Changeset 4627 for Tutorials


Ignore:
Timestamp:
Oct 27, 2020 10:46:08 AM (11 months ago)
Author:
toby
Message:

final (I hope) tutorial edit

Location:
Tutorials/RigidBody
Files:
47 added
31 deleted
1 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/RigidBody/RigidBodyRef.html

    r4624 r4627  
    2323  <o:Author>Toby, Brian H.</o:Author>
    2424  <o:LastAuthor>Toby, Brian H.</o:LastAuthor>
    25   <o:Revision>89</o:Revision>
    26   <o:TotalTime>3358</o:TotalTime>
    27   <o:Created>2020-09-21T20:56:00Z</o:Created>
    28   <o:LastSaved>2020-10-27T02:29:00Z</o:LastSaved>
    29   <o:Pages>30</o:Pages>
    30   <o:Words>4277</o:Words>
    31   <o:Characters>24385</o:Characters>
    32   <o:Lines>203</o:Lines>
    33   <o:Paragraphs>57</o:Paragraphs>
    34   <o:CharactersWithSpaces>28605</o:CharactersWithSpaces>
     25  <o:Revision>7</o:Revision>
     26  <o:TotalTime>3442</o:TotalTime>
     27  <o:Created>2020-10-27T03:04:00Z</o:Created>
     28  <o:LastSaved>2020-10-27T15:43:00Z</o:LastSaved>
     29  <o:Pages>31</o:Pages>
     30  <o:Words>4443</o:Words>
     31  <o:Characters>25328</o:Characters>
     32  <o:Lines>211</o:Lines>
     33  <o:Paragraphs>59</o:Paragraphs>
     34  <o:CharactersWithSpaces>29712</o:CharactersWithSpaces>
    3535  <o:Version>16.00</o:Version>
    3636 </o:DocumentProperties>
     
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     1388@list l4:level3
    16161389        {mso-level-number-format:bullet;
    16171390        mso-level-text:;
     
    16201393        text-indent:-.25in;
    16211394        font-family:Wingdings;}
    1622 @list l8:level4
     1395@list l4:level4
    16231396        {mso-level-number-format:bullet;
    16241397        mso-level-text:;
     
    16271400        text-indent:-.25in;
    16281401        font-family:Symbol;}
    1629 @list l8:level5
     1402@list l4:level5
    16301403        {mso-level-number-format:bullet;
    16311404        mso-level-text:o;
     
    16341407        text-indent:-.25in;
    16351408        font-family:"Courier New";}
    1636 @list l8:level6
     1409@list l4:level6
    16371410        {mso-level-number-format:bullet;
    16381411        mso-level-text:;
     
    16411414        text-indent:-.25in;
    16421415        font-family:Wingdings;}
    1643 @list l8:level7
     1416@list l4:level7
    16441417        {mso-level-number-format:bullet;
    16451418        mso-level-text:;
     
    16481421        text-indent:-.25in;
    16491422        font-family:Symbol;}
    1650 @list l8:level8
     1423@list l4:level8
    16511424        {mso-level-number-format:bullet;
    16521425        mso-level-text:o;
     
    16551428        text-indent:-.25in;
    16561429        font-family:"Courier New";}
    1657 @list l8:level9
     1430@list l4:level9
    16581431        {mso-level-number-format:bullet;
    16591432        mso-level-text:;
     
    17071480<p class=MsoNormal><span style='font-size:12.0pt;mso-bidi-font-size:14.0pt;
    17081481font-family:"Times New Roman",serif'>Note: Exercise files are found <a
    1709 href="data" target="_blank">here</a></span><span style='font-size:12.0pt;
     1482href="data/" target="_blank">here</a></span><span style='font-size:12.0pt;
    17101483font-family:"Times New Roman",serif'><o:p></o:p></span></p>
    17111484
    17121485<h2>Introduction</h2>
    17131486
    1714 <p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>It is a common situation
    1715 that a powder diffraction dataset will not provide enough observations to allow
    1716 refinement of all atoms independently. This is not only a problem for powder
    1717 diffraction; it is usually the case in single-crystal protein refinement as
    1718 well, as few datasets for that can be collected to atomic resolution. When the
    1719 number of parameters is not sufficient to discern individual atomic positions,
    1720 it is necessary to simplify the crystallographic model to require fewer
    1721 parameters through use of constraints. A common constraint is to group <span
     1487<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>It is a common
     1488situation that a powder diffraction dataset will not provide enough
     1489observations to allow refinement of all atoms independently. This is not only a
     1490problem for powder diffraction; it is usually the case in single-crystal
     1491protein structure determination as well, as few datasets for that can be
     1492collected to atomic resolution. When the number of parameters is not sufficient
     1493to discern individual atomic positions, it is necessary to apply constraints and/or
     1494restraints. Constraints simplify the crystallographic model by reducing the
     1495number of parameters. Restraints treat assumptions about the model as experimental
     1496observations. <span style='mso-spacerun:yes'> </span>Examples of restraints
     1497include providing target values for bond distances and angles, or penalizing a
     1498refinement if atoms diverge from a plane. One common constraint is to group <span
    17221499class=SpellE>U<sub>iso</sub></span> values so that a single value is used for
    1723 all atoms of a particular type or in a common bonding environment. Also common
    1724 is to apply restraints, which effectively allows assumptions about the model to
    1725 be used as if they were experimental observations. Examples of restraints
    1726 include providing target values for bond distances and angles, or penalizing a
    1727 refinement if atoms diverge from a plane. <o:p></o:p></span></p>
     1500all atoms of a particular type or in a common bonding environment. <o:p></o:p></span></p>
    17281501
    17291502<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     
    17321505powerful types of constraints in GSAS-II is to constrain a group of atoms so
    17331506that their relative positions are fixed. Such a group of atoms is known as a
    1734 rigid body. The core concept in a rigid body refinement is that 3 parameters for
    1735 an origin and 3 orientation parameters are needed to locate a rigid body,
    1736 though in some cases symmetry can reduce the number of refinable parameters
    1737 below 6. In contrast, 3 position parameters are needed for every atom in a
    1738 structure on a general position. Thus, a four-atom group requires 12 positional
    1739 parameters and a 6-atom group requires 18 positional parameters, when modeled
    1740 with individual atoms, but as rigid-bodies only 6 parameters will be needed.
    1741 Also, a more chemically reasonable result will be obtained. <o:p></o:p></span></p>
     1507rigid body. The core concept behind rigid body refinement is that 3 parameters define
     1508an origin and only 3 orientation parameters are needed to locate a rigid body,
     1509so that only 6 parameters are needed to locate and orient the body, though in
     1510some cases symmetry will constrain some of these values and the number of
     1511refinable parameters will thus be reduced. In contrast, 3 position parameters
     1512are needed for every atom in a structure on a general position. Thus, a
     1513four-atom group requires 12 positional parameters and a 6-atom group requires
     151418 positional parameters, when modeled with individual atoms, but as
     1515rigid-bodies only 6 parameters will be needed. Also, since the relative
     1516positions are fixed, rigid bodies result in a more chemically reasonable structure.
     1517<o:p></o:p></span></p>
    17421518
    17431519<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    17441520
    17451521<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>GSAS-II offers two
    1746 types of rigid bodies. This tutorial will demonstrate use of one type, residue
    1747 rigid bodies, which allow incorporation of optional torsional parameters. The second
    1748 type, vector rigid bodies, offer one or more refinable size parameters, which
    1749 can allow for refinement of selected bond distances or geometrical factors, but
    1750 this is less commonly needed compared to torsions. <o:p></o:p></span></p>
     1522types of rigid bodies. This tutorial will demonstrate use of one type, <i>residue
     1523rigid bodies</i>, which allow incorporation of optional torsional parameters.
     1524The second type, <i>vector rigid bodies</i>, offer one or more refinable size
     1525parameters, which can allow for refinement of selected bond distances or
     1526geometrical factors, but this is less commonly needed, compared to torsions. <o:p></o:p></span></p>
    17511527
    17521528<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    17531529
    17541530<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>In the supplied
    1755 example GSAS-II project file, a powder diffraction dataset is supplied for a sample
    1756 where there are two independent copies of the chiral <a
     1531example GSAS-II project file, a powder diffraction dataset is supplied for a
     1532sample where there are two independent copies of the chiral <a
    17571533href="https://pubchem.ncbi.nlm.nih.gov/compound/676113">R-(+)-Carbidopa
    17581534molecule</a> (shown below) as well as two water molecules in the asymmetric
     
    17931569bonded to them, will lie in a plane, and since bond distances and angles are
    17941570well known for those atoms, there is no reason to give these atoms any degrees
    1795 of freedom in the model used to fit the diffraction data, beyond the orientation
    1796 and position of the group. The positions for the remaining non-H atom can be
    1797 determined with only 4 additional parameters, noting that rotation is possible
    1798 around the four bonds circled below. <o:p></o:p></span></p>
     1571of freedom in the model used to fit the diffraction data, beyond the
     1572orientation and position of the group. The positions for the remaining non-H
     1573atom can be determined with only 4 additional parameters, noting that rotation
     1574is possible around the four bonds circled below. <o:p></o:p></span></p>
    17991575
    18001576<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     
    18051581</v:shape><![endif]--><![if !vml]><img border=0 width=170 height=210
    18061582src="RigidBodyRef.fld/image002.png" v:shapes="Picture_x0020_7"><![endif]></span><span
    1807 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    1808 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    1809 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1583style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    18101584
    18111585<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Thus, all 16
    18121586non-hydrogen atoms can be positioned with 10 parameters: 3 coordinates, 3
    1813 orientation parameters and 4 torsions. Compare this to the 48 positional
    1814 parameters needed for 16 unconstrained atoms. If we had neutron data that would
    1815 allow location of hydrogen atoms, adding 5 more torsions would allow for the
    1816 hydrogen atoms to be positioned as well, where a total of 30 atoms would be
    1817 located from 15 parameters.</span><span lang=HE dir=RTL style='mso-bidi-font-size:
    1818 14.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    1819 mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
    1820 minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1587orientation parameters and 4 torsions. This is almost a five-fold
     1588simplification compared to the 48 positional parameters needed for 16
     1589unconstrained atoms. If we had neutron data that would allow location of
     1590hydrogen atoms, adding 5 more torsions would allow for the hydrogen atoms to be
     1591positioned as well, where a total of 30 atoms would be located from 15
     1592parameters.</span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     1593font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     1594minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     1595mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    18211596
    18221597<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     
    18291604agreement to the observed data, but closer examination shows that the bond
    18301605distances and angles of the two molecular groups are quite irregular. Since
    1831 this distorted structure is not physically reasonable, this model is not acceptable.
    1832 This well-fitting but poor-quality model arises because too many parameters
    1833 were introduced, which is sometimes called overfitting. In this tutorial, a
    1834 better model will be developed using rigid bodies for the two molecules,
    1835 providing a more chemically reasonable representation with fewer parameters -- simply
    1836 a better fit. </span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    1837 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    1838 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1839 mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1606this distorted structure is not physically reasonable, this model is not
     1607acceptable. This well-fitting but poor-quality model arises because too many
     1608parameters were introduced, which is sometimes called overfitting. In this
     1609tutorial, a better model will be developed using rigid bodies for the two
     1610molecules, providing a more chemically reasonable representation with fewer
     1611parameters -- simply a better fit. </span><span lang=HE dir=RTL
     1612style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1613mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1614Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    18401615
    18411616<h2>Step 1. Export Cartesian coordinates for R<span class=GramE>-(</span>+)-Carbidopa
     
    18511626This can be done with low-accuracy forcefield computations or varying levels of
    18521627improved theory. A good tool for simple forcefield minimization is the free
    1853 cross-platform <a href="https://avogadro.cc/">Avogadro program</a>. <o:p></o:p></span></p>
     1628cross-platform <a href="https://avogadro.cc/">Avogadro program</a>. </span><span
     1629lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1630mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1631Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    18541632
    18551633<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     
    18621640<a
    18631641href="https://pubchem.ncbi.nlm.nih.gov/compound/676113#section=Canonical-SMILES">a
    1864 SMILES description</a> of the atomic bonding [C[C@@](CC1=CC(=C(C=C1)O)O)(C(=O)O)NN],
    1865 that description could also be used using the Avogadro Build/Insert/SMILES…
    1866 menu command, but in this step we will use a more general method to input a
    1867 molecular fragment to Avogadro, so that it can be regularized. <o:p></o:p></span></p>
     1642SMILES description</a> of the atomic bonding
     1643[C[C@@](CC1=CC(=C(C=C1)O)O)(C(=O)O)NN], that description could also be used
     1644using the Avogadro Build/Insert/SMILES… menu command, but in this step we will
     1645use a more general method to input a molecular fragment to Avogadro, so that it
     1646can be regularized. <o:p></o:p></span></p>
    18681647
    18691648<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     
    18721651style='mso-bidi-font-size:14.0pt'>For this tutorial, we will export coordinates
    18731652from GSAS-II in a form to be read Avogadro. They will be regularized in the
    1874 next step. </span></i><i><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     1653next step. <o:p></o:p></span></i></p>
     1654
     1655<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    18751656font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    18761657minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1877 mso-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>
     1658mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    18801659
    18811660<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Begin by <u>starting
     
