion of
     3178the rigid body motion/disorder description will produce an even better fit,
     3179although it is clear that the crystallographic fit is already quite good
     3180considering the limited resolution and high background levels. Refining 24 more
     3181parameters (6 T + 6 L, for each of the 2 bodies) is clearly impractical. One
     3182possible simplification would be to refine only the diagonal T &amp; L elements
     3183(which constraints translation and <span class=SpellE>libration</span> directions
     3184to crystal axes). That might be appropriate with data more sensitive to group
     3185motion, but is still impractical here. One still simpler model is to include
     3186translation and <span class=SpellE>libration</span>, but require equal
     3187amplitudes in all directions. This can be done by refining only the diagonal T
     3188and L terms, but to constrain them to be equal. If the T &amp; L values are constrained
     3189to be the same for the two groups, this means replacing the 2 group <span
     3190class=SpellE>Uiso</span> values with 2 terms (a single grouped <span
     3191class=SpellE>T<sub>jj</sub></span> and a <span class=SpellE>L<sub>jj</sub></span>
     3192term). This is easily done as shown below. </span></i><i><span lang=HE dir=RTL
     3193style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3194mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3195Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></i></p>
     3196
     3197<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3198
     3199<p class=MsoNormal><span class=MsoIntenseReference>7A)</span> <span
     3200style='mso-bidi-font-size:14.0pt'>Switch to refine the T &amp; L terms by
     3201selecting each body, in the <u>RB Models</u> phase tab, set the <u>thermal
     3202motion model to TL</u> for both rigid bodies and then <u>turn on</u> the <u>refine</u>
     3203checkbox for the <u>T11, T22, T33, L11, L22 &amp; L33 terms</u>.<span
     3204style='mso-spacerun:yes'>  </span></span><span lang=HE dir=RTL
     3205style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3206mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3207Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     3208
     3209<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     3210 id="Picture_x0020_52" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:459pt;
     3211 height:186pt;visibility:visible;mso-wrap-style:square'>
     3212 <v:imagedata src="RigidBodyRef.fld/image072.png" o:title=""/>
     3213</v:shape><![endif]--><![if !vml]><img border=0 width=459 height=186
     3214src="RigidBodyRef.fld/image072.png" v:shapes="Picture_x0020_52"><![endif]></span><span
     3215style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     3216
     3217<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     3218font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    27403219minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    27413220mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    27423221
    2743 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2744 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>The
    2745 simplest description that can be made with a rigid body is to assume that all
    2746 motion is translational and isotropic. This is equivalent to constraining all
    2747 atoms in the rigid body to have the same <span class=SpellE>Uiso</span> value,
    2748 which has already been implemented in this refinement via constraints. A
    2749 simpler way to set this up would be to select “<span class=SpellE>Uiso</span>”
    2750 for the rigid body thermal motion model. This is shown in 7A-7C, below. <o:p></o:p></span></p>
    2751 
    2752 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2753 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2754 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2755 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2756 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2757 
    2758 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>7A)</span></h3>
    2759 
    2760 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2761 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Delete the <span
    2762 class=SpellE><u>Uiso</u></span><u> constraints</u> by clicking on the
    2763 constraints tree item and <u>deleting</u> each item. Then click on phase and
    2764 the <u>Atoms tab</u> and <u>remove the U flag</u> for all atoms but the last two
    2765 (water O atoms).<o:p></o:p></span></p>
    2766 
    2767 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2768 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2769 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2770 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2771 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2772 
    2773 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>7B)</span></h3>
    2774 
    2775 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2776 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>In the <u>RB
    2777 Models</u> refine phase tab, set the <u>thermal motion model to <span
    2778 class=SpellE>Uiso</span></u> for both rigid bodies and <u>turn on</u> the <u>refine</u>
    2779 checkbox to optimize the group <span class=SpellE>Uiso</span> value.<o:p></o:p></span></p>
    2780 
    2781 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2782 embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2783  id="Picture_x0020_48" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:368pt;
    2784  height:147pt;visibility:visible;mso-wrap-style:square'>
    2785  <v:imagedata src="RigidBodyRef.fld/image036.png" o:title=""/>