    18951674style='mso-bidi-font-size:14.0pt'>in the sample input. This will read in the
    18961675coordinates for 34 atoms (two carbidopa molecules and two O atoms), from this
    1897 we want to select only one carbidopa molecule. </span><span lang=HE dir=RTL
    1898 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    1899 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    1900 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1676we want to select only one carbidopa molecule. <o:p></o:p></span></p>
    19011677
    19021678<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    19081684</v:shape><![endif]--><![if !vml]><img border=0 width=380 height=245
    19091685src="RigidBodyRef.fld/image003.png" v:shapes="Picture_x0020_1"><![endif]></span><span
    1910 style='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;
    1913 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    1914 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    1915 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    1916 
    1917 <p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
    1918 dir=LTR></span>1C)</span><span class=MsoIntenseEmphasis><span style='font-size:
    1919 16.0pt;mso-bidi-font-size:12.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1920 minor-latin'> </span></span><span style='mso-bidi-font-size:14.0pt'>Unselect
    1921 all atoms by pressing the <u>Toggle All</u> button and then <u>select the first
    1922 sixteen atoms</u> using the “Set Range” button and selecting the first [“0) C”]
    1923 and the sixteenth atom [“15) O3”]. Note that in the plot of the structure, unselected
    1924 atoms appear partially “greyed out” compared to selected atoms. <o:p></o:p></span></p>
     1686lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1687mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1688Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1689
     1690<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     1691
     1692<p class=MsoNormal><span class=MsoIntenseReference>1C)</span><span
     1693class=MsoIntenseEmphasis><span style='font-size:16.0pt;mso-bidi-font-size:12.0pt;
     1694mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> </span></span><span
     1695style='mso-bidi-font-size:14.0pt'>Unselect all atoms by pressing the <u>Toggle
     1696All</u> button and then <u>select the first sixteen atoms</u> using the “Set
     1697Range” button and selecting the first [“0) C”] and the sixteenth atom [“15)
     1698O3”]. Note that in the plot of the structure, unselected atoms appear partially
     1699“greyed out” compared to selected atoms. </span><span lang=HE dir=RTL
     1700style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1701mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1702Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    19251703
    19261704<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    19361714<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Once the 16 atoms
    19371715are selected, <u>press “Continue”</u>. The rigid body then appears in the plot
    1938 window. Note how distorted the molecule appears.</span><span lang=HE dir=RTL
    1939 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    1940 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    1941 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1716window. Note how distorted the molecule appears.<o:p></o:p></span></p>
    19421717
    19431718<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    19581733mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    19591734
    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
    1963 style='mso-bidi-font-size:14.0pt;color:black'> </span></b><span
    1964 style='mso-bidi-font-size:14.0pt'>If these coordinates were satisfactory, the
    1965 rigid body could be created at this point, but since these coordinates are
    1966 distorted, we will regularize them in Avogadro first. Export the coordinates by
    1967 pressing the <u>“export as <span class=SpellE>xyz</span>”</u> button on the
    1968 GSAS-II window.<o:p></o:p></span></p>
     1735<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     1736font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     1737minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     1738mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     1739
     1740<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     1741dir=LTR></span>1D)</span><b><span style='mso-bidi-font-size:14.0pt;color:black'>
     1742</span></b><span style='mso-bidi-font-size:14.0pt'>If these coordinates were
     1743satisfactory, the rigid body could be created at this point, but since these
     1744coordinates are distorted, we will regularize them in Avogadro first. Export
     1745the coordinates by pressing the <u>“export as <span class=SpellE>xyz</span>”</u>
     1746button on the GSAS-II window.<o:p></o:p></span></p>
    19691747
    19701748<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    19801758<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Make a note of the
    19811759file name, as it will be needed in the next step. Press <u>Cancel</u> to close
    1982 this window. It is fine to close GSAS-II, but it can also remain open. </span><span
    1983 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    1984 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    1985 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1760this window. It is fine to close GSAS-II, but it can also remain open. <o:p></o:p></span></p>
    19861761
    19871762<h2>Step 2: Regularize coordinates in Avogadro<span lang=HE dir=RTL
     
    19911766is assumed that the cross-platform software <a href="https://avogadro.cc/">Avogadro
    19921767program</a> has been installed. If you do not want to install this program,
    1993 this step can be skipped, as described at the <a href="#step3">beginning of Step
    1994 3</a>.</span></i><span style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     1768this step can be skipped, as described at the <a href="#step3">beginning of
     1769Step 3</a>.</span></i><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     1770font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     1771minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     1772mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    19951773
    19961774<p class=MsoNormal><b><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></b></p>
     
    19991777style='mso-bidi-font-size:14.0pt'>Read the coordinates into Avogadro by
    20001778starting the program and using the <u>Avogadro File/Open command</u>; select
    2001 the <u>XYZ file type</u> option and <u>read</u> the file produced in step 1D.</span><span
    2002 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2003 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2004 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1779the <u>XYZ file type</u> option and <u>read</u> the file produced in step 1D.<o:p></o:p></span></p>
    20051780
    20061781<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    20121787</v:shape><![endif]--><![if !vml]><img border=0 width=391 height=383
    20131788src="RigidBodyRef.fld/image007.png" v:shapes="Picture_x0020_8"><![endif]></span><span
    2014 style='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;
    2017 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2018 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2019 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2020 
    2021 <p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
    2022 dir=LTR></span>2B)</span><span class=Heading3Char><span style='font-size:15.0pt;
    2023 font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2024 minor-latin'> </span></span><span style='mso-bidi-font-size:14.0pt'>Note that
    2025 the program noted the correct bonding of the carboxylic acid group, where one
    2026 of the C-O bonds is noted as a double bond, but the phenyl group does not have
    2027 alternating double bonds. To fix this, we need to click on the bonds, but that
    2028 is difficult to do unless the atoms are drawn smaller. Make sure that the <u>Display
    2029 Settings</u> button is selected (shown in blue) and click on the <u>wrench
    2030 symbol</u> to bring up the “Ball and Sticks Settings” dialog, below.<o:p></o:p></span></p>
     1789lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1790mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1791Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1792
     1793<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     1794
     1795<p class=MsoNormal><span class=MsoIntenseReference>2B)</span><span
     1796class=Heading3Char><span style='font-size:15.0pt;font-family:"Calibri",sans-serif;
     1797mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> </span></span><span
     1798style='mso-bidi-font-size:14.0pt'>Note that the program noted the correct
     1799bonding of the carboxylic acid group, where one of the C-O bonds is noted as a
     1800double bond, but the phenyl group does not have alternating double bonds. To
     1801fix this, we need to click on the bonds, but that is difficult to do unless the
     1802atoms are drawn smaller. Make sure that the <u>Display Settings</u> button is
     1803selected (at top of window) and click on the <u>wrench symbol</u> to bring up
     1804the “Ball and Sticks Settings” dialog, below.</span><span lang=HE dir=RTL
     1805style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1806mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1807Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    20311808
    20321809<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    20411818
    20421819<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
    2044 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2045 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2046 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1820made smaller by <u>moving</u> the Bond Radius <u>slider to the left</u>, it
     1821becomes possible to click on bonds. <o:p></o:p></span></p>
    20471822
    20481823<p class=MsoNormal><b><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     
    20771852<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Click on directly on
    20781853every other C-C bond in the phenyl ring to <u>change the bonds</u> from single
    2079 to double. Note that when a C-C bond is clicked on, the order changes successively
    2080 from single to double and to triple and then back to single again. (Use care to
    2081 avoid clicking elsewhere than on a bond or additional atoms will be created;
    2082 use a right click to delete unneeded atoms.)</span><span lang=HE dir=RTL
    2083 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1854to double. Note that when a C-C bond is clicked on, the order changes
     1855successively from single to double and to triple and then back to single again.
     1856(Use care to avoid clicking elsewhere than on a bond or additional atoms will
     1857be created; use a right click to delete unneeded atoms.)</span><span lang=HE
     1858dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    20841859mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    20851860Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     
    20931868</v:shape><![endif]--><![if !vml]><img border=0 width=162 height=164
    20941869src="RigidBodyRef.fld/image010.png" v:shapes="Picture_x0020_12"><![endif]></span><span
    2095 style='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;
     1870lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1871mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1872Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1873
     1874<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     1875
     1876<p class=MsoNormal><span class=MsoIntenseReference>2D)</span> <span
     1877style='mso-bidi-font-size:14.0pt'>Use the <u>Build<span class=GramE>/“</span>Add
     1878Hydrogens”</u> menu item to add the remaining H atoms to the other end of the
     1879molecule. </span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    20981880font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    20991881minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2100 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2101 
    2102 <p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
    2103 dir=LTR></span>2D)</span> <span style='mso-bidi-font-size:14.0pt'>Use the <u>Build<span
    2104 class=GramE>/“</span>Add Hydrogens”</u> menu item to add the remaining H atoms
    2105 to the other end of the molecule. </span><span lang=HE dir=RTL
    2106 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2107 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2108 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1882mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    21091883
    21101884<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    21131887 type="#_x0000_t75" style='width:169pt;height:244pt;visibility:visible;
    21141888 mso-wrap-style:square'>
    2115  <v:imagedata src="RigidBodyRef.fld/image020.png" o:title=""/>
     1889 <v:imagedata src="RigidBodyRef.fld/image011.png" o:title=""/>
    21161890</v:shape><![endif]--><![if !vml]><img border=0 width=169 height=244
    2117 src="RigidBodyRef.fld/image020.png" v:shapes="Picture_x0020_13"><![endif]></span><span
    2118 style='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;
    2121 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2122 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2123 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2124 
    2125 <p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
    2126 dir=LTR></span>2E)</span> <span style='mso-bidi-font-size:14.0pt'>Optimize the
    2127 bond distances and angles using <u>Extensions<span class=GramE>/“</span>Optimize
    2128 Geometry”</u>. Use it a few times until no further changes are visible. The
    2129 molecule should appear as below. </span><span lang=HE dir=RTL style='mso-bidi-font-size:
    2130 14.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    2131 mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
    2132 minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1891src="RigidBodyRef.fld/image011.png" v:shapes="Picture_x0020_13"><![endif]></span><span
     1892lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1893mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1894Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1895
     1896<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     1897
     1898<p class=MsoNormal><span class=MsoIntenseReference>2E)</span> <span
     1899style='mso-bidi-font-size:14.0pt'>Optimize the bond distances and angles using <u>Extensions<span
     1900class=GramE>/“</span>Optimize Geometry”</u>. Use it a few times until no
     1901further changes are visible. The molecule should appear as below, with
     1902regularized bond distances and angles. </span><span lang=HE dir=RTL
     1903style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1904mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1905Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    21331906
    21341907<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    21371910 type="#_x0000_t75" style='width:172pt;height:202pt;visibility:visible;
    21381911 mso-wrap-style:square'>
    2139  <v:imagedata src="RigidBodyRef.fld/image022.png" o:title=""/>
     1912 <v:imagedata src="RigidBodyRef.fld/image012.png" o:title=""/>
    21401913</v:shape><![endif]--><![if !vml]><img border=0 width=172 height=202
    2141 src="RigidBodyRef.fld/image022.png" v:shapes="Picture_x0020_14"><![endif]></span><span
    2142 style='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;
    2145 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2146 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2147 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    2148 
    2149 <p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
    2150 dir=LTR></span>2F)</span> <span style='mso-bidi-font-size:14.0pt'>Use <u>“Save
    2151 as”</u> to write the newly generated coordinates out. Be sure to select the
    2152 file type as “<u>XYZ</u>”. I used </span><span style='mso-bidi-font-size:14.0pt;
    2153 mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>name <span
    2154 class=SpellE>regularized.xyz</span> for the file. <u>Exit</u> Avogadro. </span><span
     1914src="RigidBodyRef.fld/image012.png" v:shapes="Picture_x0020_14"><![endif]></span><span
    21551915lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     1916mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     1917Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     1918
     1919<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     1920
     1921<p class=MsoNormal><span class=MsoIntenseReference>2F)</span> <span
     1922style='mso-bidi-font-size:14.0pt'>Use <u>“Save as”</u> to write the newly
     1923generated coordinates out. Be sure to select the file type as “<u>XYZ</u>”. I
     1924used the </span><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     1925Calibri;mso-bidi-theme-font:minor-latin'>name <span class=SpellE>regularized.xyz</span>
     1926for the file. <u>Exit</u> Avogadro. </span><span lang=HE dir=RTL
     1927style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    21561928mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    21571929Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     
    21651937class=SpellE><span style='mso-bookmark:step3'><span style='mso-bidi-font-size:
    2166193814.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>regularized.xyz</span></span></span><span
    2167 style='mso-bookmark:step3'><span lang=HE dir=RTL style='mso-bidi-font-size:
    2168 14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></span></p>
     1939style='mso-bookmark:step3'><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     1940Calibri;mso-bidi-theme-font:minor-latin'> in the</span></span><span
     1941style='mso-bookmark:step3'><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     1942"Times New Roman"'> </span></span><a href="data/" target="_blank"><span
     1943style='mso-bookmark:step3'><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     1944"Times New Roman"'>Exercise files</span></span><span style='mso-bookmark:step3'></span></a><span
     1945style='mso-bookmark:step3'><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     1946"Times New Roman"'>.<o:p></o:p></span></span></p>
     1947
     1948<p class=MsoNormal><span style='mso-bookmark:step3'><span lang=HE dir=RTL
     1949style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1950minor-latin'><o:p>&nbsp;</o:p></span></span></p>
    21691951
    21701952<span style='mso-bookmark:step3'></span>
    21711953
    2172 <p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2173 Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    2174 
    2175 <p class=MsoNormal><span class=MsoIntenseReference>3A)</span> <span
    2176 style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2177 minor-latin'>To start, <u>open</u> the supplied <u>distort1.gpx file</u> in
    2178 GSAS-II. Then we will create a rigid body for this project by clicking on the <u>“Rigid
    2179 bodies”</u> tree item. Click on the <u>“Edit Residue Body”<span class=GramE>/“</span>Extract
    2180 from file”</u> menu item, select the format as <u>XYZ</u> and then select the
    2181 file written in step 2F (<span class=SpellE>regularized.xyz</span>).<span
    2182 lang=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:
    2185 Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     1954<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     1955mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     1956
     1957<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     1958dir=LTR></span>3A)</span> <span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     1959Calibri;mso-bidi-theme-font:minor-latin'>To start, in GSAS-II <u>open</u> the <u>distort1.gpx
     1960file</u> that is supplied in the</span><span style='mso-bidi-font-size:14.0pt;
     1961mso-bidi-font-family:"Times New Roman"'> <a href="data/" target="_blank">Exercise
     1962files</a>. We t</span><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     1963Calibri;mso-bidi-theme-font:minor-latin'>hen will create a rigid body for this
     1964project. Start by clicking on the <u>“Rigid bodies”</u> tree item. Click on the
     1965<u>“Edit Residue Body”<span class=GramE>/“</span>Extract from file”</u> menu
     1966item, select the format as <u>XYZ</u> and then select the file written in step
     19672F (<span class=SpellE>regularized.xyz</span>).<o:p></o:p></span></p>
     1968
     1969<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     1970mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    21861971
    21871972<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     
    21901975minor-latin'>Import XYZ<i>” menu command could also be used, but “</i>Extract
    21911976from file<i>” allows atoms to be selected, recomputes the origin as the
    2192 midpoint between atoms and allows rigid body axes and the origin to be defined based
    2193 on user preferences. With “</i>Import XYZ<i>” the coordinates would be used
    2194 exactly 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:
    2197 Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    2198 
    2199 <p class=MsoNormal><span class=MsoIntenseReference>3B)</span><span
    2200 style='mso-bidi-font-size:14.0pt'> </span><span style='mso-bidi-font-size:14.0pt;
    2201 mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>After the <span
    2202 class=SpellE>regularized.xyz</span> file is opened and read; all atoms are selected
    2203 by default. Note that H atoms are not moved when torsional groups are rotated,
    2204 so we do not want to include any of the non-phenyl H atoms. For simplicity <span
    2205 class=GramE>here</span> we will remove all of the H atoms. (They could be
    2206 regenerated later, if desired). <u>Select only atoms #0-#15</u> (as below) and
    2207 press <u>Continue</u>.<o:p></o:p></span></p>
     1977midpoint between atoms and allows rigid body axes and the origin to be defined
     1978based on user preferences. With “</i>Import XYZ<i>” the coordinates would be
     1979used exactly as in created by Avogadro.<o:p></o:p></i></span></p>
     1980
     1981<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     1982mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     1983
     1984<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     1985dir=LTR></span>3B)</span><span style='mso-bidi-font-size:14.0pt'> </span><span
     1986style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1987minor-latin'>After the <span class=SpellE>regularized.xyz</span> file is opened
     1988and read; all atoms are selected by default. Note that H atoms are not moved
     1989when torsional groups are rotated, so we do not want to include any of the
     1990non-phenyl H atoms. For simplicity, here we will remove all of the H atoms.
     1991(They could be regenerated later, if desired). <u>Select only atoms #0-#15</u>
     1992(as below) and press <u>Continue</u>.<o:p></o:p></span></p>
    22081993
    22091994<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    22121997 id="Picture_x0020_20" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:326pt;
    22131998 height:303pt;visibility:visible;mso-wrap-style:square'>
    2214  <v:imagedata src="RigidBodyRef.fld/image042.png" o:title=""/>
     1999 <v:imagedata src="RigidBodyRef.fld/image013.png" o:title=""/>
    22152000</v:shape><![endif]--><![if !vml]><img border=0 width=326 height=303
    2216 src="RigidBodyRef.fld/image042.png" v:shapes="Picture_x0020_20"><![endif]></span><span
     2001src="RigidBodyRef.fld/image013.png" v:shapes="Picture_x0020_20"><![endif]></span><span
    22172002dir=RTL></span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    22182003mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span dir=RTL></span><span
     
    22202005mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
    22212006
    2222 <p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    2223 mso-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
    2226 dir=LTR></span>3C)</span> <i><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2227 Calibri;mso-bidi-theme-font:minor-latin'>Note that there are several other
    2228 things that can be done on the window that is now created. These include:
    2229 defining axes and reordering the atoms by dragging rows in the list. As an
    2230 example, selecting the atoms in the phenyl ring and pressing “Place in plane”, where
    2231 the adjacent button has “<span class=SpellE>xy</span>” selected, will orient
    2232 the z axis as normal to the plane of the ring. Selecting a single atom and
    2233 pressing “Set origin” will place that atom as the origin, or if two atoms are
    2234 selected the origin will be the midpoint between the two atoms. None of this is
    2235 needed here, but such actions will likely be needed for bodies that will be
    2236 placed at high-symmetry locations in a unit cell. <span lang=HE dir=RTL><o:p></o:p></span></span></i></p>
     2007<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2008Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     2009
     2010<p class=MsoNormal><span class=MsoIntenseReference>3C)</span> <i><span
     2011style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2012minor-latin'>Note that there are several other things that can be done on the
     2013window that is now created. These include: defining axes and reordering the
     2014atoms by dragging rows in the list. As an example, selecting the atoms in the
     2015phenyl ring and pressing “Place in plane”, where the adjacent button has “<span
     2016class=SpellE>xy</span>” selected, will orient the z axis as normal to the plane
     2017of the ring. Selecting a single atom and pressing “Set origin” will place that
     2018atom as the origin, or if two atoms are selected the origin will be the
     2019midpoint between the two atoms. None of this is needed here, but such actions
     2020will likely be needed for bodies that will be placed at high-symmetry locations
     2021in a unit cell. <span lang=HE dir=RTL><o:p></o:p></span></span></i></p>
    22372022
    22382023<p class=MsoNormal><span lang=HE dir=RTL style='font-size:15.0pt;mso-ansi-font-size:
     
    22502035 id="Picture_x0020_21" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:429pt;
    22512036 height:215pt;visibility:visible;mso-wrap-style:square'>
    2252  <v:imagedata src="RigidBodyRef.fld/image046.png" o:title=""/>
     2037 <v:imagedata src="RigidBodyRef.fld/image014.png" o:title=""/>
    22532038</v:shape><![endif]--><![if !vml]><img border=0 width=429 height=215
    2254 src="RigidBodyRef.fld/image046.png" v:shapes="Picture_x0020_21"><![endif]></span><span
     2039src="RigidBodyRef.fld/image014.png" v:shapes="Picture_x0020_21"><![endif]></span><span
    22552040dir=RTL></span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    22562041mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span dir=RTL></span><span
    2257 style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:14.0pt;
    2258 mso-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;
    2261 mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     2042style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
     2043
     2044<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2045Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    22622046
    22632047<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     
    22702054 id="Picture_x0020_22" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:438pt;
    22712055 height:220pt;visibility:visible;mso-wrap-style:square'>
    2272  <v:imagedata src="RigidBodyRef.fld/image047.png" o:title=""/>
     2056 <v:imagedata src="RigidBodyRef.fld/image015.png" o:title=""/>
    22732057</v:shape><![endif]--><![if !vml]><img border=0 width=438 height=220
    2274 src="RigidBodyRef.fld/image047.png" v:shapes="Picture_x0020_22"><![endif]></span><span
    2275 style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2276 minor-latin'><o:p></o:p></span></p>
     2058src="RigidBodyRef.fld/image015.png" v:shapes="Picture_x0020_22"><![endif]></span><span
     2059lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;
     2060mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     2061
     2062<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2063Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    22772064
    22782065<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    22792066mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    22802067
    2281 <p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2282 Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    2283 
    2284 <p class=MsoNormal><span class=MsoIntenseReference>3D) Find atoms in torsions<o:p></o:p></span></p>
     2068<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2069dir=LTR></span>3D) Find atoms in torsions<o:p></o:p></span></p>
    22852070
    22862071<p class=MsoNormal><u><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     
    22882073style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    22892074minor-latin'> to see the rigid body. Note that dragging with the left mouse
    2290 button held down is needed to see all the atom labels, as below.<span lang=HE
    2291 dir=RTL><o:p></o:p></span></span></p>
     2075button held down is needed to see all the atom labels, as below.<o:p></o:p></span></p>
    22922076
    22932077<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    22962080 id="Picture_x0020_23" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:341pt;
    22972081 height:231pt;visibility:visible;mso-wrap-style:square'>
    2298  <v:imagedata src="RigidBodyRef.fld/image048.png" o:title=""/>
     2082 <v:imagedata src="RigidBodyRef.fld/image016.png" o:title=""/>
    22992083</v:shape><![endif]--><![if !vml]><img border=0 width=341 height=231
    2300 src="RigidBodyRef.fld/image048.png" v:shapes="Picture_x0020_23"><![endif]></span><span
     2084src="RigidBodyRef.fld/image016.png" v:shapes="Picture_x0020_23"><![endif]></span><span
    23012085dir=RTL></span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    23022086mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><span dir=RTL></span><span
    2303 style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:14.0pt;
    2304 mso-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;
    2307 mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     2087style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
     2088
     2089<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2090Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    23082091
    23092092<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    23102093Calibri;mso-bidi-theme-font:minor-latin'>From this it can be seen that the four
    2311 bonds 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
     2094bonds with possible torsional rotations are:<span lang=HE dir=RTL><o:p></o:p></span></span></p>
     2095
     2096<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
    23142097style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    23152098minor-latin'><span style='mso-list:Ignore'>a)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     
    2317210014.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>C3-C5, <o:p></o:p></span></p>
    23182101
    2319 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo9'><![if !supportLists]><span
     2102<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
    23202103style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    23212104minor-latin'><span style='mso-list:Ignore'>b)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
     
    2323210614.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>C5-C7, <o:p></o:p></span></p>
    23242107
    2325 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo9'><![if !supportLists]><span
     2108<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
    23262109style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    23272110minor-latin'><span style='mso-list:Ignore'>c)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     
    2329211214.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>C7-N2 and <o:p></o:p></span></p>
    23302113
    2331 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l4 level1 lfo9'><![if !supportLists]><span
     2114<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
    23322115style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    23332116minor-latin'><span style='mso-list:Ignore'>d)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    23342117</span></span></span><![endif]><span dir=LTR></span><span style='mso-bidi-font-size:
    2335 14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>C7-C9. <span
    2336 lang=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:
    2339 Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    2340 
    2341 <p class=MsoNormal><span class=MsoIntenseReference>3E) Define the torsions</span><span
    2342 class=MsoIntenseReference><span lang=HE dir=RTL style='font-size:12.0pt;
    2343 mso-ansi-font-size:14.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:
    2344 Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;
    2345 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></span></p>
     211814.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>C7-C9. <o:p></o:p></span></p>
     2119
     2120<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2121mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
     2122
     2123<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2124dir=LTR></span>3E) Define the torsions<o:p></o:p></span></p>
    23462125
    23472126<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    23482127Calibri;mso-bidi-theme-font:minor-latin'>Press the <u>“Edit Residue Body”<span
    2349 class=GramE>/”Define</span> torsion”</u> menu item. This opens a window to select
    2350 an origin atom. Once that is selected, you are offered a choice of atoms that
    2351 are 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:
    2354 Calibri;mso-bidi-theme-font:minor-latin'>Thus, for the C3-C5 bond, if <u>C3 is
    2355 selected first</u> as the origin atom, the options in the second menu for pivot
    2356 atom are: C1, C5 or C8. <u>Select C5</u>. (Note that if C5 had been selected
    2357 first as origin, then the pivot choices would be C3 and C7.)<o:p></o:p></span></p>
     2128class=GramE>/”Define</span> torsion”</u> menu item. This opens a window to
     2129select an origin atom. Once that is selected, you are offered a choice of atoms
     2130that are bonded to the selected atom. Thus, for the C3-C5 bond, <u>select C3</u>
     2131first to be the origin atom and press OK<span class=GramE>. </span>This will
     2132open a second menu with options for the pivot atom: C1, C5 or C8. <u>Select C5</u>.
     2133(Note that if C5 had been selected first as origin, then the pivot choices
     2134would be C3 and C7.)<o:p></o:p></span></p>
    23582135
    23592136<p class=MsoNormal align=right style='text-align:right'><span style='mso-no-proof:
     