    2786 </v:shape><![endif]--><![if !vml]><img border=0 width=368 height=147
    2787 src="RigidBodyRef.fld/image036.png" v:shapes="Picture_x0020_48"><![endif]></span><span
    2788 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    2789 
    2790 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2791 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2792 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2793 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2794 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2795 
    2796 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>7C) </span></h3>
    2797 
    2798 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2799 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Carry out a
    2800 refinement to confirm that the profile <span class=SpellE>Rw</span> returns to
    2801 2.5%. <o:p></o:p></span></p>
    2802 
    2803 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2804 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2805 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2806 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2807 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2808 
    2809 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2810 unicode-bidi:embed'><i><span dir=LTR style='mso-bidi-font-size:14.0pt'>It makes
    2811 sense to see if further expansion of the rigid body motion/disorder description
    2812 will produce an even better fit, although it is clear that the crystallographic
    2813 fit is already quite good considering the limited resolution and high
    2814 background levels. Refining 24 more parameters (6 T + 6 L x 2 bodies) is
    2815 clearly impractical. One possible simplification would be to refine only the
    2816 diagonal T &amp; L elements (which constraints translation and <span
    2817 class=SpellE>libration</span> directions to crystal axes). That might be
    2818 appropriate with data more sensitive to group motion, but is still impractical
    2819 here. One still simpler model is to include translation and <span class=SpellE>libration</span>,
    2820 but make then isotropic. This can be done by refining only the diagonal T and L
    2821 terms, but constrain them to be equal for both groups. This means replacing the
    2822 2 group <span class=SpellE>Uiso</span> values with 2 terms (a single grouped <span
    2823 class=SpellE>T<sub>jj</sub></span> and a <span class=SpellE>L<sub>jj</sub></span>
    2824 term). This is easily done as shown below. <o:p></o:p></span></i></p>
    2825 
    2826 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2827 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2828 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2829 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2830 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2831 
    2832 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>7D)</span></h3>
    2833 
    2834 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2835 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Switch to
    2836 refine the T &amp; L terms by selecting each body, in the <u>RB Models</u>
    2837 phase tab, set the <u>thermal motion model to TL</u> for both rigid bodies and
    2838 then <u>turn on</u> the <u>refine</u> checkbox for the <u>T11, T22, T33, L11,
    2839 L22 &amp; L33 terms</u>.<span style='mso-spacerun:yes'>  </span><o:p></o:p></span></p>
    2840 
    2841 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2842 embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2843  id="Picture_x0020_52" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:459pt;
    2844  height:186pt;visibility:visible;mso-wrap-style:square'>
    2845  <v:imagedata src="RigidBodyRef.fld/image037.png" o:title=""/>
    2846 </v:shape><![endif]--><![if !vml]><img border=0 width=459 height=186
    2847 src="RigidBodyRef.fld/image037.png" v:shapes="Picture_x0020_52"><![endif]></span><span
    2848 lang=HE style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2849 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2850 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2851 
    2852 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2853 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2854 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2855 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2856 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2857 
    2858 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>7E)</span></h3>
    2859 
    2860 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2861 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2862 Calibri;mso-bidi-theme-font:minor-latin'>Create constraints on the <span
    2863 class=SpellE>T<sub>jj</sub></span> and <span class=SpellE>L<sub>jj</sub></span>
    2864 terms through use of the <u>Constraints</u> tree item. To constrain the <span
    2865 class=SpellE>T<sub>jj</sub></span> terms, one needs to know their variable name
    2866 is <span class=GramE>RBRT<i>jj</i>:<i>b</i></span>:0 for body #<i>b</i> of type
    2867 0. <o:p></o:p></span></p>
    2868 
    2869 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2870 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2871 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2872 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2873 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2874 
    2875 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2876 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>On the <u>Phase
    2877 tab</u> (loaded by default), use the <u>“Edit Constr.”<span class=GramE>/“</span>Add
    2878 Equivalence”</u> menu item and enter <u>RBRT</u> in the search <u>filter</u>.
    2879 The first term is one of the six that needs to be constrained, so select it as
    2880 the 1<sup>st</sup> variable and press OK.<span style='mso-no-proof:yes'> <o:p></o:p></span></span></p>
    2881 
    2882 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2883 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     3222<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     3223dir=LTR></span>7B)</span> Delete the two existing <span style='mso-bidi-font-size:
     322414.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>constraints
     3225on <span class=SpellE>Uiso</span> values: Use the <u>Constraints</u> tree item
     3226and the Phase tab and <u>delete the two entries</u>. These constraints are
     3227actually ignored with rigid body group motion, so this does not actually have
     3228any effect, but they could lead to confusion. <o:p></o:p></span></p>
     3229
     3230<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     3231Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     3232
     3233<p class=MsoNormal><span class=MsoIntenseReference>7C)</span> <span
     3234style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3235minor-latin'>Create constraints on the <span class=SpellE>T<sub>jj</sub></span>
     3236and <span class=SpellE>L<sub>jj</sub></span> terms through use of the <u>Constraints</u>
     3237tree item. To constrain the <span class=SpellE>T<sub>jj</sub></span> terms, one
     3238needs to know their variable names are <span class=GramE>RBRT<i>jj</i>:<i>b</i></span>:0
     3239for body #<i>b</i> of type 0 where j = 1, 2 or 3.<span lang=HE dir=RTL><o:p></o:p></span></span></p>
     3240
     3241<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3242
     3243<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>On the <u>Phase tab</u>
     3244(loaded by default), use the <u>“Edit Constr.”<span class=GramE>/“</span>Add Equivalence”</u>
     3245menu item and enter <u>RBRT</u> in the search <u>filter</u>. The first term is
     3246one of the six that needs to be constrained, so select it as the 1<sup>st</sup>
     3247variable and press OK.<span style='mso-no-proof:yes'> </span></span><span
     3248lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3249mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3250Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi;
     3251mso-no-proof:yes'><o:p></o:p></span></p>
     3252
     3253<p class=MsoNormal><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    28843254Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_54"
    28853255 o:spid="_x0000_i1028" type="#_x0000_t75" style='width:423pt;height:177pt;
    28863256 visibility:visible;mso-wrap-style:square'>
    2887  <v:imagedata src="RigidBodyRef.fld/image038.png" o:title=""/>
     3257 <v:imagedata src="RigidBodyRef.fld/image073.png" o:title=""/>
    28883258</v:shape><![endif]--><![if !vml]><img border=0 width=423 height=177
    2889 src="RigidBodyRef.fld/image038.png" v:shapes="Picture_x0020_54"><![endif]></span><span
    2890 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    2891 
    2892 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2893 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2894 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2895 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2896 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2897 
    2898 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2899 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>On the next
    2900 window select the remaining 11, 22 and 33 terms<o:p></o:p></span></p>
    2901 
    2902 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2903 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>and press
    2904 OK:<o:p></o:p></span></p>
    2905 
    2906 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2907 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     3259src="RigidBodyRef.fld/image073.png" v:shapes="Picture_x0020_54"><![endif]></span><span
     3260style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     3261
     3262<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3263
     3264<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>On the next window
     3265select the remaining five 11, 22 and 33 terms</span><span lang=HE dir=RTL
     3266style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3267mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3268Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     3269
     3270<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>and press OK:<o:p></o:p></span></p>
     3271
     3272<p class=MsoNormal><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    29083273Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_55"