    23632140 type="#_x0000_t75" style='width:133pt;height:140pt;visibility:visible;
    23642141 mso-wrap-style:square'>
    2365  <v:imagedata src="RigidBodyRef.fld/image049.png" o:title=""/>
     2142 <v:imagedata src="RigidBodyRef.fld/image017.png" o:title=""/>
    23662143</v:shape><![endif]--><![if !vml]><img border=0 width=133 height=140
    2367 src="RigidBodyRef.fld/image049.png" v:shapes="Picture_x0020_42"><![endif]></span><span
     2144src="RigidBodyRef.fld/image017.png" v:shapes="Picture_x0020_42"><![endif]></span><span
    23682145style='mso-no-proof:yes'><span style='mso-spacerun:yes'> </span><!--[if gte vml 1]><v:shape
    23692146 id="Picture_x0020_44" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:121pt;
    23702147 height:90pt;visibility:visible;mso-wrap-style:square'>
    2371  <v:imagedata src="RigidBodyRef.fld/image050.png" o:title=""/>
     2148 <v:imagedata src="RigidBodyRef.fld/image018.png" o:title=""/>
    23722149</v:shape><![endif]--><![if !vml]><img border=0 width=121 height=90
    2373 src="RigidBodyRef.fld/image050.png" v:shapes="Picture_x0020_44"><![endif]></span><span
    2374 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;
    2375 mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     2150src="RigidBodyRef.fld/image018.png" v:shapes="Picture_x0020_44"><![endif]></span><span
     2151style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2152minor-latin'><o:p></o:p></span></p>
     2153
     2154<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2155mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    23762156
    23772157<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2378 Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></p>
    2379 
    2380 <p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    2381 Calibri;mso-bidi-theme-font:minor-latin'>After defining C3 and C5 for a
    2382 torsion, 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
    2384 bottom of the window, as shown below:<span lang=HE dir=RTL><o:p></o:p></span></span></p>
     2158Calibri;mso-bidi-theme-font:minor-latin'>After defining the C3-C5 for a
     2159torsion, <u>repeat</u> this to define a total of <u>4 torsions</u>, by adding <u>C5-C7</u>,
     2160<u>C7-N2</u> and <u>C7-C9</u>. The torsions are displayed at the bottom of the
     2161window, as shown below:<o:p></o:p></span></p>
    23852162
    23862163<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    23892166 id="Picture_x0020_24" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:493pt;
    23902167 height:251pt;visibility:visible;mso-wrap-style:square'>
    2391  <v:imagedata src="RigidBodyRef.fld/image051.png" o:title=""/>
     2168 <v:imagedata src="RigidBodyRef.fld/image019.png" o:title=""/>
    23922169</v:shape><![endif]--><![if !vml]><img border=0 width=493 height=251
    2393 src="RigidBodyRef.fld/image051.png" v:shapes="Picture_x0020_24"><![endif]></span><span
    2394 style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2395 minor-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;
    2398 mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></i></p>
     2170src="RigidBodyRef.fld/image019.png" v:shapes="Picture_x0020_24"><![endif]></span><span
     2171lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;
     2172mso-bidi-theme-font:minor-latin'><o:p></o:p></span></p>
     2173
     2174<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     2175Calibri;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></i></p>
    23992176
    24002177<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     
    24062183Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></i></p>
    24072184
    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
    2411 body has been defined, the next step is to insert it into the crystal structure
     2185<h2>Introduction to Steps 4 &amp; 5<span lang=HE dir=RTL style='font-size:13.0pt;
     2186mso-ansi-font-size:16.0pt'><o:p></o:p></span></h2>
     2187
     2188<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Now that the rigid body
     2189has been defined, the next step is to insert it into the crystal structure
    24122190model. This means defining where the rigid body is located, oriented and how it
    24132191is mapped to atoms in the asymmetric unit. The origin of the rigid body
    24142192Cartesian system is placed at a specified location (in fractional coordinates)
    24152193and a quaternion defines the rigid body orientation. The same rigid body may be
    2416 used multiple times in the asymmetric unit. There will need to be a set of
    2417 atoms, an origin, a quaternion for each insertion of each body. There will also
    2418 be a set of torsion values angle values associated with each body use. <o:p></o:p></span></p>
     2194inserted multiple times in the asymmetric unit. Each insertion of each body will
     2195have a corresponding set of atoms in the asymmetric unit, an origin, a
     2196quaternion for orientation. There will also be a set of torsion angle values
     2197associated with each body insertion.<o:p></o:p></span></p>
    24192198
    24202199<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    24212200
    24222201<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Note that
    2423 understanding GSAS-II’s 3D visualization can be key to managing rigid bodies.
    2424 It is valuable to move and rotate the representation, so that distances along
    2425 all axes can be visualized. For this it is valuable to understand that as the
    2426 structure is viewed, movement of the mouse while holding down a button (also
    2427 called dragging) changes the view of the crystal structure, as described here):</span><span
    2428 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2429 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2430 Calibri;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>
     2202understanding GSAS-II’s 3D visualization system is key to managing rigid
     2203bodies. It is valuable to move and rotate the representation, so that distances
     2204along all axes can be visualized. For this it is valuable to understand that as
     2205the structure is viewed, movement of the mouse while holding down a button
     2206(also called dragging) changes the view of the crystal structure, as described
     2207here:<o:p></o:p></span></p>
     2208
     2209<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2210font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2211minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     2212mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    24332213
    24342214<p class=MsoListParagraphCxSpFirst style='margin-left:.75in;mso-add-space:auto;
    2435 text-indent:-.25in;mso-list:l1 level1 lfo3'><![if !supportLists]><span
     2215text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    24362216style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
    24372217Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
     
    24392219dir=LTR></span><span style='mso-bidi-font-size:14.0pt'>Dragging with the right
    24402220button down: moves the viewpoint, which is kept at the center of the screen
    2441 (effectively translating the structure)</span><span lang=HE dir=RTL
    2442 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2443 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2444 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2221(effectively translating the structure).<o:p></o:p></span></p>
    24452222
    24462223<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    2447 auto;text-indent:-.25in;mso-list:l1 level1 lfo3'><![if !supportLists]><span
     2224auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    24482225style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
    24492226Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
     
    24512228dir=LTR></span><span style='mso-bidi-font-size:14.0pt'>Dragging with the left
    24522229button down: rotates axes around screen x &amp; y. Rotation is around the
    2453 viewpoint<o:p></o:p></span></p>
     2230viewpoint.</span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2231font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2232minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     2233mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    24542234
    24552235<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    2456 auto;text-indent:-.25in;mso-list:l1 level1 lfo3'><![if !supportLists]><span
     2236auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    24572237style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
    24582238Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
    24592239style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    24602240dir=LTR></span><span style='mso-bidi-font-size:14.0pt'>Dragging with the center
    2461 button down: rotates axes around screen z</span><span lang=HE dir=RTL
    2462 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2463 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2464 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2241button down: rotates axes around screen z.<o:p></o:p></span></p>
    24652242
    24662243<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto;
    2467 text-indent:-.25in;mso-list:l1 level1 lfo3'><![if !supportLists]><span
     2244text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    24682245style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
    24692246Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
    24702247style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    24712248dir=LTR></span><span style='mso-bidi-font-size:14.0pt'>Rotating the scroll
    2472 wheel: changes “camera position” (zoom in/out)</span><span lang=HE dir=RTL
     2249wheel: changes “camera position” (zoom in/out).</span><span lang=HE dir=RTL
    24732250style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    24742251mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    24752252Calibri;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:
    2480 14.0pt'>Note that the screen axes are x: horizontal, y: vertical and z: out of
    2481 screen. Also, additional plot controls are available by pressing on the “Draw
    2482 Options” tab. </span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    2483 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2484 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2485 mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    24862253
    24872254<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     
    24902257mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    24912258
     2259<p class=MsoNormal style='margin-left:.5in'><span style='mso-bidi-font-size:
     226014.0pt'>Note that the screen axes are x: horizontal; y: vertical; and z: out of
     2261screen. Also, there are additional plot controls available by pressing on the
     2262“Draw Options” tab. <o:p></o:p></span></p>
     2263
     2264<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2265font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2266minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     2267mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     2268
    24922269<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>When inserting a
    2493 rigid body into a unit cell, as described in the next section, the rigid body can
    2494 be is being located into the unit cell, a second set of actions can be accessed
    2495 with the mouse that affect the rigid body only. This is done by holding the Alt
    2496 keyboard key down while “dragging” the mouse. <o:p></o:p></span></p>
     2270rigid body into a unit cell, as described in the next section, as the rigid
     2271body is being located into the unit cell, a second set of actions can be
     2272accessed with the mouse that affect the rigid body positioning. This is done by
     2273holding the Alt keyboard key down while “dragging” the mouse. </span><span
     2274lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2275mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2276Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    24972277
    24982278<p class=MsoListParagraphCxSpFirst style='margin-left:.75in;mso-add-space:auto;
    2499 text-indent:-.25in;mso-list:l8 level1 lfo4'><![if !supportLists]><span
     2279text-indent:-.25in;mso-list:l4 level1 lfo6'><![if !supportLists]><span
    25002280style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
    25012281Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
    25022282style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    25032283dir=LTR></span><span class=SpellE><span style='mso-bidi-font-size:14.0pt'>Alt+right</span></span><span
    2504 style='mso-bidi-font-size:14.0pt'> mouse dragging changes the rigid body
    2505 origin, <o:p></o:p></span></p>
     2284style='mso-bidi-font-size:14.0pt'> mouse dragging moves the rigid body by shifting
     2285the origin.<o:p></o:p></span></p>
    25062286
    25072287<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    2508 auto;text-indent:-.25in;mso-list:l8 level1 lfo4'><![if !supportLists]><span
     2288auto;text-indent:-.25in;mso-list:l4 level1 lfo6'><![if !supportLists]><span
    25092289style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
    25102290Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
     
    25152295
    25162296<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    2517 auto;text-indent:-.25in;mso-list:l8 level1 lfo4'><![if !supportLists]><span
     2297auto;text-indent:-.25in;mso-list:l4 level1 lfo6'><![if !supportLists]><span
    25182298style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
    25192299Symbol;mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>·<span
    25202300style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    25212301dir=LTR></span><span class=SpellE><span style='mso-bidi-font-size:14.0pt'>Alt+left</span></span><span
    2522 style='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>
     2302style='mso-bidi-font-size:14.0pt'> button dragging rotates the body around the
     2303x &amp; y screen axes. <o:p></o:p></span></p>
    25242304
    25252305<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto'><span
     
    25362316molecules are already found. There are two ways to do this. One is that if
    25372317specified atoms in the rigid body are paired to atoms in the crystal, the
    2538 origin and/or quaternion can be optimized to best collocate the pairs of atoms.
    2539 This will be shown in Step 4. Another choice is to visually move the rigid body
    2540 to the desired location, which will be shown in Step 5. That process might be
    2541 needed to insert a molecule into a region of a Fourier map.</span></i><span
     2318origin and/or quaternion can be optimized to best collocate those pairs of
     2319atoms. This will be shown in Step 4. Another choice is to visually move the
     2320rigid body to the desired location, which will be shown in Step 5. That process
     2321might be needed to insert a molecule into a specific region of a structure to
     2322fill a void or to account for density in a Fourier map.</span></i><span
    25422323style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    25432324
     
    25452326
    25462327<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt'>In this step we
    2547 will assign pairs of atoms that match between the rigid body and the crystal asymmetric
    2548 unit and have the best rigid body location be computed. </span></i><i><span
    2549 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2550 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2551 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></i></p>
     2328will assign matching pairs of atoms between the rigid body and the crystal
     2329asymmetric unit and use them to determine the rigid body location. <o:p></o:p></span></i></p>
    25522330
    25532331<p class=MsoNormal><b><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     
    25572335
    25582336<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
    2559 dir=LTR></span>4A) </span><span style='mso-bidi-font-size:14.0pt'>To insert a
    2560 rigid body into a structure, select the desired phase in the data tree (here
    2561 there 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
    2563 to select which body would be offered. A window is displayed with options to
    2564 define where the rigid body will be placed, as below. </span><span lang=HE
    2565 dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2337dir=LTR></span>4A) </span><span style='mso-bidi-font-size:14.0pt'>To start the
     2338process of inserting a rigid body into a structure, select the desired phase in
     2339the data tree (here there is only one choice) and then select the <u>“Edit
     2340Body”<span class=GramE>/“</span>Locate &amp; Insert Rigid Body”</u> menu item.
     2341If more than one body were defined, a window to select which body would be
     2342offered. A <span class=SpellE>farily</span> complex window is displayed with
     2343options to define where the rigid body will be placed, as below. </span><span
     2344lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    25662345mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    25672346Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     
    25712350 o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;height:313pt;
    25722351 visibility:visible;mso-wrap-style:square'>
    2573  <v:imagedata src="RigidBodyRef.fld/image052.png" o:title=""/>
     2352 <v:imagedata src="RigidBodyRef.fld/image020.png" o:title=""/>
    25742353</v:shape><![endif]--><![if !vml]><img border=0 width=468 height=313
    2575 src="RigidBodyRef.fld/image052.png" v:shapes="Picture_x0020_46"><![endif]></span><span
    2576 style='mso-bidi-font-size:14.0pt'><span style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
     2354src="RigidBodyRef.fld/image020.png" v:shapes="Picture_x0020_46"><![endif]></span><span
     2355style='mso-bidi-font-size:14.0pt'><span style='mso-spacerun:yes'> </span></span><span
     2356lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2357mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2358Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    25772359
    25782360<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     
    25802362<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Also shown in the
    25812363GSAS-II graphics window is a plot of the structure, along with the rigid body
    2582 location. Note that by default the asymmetric unit is shown with van der Waals
    2583 spheres. The rigid body is displayed as a ball-and-stick model with green
    2584 bonds. Note that the origin of the rigid body is shown with a triplet of red,
    2585 green and blue lines (for x, y, &amp; z, respectively) as well as a white line
    2586 that 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;
    2589 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2590 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2591 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     2364location. The structure will be plotted as was set in the Draw Atoms tab. Note
     2365that here, by default, the asymmetric unit is shown with van der Waals spheres.
     2366The rigid body is always displayed as a ball-and-stick model with green bonds.
     2367Note that the origin of the rigid body is shown with a triplet of red, green
     2368and blue lines (for x, y, &amp; z, respectively). A white line is also shown that
     2369displays the orientation vector. The red, green and blue lines (for x, y, &amp;
     2370z, respectively) of the unit cell outline show the origin and axes of the
     2371crystal. The same color sequence <span class=GramE>show</span> these axes on the
     2372viewpoint. <o:p></o:p></span></p>
    25922373
    25932374<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     
    25952376 o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt;height:220pt;
    25962377 visibility:visible;mso-wrap-style:square'>
    2597  <v:imagedata src="RigidBodyRef.fld/image053.png" o:title=""/>
     2378 <v:imagedata src="RigidBodyRef.fld/image021.png" o:title=""/>
    25982379</v:shape><![endif]--><![if !vml]><img border=0 width=468 height=220
    2599 src="RigidBodyRef.fld/image053.png" v:shapes="Picture_x0020_47"><![endif]></span><span
     2380src="RigidBodyRef.fld/image021.png" v:shapes="Picture_x0020_47"><![endif]></span><span
    26002381lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    26012382mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    26022383Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2384
     2385<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    26032386
    26042387<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Change the crystal
     