    29093274 o:spid="_x0000_i1027" type="#_x0000_t75" style='width:422pt;height:255pt;
    29103275 visibility:visible;mso-wrap-style:square'>
    2911  <v:imagedata src="RigidBodyRef.fld/image039.png" o:title=""/>
     3276 <v:imagedata src="RigidBodyRef.fld/image074.png" o:title=""/>
    29123277</v:shape><![endif]--><![if !vml]><img border=0 width=422 height=255
    2913 src="RigidBodyRef.fld/image039.png" v:shapes="Picture_x0020_55"><![endif]></span><span
    2914 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    2915 
    2916 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2917 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-no-proof:
    2918 yes'><span style='mso-spacerun:yes'> </span></span><span dir=LTR
     3278src="RigidBodyRef.fld/image074.png" v:shapes="Picture_x0020_55"><![endif]></span><span
    29193279style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    29203280
    2921 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2922 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><span
    2923 style='mso-spacerun:yes'> </span></span><sub><span lang=HE style='mso-bidi-font-size:
    2924 14.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    2925 mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
    2926 minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></sub></p>
    2927 
    2928 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2929 unicode-bidi:embed'><sub><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></sub></p>
    2930 
    2931 <h3 dir=RTL><span dir=LTR>7F)</span></h3>
    2932 
    2933 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2934 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     3281<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><span
     3282style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     3283
     3284<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><span
     3285style='mso-spacerun:yes'> </span><sub><o:p></o:p></sub></span></p>
     3286
     3287<p class=MsoNormal><sub><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     3288font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     3289minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     3290mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></sub></p>
     3291
     3292<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     3293dir=LTR></span>7D)</span> <span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    29353294Calibri;mso-bidi-theme-font:minor-latin'>Create constraints on the <span
    29363295class=SpellE>L<sub>jj</sub></span> terms through use of the <u>Constraints</u>
     
    29383297Again use the <u>“Edit Constr.”/“Add Equivalence”</u> menu item and enter <u>RBRL</u>
    29393298in the search <u>filter</u>. The first term is one of the six that needs to be
    2940 constrained, and on the next screen select the remaining 11, 22 and 33 terms
    2941 and press OK. Constraints should appear as:<span style='mso-no-proof:yes'> <o:p></o:p></span></span></p>
    2942 
    2943 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2944 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     3299constrained, and on the next screen select the remaining five 11, 22 and 33
     3300terms and press OK. Constraints should appear as:<span style='mso-no-proof:
     3301yes'> <span lang=HE dir=RTL><o:p></o:p></span></span></span></p>
     3302
     3303<p class=MsoNormal><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    29453304Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_56"
    29463305 o:spid="_x0000_i1026" type="#_x0000_t75" style='width:578pt;height:133pt;
    29473306 visibility:visible;mso-wrap-style:square'>
    2948  <v:imagedata src="RigidBodyRef.fld/image040.png" o:title=""/>
     3307 <v:imagedata src="RigidBodyRef.fld/image075.png" o:title=""/>
    29493308</v:shape><![endif]--><![if !vml]><img border=0 width=578 height=133
    2950 src="RigidBodyRef.fld/image040.png" v:shapes="Picture_x0020_56"><![endif]></span><span
    2951 dir=LTR style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><o:p></o:p></span></p>
    2952 
    2953 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2954 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    2955 
    2956 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2957 unicode-bidi:embed'><span lang=HE style='mso-bidi-font-size:14.0pt;font-family:
    2958 "Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     3309src="RigidBodyRef.fld/image075.png" v:shapes="Picture_x0020_56"><![endif]></span><span
     3310style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><o:p></o:p></span></p>
     3311
     3312<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3313
     3314<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3315
     3316<p class=MsoNormal><span class=MsoIntenseReference>7E)</span> <span
     3317style='mso-bidi-font-size:14.0pt'>Then <u>refine</u> with these parameters and