    26112394minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    26122395
    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
    2616 table at the lower part of the window shows each atom in the rigid body and the
    2617 closest atom in the crystal structure and the distance to that atom. In the
    2618 column labeled as “Assign as atom” to the extreme right of the table, we can assign
    2619 specific pairing between atoms in the rigid body and atoms in the crystal
    2620 structure that will override the closest atom pairing. Scrolling or expanding
    2621 the window so the entire table is visible will make subsequent steps easier (as
    2622 seen below). As the rigid body is moved, the distances will be updated. The
    2623 closest 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
    2628 style='mso-bidi-font-size:14.0pt'>We will align the rigid body to the molecule
    2629 in the cell closest to the upper right corner by assigning rigid body atoms to
    2630 the matching atoms in the unit cell. </span><span lang=HE dir=RTL
    2631 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2632 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2633 Calibri;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
    2638 the 2<sup>nd</sup> row</u> in the table (with row label “C2”), the row is
    2639 highlighted </span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    2640 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2641 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2642 mso-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
    2645 lang=HE style='mso-no-proof:yes'><span dir=LTR></span><span
    2646 style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:14.0pt;
    2647 mso-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
    2651 src="RigidBodyRef.fld/image054.png" v:shapes="_x0000_i1046"><![endif]></span><span
    2652 style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    2653 
    26542396<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    26552397font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     
    26572399mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    26582400
     2401<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt'>Note that the
     2402table at the lower part of the window (as seen below) shows each atom in the
     2403rigid body and the closest atom in the crystal structure as well as the
     2404distance to that atom. In the column labeled as “Assign as atom” to the extreme
     2405right of the table, we can assign specific pairing between atoms in the rigid
     2406body and atoms in the crystal structure that will override the closest atom
     2407pairing. As the rigid body is moved, the distances will be updated. Unless <span
     2408class=SpellE>a</span> pairing assignment has been made, the closest atom pairing
     2409may change as the body moves. <o:p></o:p></span></i></p>
     2410
     2411<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2412
     2413<p class=MsoNormal><span class=MsoIntenseReference>4B) </span><span
     2414style='mso-bidi-font-size:14.0pt'>We will align the rigid body to the molecule
     2415in the cell closest to the upper right corner by assigning rigid body atoms to
     2416the matching atoms in the unit cell. <i>Scrolling or expanding the window so
     2417the entire table is visible will make subsequent steps easier </i><o:p></o:p></span></p>
     2418
     2419<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2420font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2421minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     2422mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     2423
     2424<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>If we <u>click on
     2425the 2<sup>nd</sup> row</u> in the table (with row label “C2”), the row is
     2426highlighted. <o:p></o:p></span></p>
     2427
     2428<p class=MsoNormal align=right style='text-align:right'><span style='mso-no-proof:
     2429yes'><span style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:
     243014.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_61"
     2431 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:412pt;height:230pt;
     2432 visibility:visible;mso-wrap-style:square'>
     2433 <v:imagedata src="RigidBodyRef.fld/image022.png" o:title=""/>
     2434</v:shape><![endif]--><![if !vml]><img border=0 width=412 height=230
     2435src="RigidBodyRef.fld/image022.png" v:shapes="Picture_x0020_61"><![endif]></span><span
     2436lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2437mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2438Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2439
     2440<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2441
    26592442<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Note that atom C2 in
    2660 the rigid body is highlighted by the ball color changing to green, as well as
    2661 its matching atom in the crystal structure (C6), as shown below. </span><span
     2443the rigid body is highlighted by the ball color changing to green, as well as its
     2444paired atom in the crystal structure (C6), as shown below. </span><span
    26622445lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    26632446mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     
    26692452 type="#_x0000_t75" style='width:391pt;height:154pt;visibility:visible;
    26702453 mso-wrap-style:square'>
    2671  <v:imagedata src="RigidBodyRef.fld/image055.png" o:title=""/>
     2454 <v:imagedata src="RigidBodyRef.fld/image023.png" o:title=""/>
    26722455</v:shape><![endif]--><![if !vml]><img border=0 width=391 height=154
    2673 src="RigidBodyRef.fld/image055.png" v:shapes="Picture_x0020_29"><![endif]></span><span
    2674 style='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;
    2677 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    2678 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2679 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     2456src="RigidBodyRef.fld/image023.png" v:shapes="Picture_x0020_29"><![endif]></span><span
     2457lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2458mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2459Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2460
     2461<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    26802462
    26812463<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>The crystal
     
    26892471Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    26902472
    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
    2694 style='mso-bidi-font-size:14.0pt'>C11 in the crystal structure to be paired to
    2695 C2 by clicking in the <u>right-most box </u>in the C2 row of the table and <u>selecting
    2696 atom 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:
    2699 14.0pt;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;
    2701  visibility:visible;mso-wrap-style:square'>
    2702  <v:imagedata src="RigidBodyRef.fld/image056.png" o:title=""/>
    2703 </v:shape><![endif]--><![if !vml]><img border=0 width=329 height=166
    2704 src="RigidBodyRef.fld/image056.png" v:shapes="Picture_x0020_50"><![endif]></span><span
    2705 style='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
    2709 shown in the table. Likewise, pressing “Set Origin” will translate the rigid
    2710 body to best match the assigned atoms. Since there is only one assigned atom,
    2711 the distance will be zero. </span><span lang=HE dir=RTL style='mso-bidi-font-size:
    2712 14.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    2713 mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
    2714 minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    2715 
    2716 <p class=MsoNormal><span dir=LTR></span><span lang=HE style='mso-no-proof:yes'><span
    2717 dir=LTR></span><span style='mso-spacerun:yes'> </span></span><span
    2718 style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    2719 
    27202473<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    27212474font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     
    27242477
    27252478<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
    2726 dir=LTR></span>4D)</span> <span style='mso-bidi-font-size:14.0pt'>Setting the
    2727 orientation and origin requires assignment of at least two more atoms and
    2728 preferably more. Select another easy to identify an atom in the rigid body by <u>click</u>ing
    2729 on the <u>C4 row</u> in the table. (Alternately, press Alt-Tab to highlight
    2730 different rigid body atoms.) Using Tab, it can be seen that crystal structure
    2731 atom C13 should be paired. <u>Select atom C13</u> in the “Assign as atom” cell
    2732 for C4.</span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    2733 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2479dir=LTR></span>4C)</span> Assign <span style='mso-bidi-font-size:14.0pt'>C11 in
     2480the crystal structure to be paired to C2 by clicking in the <u>right-most box </u>in
     2481the C2 row of the table and <u>selecting atom C11</u> from the dropdown list,
     2482as seen below. <o:p></o:p></span></p>
     2483
     2484<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     248514.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_66"
     2486 o:spid="_x0000_i1044" type="#_x0000_t75" style='width:339pt;height:171pt;
     2487 visibility:visible;mso-wrap-style:square'>
     2488 <v:imagedata src="RigidBodyRef.fld/image024.png" o:title=""/>
     2489</v:shape><![endif]--><![if !vml]><img border=0 width=339 height=171
     2490src="RigidBodyRef.fld/image024.png" v:shapes="Picture_x0020_66"><![endif]></span><span
     2491style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2492
     2493<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     249414.0pt'><o:p>&nbsp;</o:p></span></p>
     2495
     2496<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Optional: press “Update
     2497Assignments” button and the distance between RB C2 and unit cell C11 will be
     2498shown in the table. Likewise, pressing “Set Origin” will translate the rigid
     2499body to best match the assigned atoms. Since there is only one assigned atom,
     2500the distance will be zero. <o:p></o:p></span></p>
     2501
     2502<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2503
     2504<p class=MsoNormal><span class=MsoIntenseReference>4D)</span> <span
     2505style='mso-bidi-font-size:14.0pt'>Setting the orientation and origin requires
     2506assignment of at least two more atoms and preferably more. Select another easy
     2507to identify an atom in the rigid body by <u>click</u>ing on the <u>C4 row</u> in
     2508the table. (Alternately, press Alt-Tab to highlight different rigid body
     2509atoms.) Using Tab, it can be seen that crystal structure atom C13 should be
     2510paired to RB atoms C4. <u>Select atom C13</u> in the “Assign as atom” cell for
     2511C4.</span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:
     2512"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    27342513minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    27352514mso-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
    2740 atom C5 should be assigned to crystal structure atom C14 by <u>selecting atom
    2741 C14</u> in the “Assign as atom” cell for C5.</span><span lang=HE dir=RTL
    2742 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2743 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2744 Calibri;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
    2749 style='mso-bidi-font-size:14.0pt'>Then <u>press</u> the <u>“Set Both”</u>
    2750 button and the phenyl ring positions are approximately matched, as below. </span><span
    2751 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2752 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2753 Calibri;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:
    2756 14.0pt;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
    2761 src="RigidBodyRef.fld/image057.png" v:shapes="Picture_x0020_32"><![endif]></span><span
    2762 style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    27632515
    27642516<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     
    27672519mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    27682520
    2769 <p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
    2770 dir=LTR></span>4F)</span> <span style='mso-bidi-font-size:14.0pt'>The agreement
    2771 in atom positions at the other end of the molecule is still not very good, but
    2772 this can be improved by <b>repositioning the view</b> (dragging with the left
    2773 mouse button) to look approximately along the plane of the ring. When this is
    2774 done, it becomes clear that the agreement can be improved significantly by
    2775 rotating around the <u>first torsion</u> angle by <u>moving the slider</u>. An
    2776 angle of ~23 degrees brings the atoms much closer, but there are still atoms as
    2777 much as 1 Å in disagreement, since the crystal structure molecule is rather
    2778 distorted. </span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2521<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Likewise, rigid body
     2522atom C5 should be assigned to crystal structure atom C14 by <u>selecting atom
     2523C14</u> in the “Assign as atom” cell for C5.<o:p></o:p></span></p>
     2524
     2525<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    27792526font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    27802527minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    2781 mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2528mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     2529
     2530<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2531dir=LTR></span>4E)</span> <span style='mso-bidi-font-size:14.0pt'>Then <u>press</u>
     2532the <u>“Set Both”</u> button and the phenyl ring positions are approximately
     2533matched, as below. <o:p></o:p></span></p>
     2534
     2535<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     253614.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1043" type="#_x0000_t75"
     2537 style='width:468pt;height:189pt;visibility:visible;mso-wrap-style:square'>
     2538 <v:imagedata src="RigidBodyRef.fld/image025.png" o:title=""/>
     2539</v:shape><![endif]--><![if !vml]><img border=0 width=468 height=189
     2540src="RigidBodyRef.fld/image025.png" v:shapes="_x0000_i1043"><![endif]></span><span
     2541lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2542mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2543Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2544
     2545<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2546
     2547<p class=MsoNormal><span class=MsoIntenseReference>4F)</span> <span
     2548style='mso-bidi-font-size:14.0pt'>The agreement in atom positions at the other
     2549end of the molecule is still not very good, and this can be improved by <b>repositioning
     2550the view</b> (dragging with the left mouse button) to look approximately along
     2551the plane of the ring. When this is done, it becomes clear that the agreement
     2552can be improved significantly by rotating around the <u>first torsion</u> angle
     2553by <u>moving the slider</u>. An angle of ~23 degrees brings the atoms much
     2554closer, but there are still atoms as much as 1 Å in disagreement, since the molecule
     2555in the crystal structure is rather distorted. </span><span lang=HE dir=RTL
     2556style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2557mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2558Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    27822559
    27832560<p class=MsoNormal align=right style='text-align:right'><span dir=LTR></span><span
     
    27862563 id="Picture_x0020_33" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:225pt;
    27872564 height:181pt;visibility:visible;mso-wrap-style:square'>
    2788  <v:imagedata src="RigidBodyRef.fld/image058.png" o:title="" croptop="7159f"
     2565 <v:imagedata src="RigidBodyRef.fld/image026.png" o:title="" croptop="7159f"
    27892566  cropright="6357f"/>
    27902567</v:shape><![endif]--><![if !vml]><img border=0 width=225 height=181
    2791 src="RigidBodyRef.fld/image012.png" v:shapes="Picture_x0020_33"><![endif]></span><span
     2568src="RigidBodyRef.fld/image027.png" v:shapes="Picture_x0020_33"><![endif]></span><span
    27922569style='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=""/>
     2570 id="_x0000_i1041" type="#_x0000_t75" style='width:212pt;height:181pt;
     2571 visibility:visible;mso-wrap-style:square'>
     2572 <v:imagedata src="RigidBodyRef.fld/image028.png" o:title=""/>
    27962573</v:shape><![endif]--><![if !vml]><img border=0 width=212 height=181
    2797 src="RigidBodyRef.fld/image060.png" v:shapes="Picture_x0020_34"><![endif]></span><o:p></o:p></span></p>
     2574src="RigidBodyRef.fld/image028.png" v:shapes="_x0000_i1041"><![endif]></span></span><span
     2575lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2576mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2577Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    27982578
    27992579<p class=MsoNormal align=right style='text-align:right'><span lang=HE
    28002580style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
    2801 HE;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=""/>
     2581HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1040" type="#_x0000_t75"
     2582 style='width:230pt;height:215pt;visibility:visible;mso-wrap-style:square'>
     2583 <v:imagedata src="RigidBodyRef.fld/image029.png" o:title=""/>
    28052584</v:shape><![endif]--><![if !vml]><img border=0 width=230 height=215
    2806 src="RigidBodyRef.fld/image061.png" v:shapes="Picture_x0020_36"><![endif]></span><span
    2807 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2808 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2809 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2585src="RigidBodyRef.fld/image029.png" v:shapes="_x0000_i1040"><![endif]></span><span
     2586style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    28102587
    28112588<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     
    28162593<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
    28172594dir=LTR></span>4G)</span> <span style='mso-bidi-font-size:14.0pt'>Note that the
    2818 table now shows that the rigid body has crystal structure atoms 16-31 paired consecutively,
    2819 which is to be expected since the atom order was never changed.<span
    2820 style='mso-spacerun:yes'>  </span><u>Press Add</u> to define these atoms from
    2821 the rigid body parameters shown in the window. A warning is displayed, since
    2822 some of the distances are larger than 0.5 Å, but <u>press Yes</u> since this is
    2823 about as good as we can do.</span><span lang=HE dir=RTL style='mso-bidi-font-size:
    2824 14.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    2825 mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
    2826 minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2595table now shows that the rigid body has crystal structure atoms 16-31 paired.
     2596The pairing is consecutive, which is to be expected since the ordering of atoms
     2597was never changed, but this is not required.<span style='mso-spacerun:yes'> 
     2598</span><u>Press Add</u> to insert the rigid body, using the parameters shown in
     2599the window. A warning is displayed, since some of the distances are larger than
     26000.5 Å, but <u>press Yes</u> since this is about as good as we can do.</span><span
     2601lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2602mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2603Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    28272604
    28282605<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    28312608 type="#_x0000_t75" style='width:262pt;height:95pt;visibility:visible;
    28322609 mso-wrap-style:square'>
    2833  <v:imagedata src="RigidBodyRef.fld/image062.png" o:title=""/>
     2610 <v:imagedata src="RigidBodyRef.fld/image030.png" o:title=""/>
    28342611</v:shape><![endif]--><![if !vml]><img border=0 width=262 height=95
    2835 src="RigidBodyRef.fld/image062.png" v:shapes="Picture_x0020_37"><![endif]></span><span
    2836 style='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
     2612src="RigidBodyRef.fld/image030.png" v:shapes="Picture_x0020_37"><![endif]></span><span
     2613lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2614mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2615Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2616
     2617<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2618
     2619<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Pressing Add causes any
    28392620unpaired (shown as “create new”) to be added to the Atoms list and then every
    2840 atom in the rigid body is linked to an atom in the asymmetric unit. <span
    2841 style='mso-spacerun:yes'> </span>The rigid-body constrained atoms are now shown
    2842 with bonds in orange (unless “Show Rigid Bodies” is unchecked on the “Draw
    2843 Options” tab.) The atom coordinates are shown with a grey background on the
    2844 Atoms tab. Press the c key (with the graphics window active) to see the view
    2845 below.<o:p></o:p></span></p>
     2621atom in the rigid body is linked to an atom in the asymmetric unit.<span
     2622style='mso-spacerun:yes'>  </span>The rigid-body constrained atoms are now
     2623shown with bonds in orange (unless “Show Rigid Bodies” is unchecked on the
     2624“Draw Options” tab.) The atom coordinates are shown with a grey background on
     2625the Atoms tab. Press the c key (with the graphics window active) to see the
     2626view below.<o:p></o:p></span></p>
    28462627
    28472628<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     
    28502631 type="#_x0000_t75" style='width:322pt;height:113pt;visibility:visible;
    28512632 mso-wrap-style:square'>
    2852  <v:imagedata src="RigidBodyRef.fld/image063.png" o:title=""/>
     2633 <v:imagedata src="RigidBodyRef.fld/image031.png" o:title=""/>
    28532634</v:shape><![endif]--><![if !vml]><img border=0 width=322 height=113
    2854 src="RigidBodyRef.fld/image063.png" v:shapes="Picture_x0020_38"><![endif]></span><span
    2855 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2856 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2857 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2635src="RigidBodyRef.fld/image031.png" v:shapes="Picture_x0020_38"><![endif]></span><span
     2636style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    28582637
    28592638<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     
    28682647the introduction to steps 4 &amp; 5, above, holding a mouse button down (mouse
    28692648dragging) changes the view of the crystal while holding Alt down while dragging
    2870 the mouse, moves the rigid body within the cell. In this step, to show how that
    2871 works, we will use the mouse to place the rigid body. <o:p></o:p></span></i></p>
     2649the mouse, repositions the rigid body within the cell. In this step, to show
     2650how that works, we will use the mouse to place the rigid body. </span></i><i><span
     2651lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2652mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2653Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></i></p>
    28722654
    28732655<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     
    28772659again to match the second copy of the molecule, again select the <u>“Edit Body”<span
    28782660class=GramE>/“</span>Locate &amp; Insert Rigid Body”</u> menu item. A window is
    2879 displayed as before with options to define where the rigid body will be placed
    2880 and the graphical display will look like this:<o:p></o:p></span></p>
     2661displayed as before with options to define where the rigid body will be placed.
     2662The graphical display will look like this:<o:p></o:p></span></p>
    28812663
    28822664<p class=MsoNormal align=right style='text-align:right'><b><span
     
    28842666 id="Picture_x0020_51" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:357pt;
    28852667 height:154pt;visibility:visible;mso-wrap-style:square'>
    2886  <v:imagedata src="RigidBodyRef.fld/image064.png" o:title=""/>
     2668 <v:imagedata src="RigidBodyRef.fld/image032.png" o:title=""/>
    28872669</v:shape><![endif]--><![if !vml]><img border=0 width=357 height=154
    2888 src="RigidBodyRef.fld/image064.png" v:shapes="Picture_x0020_51"><![endif]></span></b><b><span
    2889 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2890 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2891 Calibri;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
    2896 style='mso-bidi-font-size:14.0pt'>Hold the <u>Alt key down</u> and <u>drag</u>
    2897 with the <u>middle mouse</u> button to rotate the rigid body by 180 degrees, as
    2898 shown below.<span style='mso-no-proof:yes'> <o:p></o:p></span></span></p>
     2670src="RigidBodyRef.fld/image032.png" v:shapes="Picture_x0020_51"><![endif]></span></b><b><span
     2671style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></b></p>
     2672
     2673<p class=MsoNormal><b><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2674font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     2675minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     2676mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></b></p>
     2677
     2678<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2679dir=LTR></span>5B)</span> <span style='mso-bidi-font-size:14.0pt'>Hold the <u>Alt
     2680key down</u> and <u>drag</u> with the <u>middle mouse</u> button to rotate the
     2681rigid body by 180 degrees, as shown below.<span style='mso-no-proof:yes'> <o:p></o:p></span></span></p>
    28992682
    29002683<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
    2901 14.0pt;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
    2905 src="RigidBodyRef.fld/image065.png" v:shapes="_x0000_i1036"><![endif]><span
    2906 style='mso-spacerun:yes'> </span></span><span lang=HE dir=RTL style='mso-bidi-font-size:
     268414.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
     2685 o:spid="_x0000_i1036" type="#_x0000_t75" style='width:330pt;height:136pt;
     2686 visibility:visible;mso-wrap-style:square'>
     2687 <v:imagedata src="RigidBodyRef.fld/image033.png" o:title=""/>
     2688</v:shape><![endif]--><![if !vml]><img border=0 width=330 height=136
     2689src="RigidBodyRef.fld/image033.png" v:shapes="Picture_x0020_32"><![endif]><span
     2690style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2691
     2692<p class=MsoNormal align=right style='text-align:right'><span lang=HE dir=RTL
     2693style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2694mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2695Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     2696
     2697<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2698
     2699<p class=MsoNormal><span class=MsoIntenseReference>5C)</span> Again w<span
     2700style='mso-bidi-font-size:14.0pt'>ith the <u>Alt key down</u>, <u>drag</u> with
     2701the <u>right mouse</u> button and move the rigid body so that the phenyl rings
     2702are more or less aligned.</span><span lang=HE dir=RTL style='mso-bidi-font-size:
    2907270314.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    29082704mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
     
    29102706
    29112707<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
    2912 14.0pt'><o:p>&nbsp;</o:p></span></p>
     270814.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_53"
     2709 o:spid="_x0000_i1035" type="#_x0000_t75" style='width:354pt;height:155pt;
     2710 visibility:visible;mso-wrap-style:square'>
     2711 <v:imagedata src="RigidBodyRef.fld/image034.png" o:title=""/>
     2712</v:shape><![endif]--><![if !vml]><img border=0 width=354 height=155
     2713src="RigidBodyRef.fld/image034.png" v:shapes="Picture_x0020_53"><![endif]></span><span
     2714style='mso-bidi-font-size:14.0pt'><span style='mso-spacerun:yes'> </span></span><span
     2715lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2716mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2717Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2718
     2719<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2720
     2721<p class=MsoNormal><span class=MsoIntenseReference>5D)</span> <span
     2722style='mso-bidi-font-size:14.0pt'>To see how far the rings are separated in the
     2723screen z direction, we must rotate the view. <u>Drag</u> the mouse <u>upwards</u>
     2724with the <u>left button</u> down (without pressing Alt) to obtain a view
     2725similar to the one below.<o:p></o:p></span></p>
     2726
     2727<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     272814.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_34"
     2729 o:spid="_x0000_i1034" type="#_x0000_t75" style='width:358pt;height:231pt;
     2730 visibility:visible;mso-wrap-style:square'>
     2731 <v:imagedata src="RigidBodyRef.fld/image035.png" o:title=""/>
     2732</v:shape><![endif]--><![if !vml]><img border=0 width=358 height=231
     2733src="RigidBodyRef.fld/image035.png" v:shapes="Picture_x0020_34"><![endif]></span><span
     2734style='mso-bidi-font-size:14.0pt'><span style='mso-spacerun:yes'> </span></span><span
     2735lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2736mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2737Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2738
     2739<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2740
     2741<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>From this view it is
     2742clear that both a small rotation and a small translation is needed. First with
     2743the <u>Alt</u> and the <u>middle mouse</u> button both pressed, drag upwards
     2744until the two rings molecules are more parallel. Then, with the <u>Alt</u> and
     2745the <u>right mouse</u> buttons both pressed, drag upwards until the molecules
     2746are better overlapped. </span><span lang=HE dir=RTL style='mso-bidi-font-size:
     274714.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
     2748mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
     2749minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    29132750
    29142751<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     
    29182755
    29192756<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
    2920 dir=LTR></span>5C)</span> Again w<span style='mso-bidi-font-size:14.0pt'>ith
    2921 the <u>Alt key down</u>, <u>drag</u> with the <u>right mouse</u> button and
    2922 move the rigid body so that the phenyl rings are more or less aligned.</span><span
    2923 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2924 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2925 Calibri;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:
    2928 14.0pt;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
    2933 src="RigidBodyRef.fld/image066.png" v:shapes="Picture_x0020_53"><![endif]></span><span
    2934 style='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
    2939 style='mso-bidi-font-size:14.0pt'>To see how far the rings are separated in the
    2940 screen z direction, we must rotate the view. <u>Drag</u> the mouse <u>upwards</u>
    2941 with the <u>left button</u> down (without pressing Alt) to obtain a view
    2942 similar to the one below.</span><span lang=HE dir=RTL style='mso-bidi-font-size:
    2943 14.0pt;font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;
    2944 mso-ascii-theme-font:minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:
    2945 minor-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:
    2948 14.0pt;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
    2952 src="RigidBodyRef.fld/image067.png" v:shapes="_x0000_i1034"><![endif]></span><span
    2953 style='mso-bidi-font-size:14.0pt'><span style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
     2757dir=LTR></span>5E)</span> <span style='mso-bidi-font-size:14.0pt'>At the point
     2758the rigid body is pretty close to the position of the molecule in the unit
     2759cell, with distances in the table ranging from 0.1 to nearly 2 Å, but better
     2760agreement can be obtained by making small adjustments with the Alt down and
     2761successively pressing each of the three mouse buttons alternated with changing
     2762the view to see the molecules from a different perspective. Another choice is
     2763to assign several atoms and optimize, as was done in steps 4D and 4E. Choices
     2764of atoms to optimize are clear, since the atoms are properly paired in the
     2765table. Updating the C3-C5 torsion to ~20 degrees will also improve the
     2766agreement. <o:p></o:p></span></p>
    29542767
    29552768<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     
    29582771mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    29592772
    2960 <p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>From this view it is
    2961 clear that a small rotation is needed and a small translation. First with the <u>Alt</u>
    2962 and the <u>middle mouse</u> button both pressed, drag upwards until the two rings
    2963 molecules are more parallel. Then, with the <u>Alt</u> and the <u>right mouse</u>
    2964 buttons both pressed, drag upwards until the molecules are better overlapped. </span><span
    2965 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2966 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2967 Calibri;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
    2972 style='mso-bidi-font-size:14.0pt'>At the point the rigid body is pretty close
    2973 to the position of the molecule in the unit cell, with distances in the table
    2974 ranging from 0.1 to nearly 2 Å, but better agreement can be obtained by making
    2975 small adjustments with the Alt down and successively pressing each of the three
    2976 mouse buttons alternated with changing the view to see the molecules from a
    2977 different perspective. Another choice is to assign several atoms and optimize,
    2978 as was done in steps 4D and 4E. Choices of atoms to optimize are clear since
    2979 the atoms are properly paired in the table. Updating the C3-C5 torsion to ~20
    2980 degrees will also improve the agreement. </span><span lang=HE dir=RTL
    2981 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2982 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2983 Calibri;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
    2988 style='mso-bidi-font-size:14.0pt'>When the agreement is sufficient, press Add,
    2989 accept the warning and this molecule is also now constrained by the rigid body.
    2990 Now both molecules will appear as orange. </span><span lang=HE dir=RTL
    2991 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    2992 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    2993 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2773<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2774dir=LTR></span>5F)</span> <span style='mso-bidi-font-size:14.0pt'>When the
     2775agreement is sufficient, press Add, accept the warning and this molecule is
     2776also now constrained by the rigid body. Now both molecules will appear as
     2777orange. <o:p></o:p></span></p>
    29942778
    29952779<h2>Step 6: Optimize the model<span lang=HE dir=RTL style='font-size:13.0pt;
     
    30012785jumping from 2.2% with the distorted model to ~6%. This is not surprising and
    30022786only a few refinement steps will provide a more realistic model with comparable
    3003 agreement, but far fewer parameters.<o:p></o:p></span></p>
     2787agreement, but far fewer parameters.</span><span lang=HE dir=RTL
     2788style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2789mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2790Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    30042791
    30052792<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    30062793
    30072794<p class=MsoNormal><span class=MsoIntenseReference>6A)</span> <span
    3008 style='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
    3010 all boxes unchecked and press OK). Note that the X flag for the atoms in the rigid
    3011 bodies would be ignored anyway. <o:p></o:p></span></p>
     2795style='mso-bidi-font-size:14.0pt'>Initially, <u>turn off refinement of all
     2796atoms</u>. (Select the <u>Atoms tab</u>, double-click on the refine column
     2797label and then leave all boxes unchecked and press OK). Note that the X flag
     2798for the atoms in the rigid bodies would be ignored anyway. <o:p></o:p></span></p>
    30122799
    30132800<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
    3014 14.0pt;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=""/>
     280114.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_35"
     2802 o:spid="_x0000_i1033" type="#_x0000_t75" style='width:433pt;height:205pt;
     2803 visibility:visible;mso-wrap-style:square'>
     2804 <v:imagedata src="RigidBodyRef.fld/image036.png" o:title=""/>
    30172805</v:shape><![endif]--><![if !vml]><img border=0 width=433 height=205
    3018 src="RigidBodyRef.fld/image068.png" v:shapes="_x0000_i1033"><![endif]></span><span
     2806src="RigidBodyRef.fld/image036.png" v:shapes="Picture_x0020_35"><![endif]></span><span
    30192807style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    30202808
     