     3318the <span class=SpellE>Rwp</span> remains at 2.5%, but I would argue this is a
     3319more reasonable model than the <span class=SpellE>Uiso</span> model. If the
     3320thermal ellipsoids are plotted, they get larger further away from the origin as
     3321one might expect. </span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     3322font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    29593323minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2960 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2961 
    2962 <h3 dir=RTL><span dir=LTR></span><span dir=LTR><span dir=LTR></span>7G)</span></h3>
    2963 
    2964 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2965 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'>Then <u>refine</u>
    2966 with these parameters and the <span class=SpellE>Rwp</span> remains at 2.5%,
    2967 but I would argue this is a more reasonable model than the <span class=SpellE>Uiso</span>
    2968 model as the thermal ellipsoids are plotted, they get larger further away from
    2969 the origin. <o:p></o:p></span></p>
    2970 
    2971 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2972 unicode-bidi:embed'><span dir=LTR style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    2973 
    2974 <h3 dir=RTL><span dir=LTR>7H)</span><span lang=HE><o:p></o:p></span></h3>
    2975 
    2976 <p class=MsoNormal align=right dir=RTL style='text-align:left;direction:rtl;
    2977 unicode-bidi:embed'><i><span dir=LTR style='mso-bidi-font-size:14.0pt'>An even
    2978 more relaxed model would be to allow the <span class=SpellE>T<sub>jj</sub></span>
    2979 and <span class=SpellE>L<sub>jj</sub></span> terms to differ between the two
    2980 bodies, with constraints as shown below, but this produces no improvement in
    2981 the <span class=SpellE>Rwp</span>. Further it has a non-physical negative <span
    2982 class=SpellE>L<sub>jj</sub></span> value for one of the two bodies, so this is
    2983 not a better model.<o:p></o:p></span></i></p>
    2984 
    2985 <p class=MsoNormal dir=RTL style='text-align:right;direction:rtl;unicode-bidi:
    2986 embed'><span lang=HE dir=LTR style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     3324mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     3325
     3326<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3327
     3328<p class=MsoNormal><span class=MsoIntenseReference>7F)</span> <i><span
     3329style='mso-bidi-font-size:14.0pt'>An even more relaxed model would be to allow
     3330the <span class=SpellE>T<sub>jj</sub></span> and <span class=SpellE>L<sub>jj</sub></span>
     3331terms to differ between the two bodies, with constraints as shown below, but
     3332this produces no improvement in the <span class=SpellE>Rwp</span>. Further it
     3333has a non-physical negative <span class=SpellE>L<sub>jj</sub></span> value for
     3334one of the two bodies, so this is not a better model.</span></i><i><span
     3335lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3336mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3337Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></i></p>
     3338
     3339<p class=MsoNormal><span lang=HE style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    29873340Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_49"
    29883341 o:spid="_x0000_i1025" type="#_x0000_t75" style='width:520pt;height:236pt;
    29893342 visibility:visible;mso-wrap-style:square'>
    2990  <v:imagedata src="RigidBodyRef.fld/image041.png" o:title=""/>
     3343 <v:imagedata src="RigidBodyRef.fld/image076.png" o:title=""/>
    29913344</v:shape><![endif]--><![if !vml]><img border=0 width=520 height=236
    2992 src="RigidBodyRef.fld/image041.png" v:shapes="Picture_x0020_49"><![endif]></span><span
    2993 dir=LTR style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     3345src="RigidBodyRef.fld/image076.png" v:shapes="Picture_x0020_49"><![endif]></span><span
     3346style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     3347
     3348<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3349
     3350<h2>Conclusion</h2>
     3351
     3352<p class=MsoNormal>In the tutorial, we have seen how to create a rigid body,
     3353using the Avogadro program to regularize the internal geometry. The body was then
     3354defined within GSAS-II, including 4 torsion angles internal to the body. The
     3355rigid body was then placed into the unit cell in previously determined positions/orientations.
     3356The positions, orientations and torsions, as well as rigid body group motion parameters,
     3357we then refined. The resulting fit was excellent with a highly realistic
     3358structure and a small number of parameters that are appropriate for the dataset
     3359being used. </p>
    29943360
    29953361</div>
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