    30222810style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
    30232811
    3024 <p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2812<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     2813
     2814<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Then select the <u>RB
     2815Models</u> tab. The first rigid body is automatically selected. Make the
     2816following changes:</span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    30252817font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    30262818minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    3027 mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    3028 
    3029 <p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>Then select the <u>RB
    3030 Models</u> tab. The first rigid body is automatically selected. Make the following
    3031 changes:<o:p></o:p></span></p>
    3032 
    3033 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l3 level1 lfo5'><![if !supportLists]><span
     2819mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2820
     2821<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo8'><![if !supportLists]><span
    30342822style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    30352823minor-latin'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     
    3037282514.0pt'>Select to <u>refine</u> the <u>Origin</u> <o:p></o:p></span></p>
    30382826
    3039 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo5'><![if !supportLists]><span
     2827<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo8'><![if !supportLists]><span
    30402828style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    30412829minor-latin'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     
    30442832flag</u><o:p></o:p></span></p>
    30452833
    3046 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo5'><![if !supportLists]><span
     2834<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo8'><![if !supportLists]><span
    30472835style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    30482836minor-latin'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     
    3050283814.0pt'>Set the “thermal motion” <u>mode to <span class=SpellE>Uiso</span></u> <o:p></o:p></span></p>
    30512839
    3052 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo5'><![if !supportLists]><span
     2840<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo8'><![if !supportLists]><span
    30532841style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    30542842minor-latin'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
     
    30572845something reasonable, say <u>0.01</u><o:p></o:p></span></p>
    30582846
    3059 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l3 level1 lfo5'><![if !supportLists]><span
     2847<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l2 level1 lfo8'><![if !supportLists]><span
    30602848style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    30612849minor-latin'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;
    30622850</span></span></span><![endif]><span dir=LTR></span><span style='mso-bidi-font-size:
    3063 14.0pt'>Set the <u>refinement flag</u> for thermal motion</span><span lang=HE
    3064 dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    3065 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    3066 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     285114.0pt'>Set the <u>refinement flag</u> for thermal motion<o:p></o:p></span></p>
    30672852
    30682853<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
    3069 14.0pt;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
    3073 src="RigidBodyRef.fld/image069.png" v:shapes="_x0000_i1032"><![endif]></span><span
    3074 style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     285414.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_36"
     2855 o:spid="_x0000_i1032" type="#_x0000_t75" style='width:333pt;height:223pt;
     2856 visibility:visible;mso-wrap-style:square'>
     2857 <v:imagedata src="RigidBodyRef.fld/image037.png" o:title=""/>
     2858</v:shape><![endif]--><![if !vml]><img border=0 width=333 height=223
     2859src="RigidBodyRef.fld/image037.png" v:shapes="Picture_x0020_36"><![endif]></span><span
     2860lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2861mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2862Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    30752863
    30762864<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     
    30782866
    30792867<p class=MsoNormal><span class=MsoIntenseReference>6B)</span> <span
    3080 style='mso-bidi-font-size:14.0pt'>Then <u>select the second rigid body</u> and
    3081 repeat the previous actions (setting the <u>refine checkbox</u>, selecting <u>AV</u>
     2868style='mso-bidi-font-size:14.0pt'>Then <u>select the second rigid body</u> and repeat
     2869the previous actions (setting the <u>refine checkbox</u>, selecting <u>AV</u>
    30822870for the orientation refinement, setting <span class=SpellE><u>Uiso</u></span><u>
    30832871mode</u>, set the <span class=SpellE><u>Uiso</u></span><u> value</u> to <u>0.01</u>
    3084 and set the thermal motion <u>refinement flag</u>.)</span><span lang=HE
    3085 dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    3086 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    3087 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2872and set the thermal motion <u>refinement flag</u>.)<o:p></o:p></span></p>
    30882873
    30892874<p class=MsoNormal align=right style='text-align:right'><span lang=HE dir=RTL
     
    30942879<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
    3095288014.0pt;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;
     2881 o:spid="_x0000_i1031" type="#_x0000_t75" style='width:336pt;height:233pt;
    30972882 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
    3100 src="RigidBodyRef.fld/image070.png" v:shapes="Picture_x0020_58"><![endif]></span><span
    3101 style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2883 <v:imagedata src="RigidBodyRef.fld/image038.png" o:title=""/>
     2884</v:shape><![endif]--><![if !vml]><img border=0 width=336 height=233
     2885src="RigidBodyRef.fld/image038.png" v:shapes="Picture_x0020_58"><![endif]></span><span
     2886lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2887mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2888Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    31022889
    31032890<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     
    31062893style='mso-bidi-font-size:14.0pt'>Set the <u>number of cycles back to 5</u> and
    31072894<u>refine</u>. The fit will converge quickly to an <span class=SpellE>wR</span>
    3108 of ~4%.</span><b><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     2895of ~4%.<b><o:p></o:p></b></span></p>
     2896
     2897<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    31092898font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    31102899minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    3111 mso-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
    3116 style='mso-bidi-font-size:14.0pt'>Add refinement of the <u>four torsion angles</u>
    3117 for each of the <u>two rigid bodies</u>. Then refine again. The <span
    3118 class=SpellE>wR</span> quickly drops to 2.5%<o:p></o:p></span></p>
     2900mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     2901
     2902<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     2903dir=LTR></span>6D)</span> <span style='mso-bidi-font-size:14.0pt'>Add
     2904refinement of the <u>four torsion angles</u> for each of the <u>two rigid
     2905bodies</u>. Then refine again. The <span class=SpellE>wR</span> quickly drops
     2906to 2.5%<o:p></o:p></span></p>
    31192907
    31202908<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     
    31222910 o:spid="_x0000_i1030" type="#_x0000_t75" style='width:322pt;height:236pt;
    31232911 visibility:visible;mso-wrap-style:square'>
    3124  <v:imagedata src="RigidBodyRef.fld/image071.png" o:title=""/>
     2912 <v:imagedata src="RigidBodyRef.fld/image039.png" o:title=""/>
    31252913</v:shape><![endif]--><![if !vml]><img border=0 width=322 height=236
    3126 src="RigidBodyRef.fld/image071.png" v:shapes="Picture_x0020_60"><![endif]></span><span
    3127 lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    3128 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    3129 Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     2914src="RigidBodyRef.fld/image039.png" v:shapes="Picture_x0020_60"><![endif]></span><span
     2915style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    31302916
    31312917<h2>Optional Step 7: Try rigid body TLS motion <span lang=HE dir=RTL
     
    31352921rigid bodies, known as the TLS description, has been worked out (<span
    31362922class=SpellE>Schomaker</span> &amp; Trueblood, Acta <span class=SpellE>Cryst</span>.
    3137 B<b>24</b>, 63-76, 1968) and consists of three tensors:<o:p></o:p></span></i></p>
     2923B<b>24</b>, 63-76, 1968) and consists of three tensors:</span></i><i><span
     2924lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     2925mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     2926Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></i></p>
    31382927
    31392928<p class=MsoListParagraphCxSpFirst style='margin-left:.75in;mso-add-space:auto;
    3140 text-indent:-.25in;mso-list:l0 level1 lfo7'><![if !supportLists]><span
     2929text-indent:-.25in;mso-list:l0 level1 lfo10'><![if !supportLists]><span
    31412930style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
    31422931Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span
     
    31462935
    31472936<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
    3148 auto;text-indent:-.25in;mso-list:l0 level1 lfo7'><![if !supportLists]><span
     2937auto;text-indent:-.25in;mso-list:l0 level1 lfo10'><![if !supportLists]><span
    31492938style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
    31502939Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span
     
    31552944
    31562945<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto;
    3157 text-indent:-.25in;mso-list:l0 level1 lfo7'><![if !supportLists]><span
     2946text-indent:-.25in;mso-list:l0 level1 lfo10'><![if !supportLists]><span
    31582947style='mso-bidi-font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:
    31592948Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span
     
    31662955<p class=MsoNormal style='margin-left:.5in'><i><span style='mso-bidi-font-size:
    3167295614.0pt'>In the full expansion there are 6 T and 6 L and 8 S terms. It is
    3168 unlikely that all of these terms can ever be used with powder data. <o:p></o:p></span></i></p>
     2957unlikely that all of these terms can ever be used with a powder dataset.<o:p></o:p></span></i></p>
    31692958
    31702959<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     
    31722961<p class=MsoNormal><i><span style='mso-bidi-font-size:14.0pt'>The simplest
    31732962description that can be made with a rigid body is to assume that all motion is
    3174 translational and isotropic. This is what we have done and would be equivalent
    3175 to refining <span class=SpellE>Uiso</span> for each atom in the rigid body, but
    3176 applying a constraint so that all atoms in the rigid body share that <span
    3177 class=SpellE>Uiso</span> value. It makes sense to see if further expansion of
    3178 the rigid body motion/disorder description will produce an even better fit,
    3179 although it is clear that the crystallographic fit is already quite good
    3180 considering the limited resolution and high background levels. Refining 24 more
    3181 parameters (6 T + 6 L, for each of the 2 bodies) is clearly impractical. One
    3182 possible simplification would be to refine only the diagonal T &amp; L elements
    3183 (which constraints translation and <span class=SpellE>libration</span> directions
    3184 to crystal axes). That might be appropriate with data more sensitive to group
    3185 motion, but is still impractical here. One still simpler model is to include
    3186 translation and <span class=SpellE>libration</span>, but require equal
     2963translational and isotropic. This is what we have done previously and is
     2964equivalent to refining <span class=SpellE>Uiso</span> for each atom in the
     2965rigid body, but applying a constraint so that all atoms in the rigid body share
     2966that <span class=SpellE>Uiso</span> value. It makes sense to see if further
     2967expansion of the rigid body motion/disorder description will produce an even
     2968better fit, although it is clear that the crystallographic fit is already quite
     2969good considering the limited resolution and high background levels. Refining 24
     2970more parameters (6 T + 6 L, for each of the 2 bodies) is clearly impractical.
     2971One possible simplification would be to refine only the diagonal T &amp; L
     2972elements (which constraints translation and <span class=SpellE>libration</span>
     2973directions to crystal axes). That might be appropriate with data more sensitive
     2974to group motion, but is still impractical here. One still simpler model is to
     2975include translation and <span class=SpellE>libration</span>, but require equal
    31872976amplitudes in all directions. This can be done by refining only the diagonal T
    3188 and L terms, but to constrain them to be equal. If the T &amp; L values are constrained
    3189 to be the same for the two groups, this means replacing the 2 group <span
    3190 class=SpellE>Uiso</span> values with 2 terms (a single grouped <span
    3191 class=SpellE>T<sub>jj</sub></span> and a <span class=SpellE>L<sub>jj</sub></span>
    3192 term). This is easily done as shown below. </span></i><i><span lang=HE dir=RTL
    3193 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    3194 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    3195 Calibri;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
    3200 style='mso-bidi-font-size:14.0pt'>Switch to refine the T &amp; L terms by
    3201 selecting each body, in the <u>RB Models</u> phase tab, set the <u>thermal
    3202 motion model to TL</u> for both rigid bodies and then <u>turn on</u> the <u>refine</u>
    3203 checkbox for the <u>T11, T22, T33, L11, L22 &amp; L33 terms</u>.<span
    3204 style='mso-spacerun:yes'>  </span></span><span lang=HE dir=RTL
    3205 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    3206 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    3207 Calibri;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
    3214 src="RigidBodyRef.fld/image072.png" v:shapes="Picture_x0020_52"><![endif]></span><span
    3215 style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     2977and L terms, but to constrain them to be equal. If the T &amp; L values are
     2978constrained to be the same for the two rigid body insertions, this means
     2979replacing the 2 grouped <span class=SpellE>Uiso</span> values with 2 terms (a
     2980single <span class=SpellE>T<sub>jj</sub></span> and a <span class=SpellE>L<sub>jj</sub></span>
     2981term applied to all rigid body atoms). This is easily done as shown below. <o:p></o:p></span></i></p>
    32162982
    32172983<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     
    32212987
    32222988<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
    3223 dir=LTR></span>7B)</span> Delete the two existing <span style='mso-bidi-font-size:
    3224 14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>constraints
    3225 on <span class=SpellE>Uiso</span> values: Use the <u>Constraints</u> tree item
    3226 and the Phase tab and <u>delete the two entries</u>. These constraints are
    3227 actually ignored with rigid body group motion, so this does not actually have
    3228 any effect, but they could lead to confusion. <o:p></o:p></span></p>
     2989dir=LTR></span>7A)</span> <span style='mso-bidi-font-size:14.0pt'>Switch to
     2990refine the T &amp; L terms by selecting each body, in the <u>RB Models</u>
     2991phase tab, set the <u>thermal motion model to TL</u> for both rigid bodies and
     2992then <u>turn on</u> the <u>refine</u> checkbox for the <u>T11, T22, T33, L11,
     2993L22 &amp; L33 terms</u>.<span style='mso-spacerun:yes'>  </span><o:p></o:p></span></p>
     2994
     2995<p class=MsoNormal align=right style='text-align:right'><span style='mso-bidi-font-size:
     299614.0pt;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_52"
     2997 o:spid="_x0000_i1029" type="#_x0000_t75" style='width:459pt;height:186pt;
     2998 visibility:visible;mso-wrap-style:square'>
     2999 <v:imagedata src="RigidBodyRef.fld/image040.png" o:title=""/>
     3000</v:shape><![endif]--><![if !vml]><img border=0 width=459 height=186
     3001src="RigidBodyRef.fld/image040.png" v:shapes="Picture_x0020_52"><![endif]></span><span
     3002lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3003mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3004Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     3005
     3006<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3007
     3008<p class=MsoNormal><span class=MsoIntenseReference>7B)</span> Delete the two
     3009existing <span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;
     3010mso-bidi-theme-font:minor-latin'>constraints on <span class=SpellE>Uiso</span>
     3011values: Use the <u>Constraints</u> tree item and the Phase tab and <u>delete
     3012the two entries</u>. These constraints are actually ignored when rigid body
     3013group motion is refined, so the presence of these constraints does not actually
     3014have any effect, but it is better to remove any unused constraints.<span
     3015lang=HE dir=RTL><o:p></o:p></span></span></p>
    32293016
    32303017<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
     
    32363023and <span class=SpellE>L<sub>jj</sub></span> terms through use of the <u>Constraints</u>
    32373024tree item. To constrain the <span class=SpellE>T<sub>jj</sub></span> terms, one
    3238 needs to know their variable names are <span class=GramE>RBRT<i>jj</i>:<i>b</i></span>:0
    3239 for 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>
     3025needs to know their variable names are </span><span class=GramE><span
     3026style='mso-bidi-font-size:14.0pt;font-family:Courier;mso-bidi-font-family:Calibri;
     3027mso-bidi-theme-font:minor-latin'>RBRT<i>jj</i>:<i>b</i></span></span><span
     3028style='mso-bidi-font-size:14.0pt;font-family:Courier;mso-bidi-font-family:Calibri;
     3029mso-bidi-theme-font:minor-latin'>:0</span><span style='mso-bidi-font-size:14.0pt;
     3030mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> for body #</span><i><span
     3031style='mso-bidi-font-size:14.0pt;font-family:Courier;mso-bidi-font-family:Calibri;
     3032mso-bidi-theme-font:minor-latin'>b</span></i><span style='mso-bidi-font-size:
     303314.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> of type 0
     3034where </span><span style='mso-bidi-font-size:14.0pt;font-family:Courier;
     3035mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>j</span><span
     3036style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3037minor-latin'> = 1, 2 or 3.<o:p></o:p></span></p>
     3038
     3039<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     3040font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
     3041minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
     3042mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
    32423043
    32433044<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>
    3245 menu item and enter <u>RBRT</u> in the search <u>filter</u>. The first term is
    3246 one of the six that needs to be constrained, so select it as the 1<sup>st</sup>
    3247 variable and press OK.<span style='mso-no-proof:yes'> </span></span><span
     3045(loaded by default), use the <u>“Edit Constr.”<span class=GramE>/“</span>Add
     3046Equivalence”</u> menu item and enter <u>RBRT</u> in the search <u>filter</u>.
     3047The first term is one of the six that needs to be constrained, so select it as
     3048the 1<sup>st</sup> variable and press OK.<span style='mso-no-proof:yes'> <o:p></o:p></span></span></p>
     3049
     3050<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     3051style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     3052HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_54" o:spid="_x0000_i1028"
     3053 type="#_x0000_t75" style='width:423pt;height:177pt;visibility:visible;
     3054 mso-wrap-style:square'>
     3055 <v:imagedata src="RigidBodyRef.fld/image041.png" o:title=""/>
     3056</v:shape><![endif]--><![if !vml]><img border=0 width=423 height=177
     3057src="RigidBodyRef.fld/image041.png" v:shapes="Picture_x0020_54"><![endif]></span><span
     3058lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3059mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3060Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     3061
     3062<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     3063
     3064<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>On the next window
     3065select the remaining five 11, 22 and 33 terms<o:p></o:p></span></p>
     3066
     3067<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'>and press OK:</span><span
     3068lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
     3069mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
     3070Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
     3071
     3072<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     3073style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     3074HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_55" o:spid="_x0000_i1027"
     3075 type="#_x0000_t75" style='width:422pt;height:255pt;visibility:visible;
     3076 mso-wrap-style:square'>
     3077 <v:imagedata src="RigidBodyRef.fld/image042.png" o:title=""/>
     3078</v:shape><![endif]--><![if !vml]><img border=0 width=422 height=255
     3079src="RigidBodyRef.fld/image042.png" v:shapes="Picture_x0020_55"><![endif]></span><span
     3080style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     3081
     3082<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><span
     3083style='mso-spacerun:yes'> </span></span><span style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     3084
     3085<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><span
     3086style='mso-spacerun:yes'> </span><sub><o:p></o:p></sub></span></p>
     3087
     3088<p class=MsoNormal><sub><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></sub></p>
     3089
     3090<p class=MsoNormal><span class=MsoIntenseReference>7D)</span> <span
     3091style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     3092minor-latin'>Create constraints on the <span class=SpellE>L<sub>jj</sub></span>
     3093terms through use of the <u>Constraints</u> tree item as was done before. Their
     3094variable name is </span><span class=GramE><span style='mso-bidi-font-size:14.0pt;
     3095font-family:Courier;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>RBRL<i>jj</i>:<i>b</i></span></span><span
     3096style='mso-bidi-font-size:14.0pt;font-family:Courier;mso-bidi-font-family:Calibri;
     3097mso-bidi-theme-font:minor-latin'>:0</span><span style='mso-bidi-font-size:14.0pt;
     3098mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>. Again use the <u>“Edit
     3099Constr.”/“Add Equivalence”</u> menu item and enter <u>RBRL</u> in the search <u>filter</u>.
     3100The first term is one of the six that needs to be constrained, and on the next
     3101screen select the remaining five 11, 22 and 33 terms and press OK. Constraints
     3102should appear as:<span style='mso-no-proof:yes'> <o:p></o:p></span></span></p>
     3103
     3104<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     3105style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     3106HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_56" o:spid="_x0000_i1026"
     3107 type="#_x0000_t75" style='width:578pt;height:133pt;visibility:visible;
     3108 mso-wrap-style:square'>
     3109 <v:imagedata src="RigidBodyRef.fld/image043.png" o:title=""/>
     3110</v:shape><![endif]--><![if !vml]><img border=0 width=578 height=133
     3111src="RigidBodyRef.fld/image043.png" v:shapes="Picture_x0020_56"><![endif]></span><span
    32483112lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    32493113mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    32503114Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi;
    32513115mso-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:
    3254 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_54"
    3255  o:spid="_x0000_i1028" type="#_x0000_t75" style='width:423pt;height:177pt;
    3256  visibility:visible;mso-wrap-style:square'>
    3257  <v:imagedata src="RigidBodyRef.fld/image073.png" o:title=""/>
    3258 </v:shape><![endif]--><![if !vml]><img border=0 width=423 height=177
    3259 src="RigidBodyRef.fld/image073.png" v:shapes="Picture_x0020_54"><![endif]></span><span
    3260 style='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
    3265 select the remaining five 11, 22 and 33 terms</span><span lang=HE dir=RTL
    3266 style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    3267 mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    3268 Calibri;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:
    3273 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_55"
    3274  o:spid="_x0000_i1027" type="#_x0000_t75" style='width:422pt;height:255pt;
    3275  visibility:visible;mso-wrap-style:square'>
    3276  <v:imagedata src="RigidBodyRef.fld/image074.png" o:title=""/>
    3277 </v:shape><![endif]--><![if !vml]><img border=0 width=422 height=255
    3278 src="RigidBodyRef.fld/image074.png" v:shapes="Picture_x0020_55"><![endif]></span><span
    3279 style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
    3280 
    3281 <p class=MsoNormal><span style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><span
    3282 style='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
    3285 style='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;
    3288 font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    3289 minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    3290 mso-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
    3293 dir=LTR></span>7D)</span> <span style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:
    3294 Calibri;mso-bidi-theme-font:minor-latin'>Create constraints on the <span
    3295 class=SpellE>L<sub>jj</sub></span> terms through use of the <u>Constraints</u>
    3296 tree item as was done before. Their variable name is <span class=GramE>RBRL<i>jj</i>:<i>b</i></span>:0.
    3297 Again use the <u>“Edit Constr.”/“Add Equivalence”</u> menu item and enter <u>RBRL</u>
    3298 in the search <u>filter</u>. The first term is one of the six that needs to be
    3299 constrained, and on the next screen select the remaining five 11, 22 and 33
    3300 terms and press OK. Constraints should appear as:<span style='mso-no-proof:
    3301 yes'> <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:
    3304 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_56"
    3305  o:spid="_x0000_i1026" type="#_x0000_t75" style='width:578pt;height:133pt;
    3306  visibility:visible;mso-wrap-style:square'>
    3307  <v:imagedata src="RigidBodyRef.fld/image075.png" o:title=""/>
    3308 </v:shape><![endif]--><![if !vml]><img border=0 width=578 height=133
    3309 src="RigidBodyRef.fld/image075.png" v:shapes="Picture_x0020_56"><![endif]></span><span
    3310 style='mso-bidi-font-size:14.0pt;mso-no-proof:yes'><o:p></o:p></span></p>
    33113116
    33123117<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     
    33193124more reasonable model than the <span class=SpellE>Uiso</span> model. If the
    33203125thermal ellipsoids are plotted, they get larger further away from the origin as
    3321 one might expect. </span><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
     3126one might expect. <o:p></o:p></span></p>
     3127
     3128<p class=MsoNormal><span lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;
    33223129font-family:"Times New Roman",serif;mso-ascii-font-family:Calibri;mso-ascii-theme-font:
    33233130minor-latin;mso-hansi-font-family:Calibri;mso-hansi-theme-font:minor-latin;
    3324 mso-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
    3329 style='mso-bidi-font-size:14.0pt'>An even more relaxed model would be to allow
    3330 the <span class=SpellE>T<sub>jj</sub></span> and <span class=SpellE>L<sub>jj</sub></span>
    3331 terms to differ between the two bodies, with constraints as shown below, but
    3332 this produces no improvement in the <span class=SpellE>Rwp</span>. Further it
    3333 has a non-physical negative <span class=SpellE>L<sub>jj</sub></span> value for
    3334 one of the two bodies, so this is not a better model.</span></i><i><span
     3131mso-bidi-theme-font:minor-bidi'><o:p>&nbsp;</o:p></span></p>
     3132
     3133<p class=MsoNormal><span dir=LTR></span><span class=MsoIntenseReference><span
     3134dir=LTR></span>7F)</span> <i><span style='mso-bidi-font-size:14.0pt'>An even
     3135more relaxed model would be to allow the <span class=SpellE>T<sub>jj</sub></span>
     3136and <span class=SpellE>L<sub>jj</sub></span> terms to differ between the two
     3137bodies, with constraints as shown below, but this produces no improvement in
     3138the <span class=SpellE>Rwp</span>. Further it has a non-physical negative <span
     3139class=SpellE>L<sub>jj</sub></span> value for one of the two bodies, so this is
     3140not a better model.<o:p></o:p></span></i></p>
     3141
     3142<p class=MsoNormal align=right style='text-align:right'><span lang=HE
     3143style='mso-bidi-font-size:14.0pt;mso-bidi-font-family:Arial;mso-ansi-language:
     3144HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_49" o:spid="_x0000_i1025"
     3145 type="#_x0000_t75" style='width:520pt;height:236pt;visibility:visible;
     3146 mso-wrap-style:square'>
     3147 <v:imagedata src="RigidBodyRef.fld/image044.png" o:title=""/>
     3148</v:shape><![endif]--><![if !vml]><img border=0 width=520 height=236
     3149src="RigidBodyRef.fld/image044.png" v:shapes="Picture_x0020_49"><![endif]></span><span
    33353150lang=HE dir=RTL style='mso-bidi-font-size:14.0pt;font-family:"Times New Roman",serif;
    33363151mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-hansi-font-family:
    3337 Calibri;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:
    3340 Arial;mso-ansi-language:HE;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_49"
    3341  o:spid="_x0000_i1025" type="#_x0000_t75" style='width:520pt;height:236pt;
    3342  visibility:visible;mso-wrap-style:square'>
    3343  <v:imagedata src="RigidBodyRef.fld/image076.png" o:title=""/>
    3344 </v:shape><![endif]--><![if !vml]><img border=0 width=520 height=236
    3345 src="RigidBodyRef.fld/image076.png" v:shapes="Picture_x0020_49"><![endif]></span><span
    3346 style='mso-bidi-font-size:14.0pt'><o:p></o:p></span></p>
     3152Calibri;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-bidi'><o:p></o:p></span></p>
    33473153
    33483154<p class=MsoNormal><span style='mso-bidi-font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
     
    33503156<h2>Conclusion</h2>
    33513157
    3352 <p class=MsoNormal>In the tutorial, we have seen how to create a rigid body,
    3353 using the Avogadro program to regularize the internal geometry. The body was then
    3354 defined within GSAS-II, including 4 torsion angles internal to the body. The
    3355 rigid body was then placed into the unit cell in previously determined positions/orientations.
    3356 The positions, orientations and torsions, as well as rigid body group motion parameters,
    3357 we then refined. The resulting fit was excellent with a highly realistic
    3358 structure and a small number of parameters that are appropriate for the dataset
    3359 being used. </p>
     3158<p class=MsoNormal>In this tutorial, we have seen how to create a rigid body, using
     3159the Avogadro program to regularize the internal geometry. The body was then imported
     3160into GSAS-II, including 4 torsion angles internal to the body. The rigid body
     3161was then placed into the unit cell in previously determined
     3162positions/orientations. The positions, orientations and torsions, as well as
     3163rigid body group motion parameters, were then refined. The resulting fit was
     3164excellent, with a highly realistic structure and a small number of parameters
     3165that are appropriate for the dataset being used. </p>
    33603166
    33613167</div>
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