Jul 6, 2011 3:35:40 PM (10 years ago)

update documentation

1 edited


  • branches/sandbox/doc/expgui2.html

    r971 r1150  
    8181<a name="xform"></a>
    82 <h4>A.2.2 Transform Coordinates</h4>
    83 <DL><DL>
    84 <img SRC="2a.gif" align=RIGHT alt="EXPGUI Screen snapshot">
    85 If one or more atoms have been selected
    86 <A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible
    87 to make changes to those atoms by pressing the "Xform atom(s)" button.
    88 This raises the window shown to the right.
    89 Note that no changes are actually made, until the
    90 "Transform Coordinates", "Set Occupancies",... buttons are pressed.
    91 <P>
    92 This window can be used
    93 to transform the coordinates coordinates of the selected atoms,
    94 globally set occupancy or Uiso (Uequiv)
    95 values for the selected atoms, or erase the selected atoms. by pressing the
    96 It is also possible to transform the selected atoms
    97 from isotropic to anisotropic, or the reverse.
    98 <P>
    99 <IMG SRC="new.gif" alt="New!">
    100 The "Xform Origin 1 to Origin 2" button is only available for those
     82<h4>A.2.2 Modify Atom</h4>
     84<img SRC="2a.jpg" align=RIGHT alt="EXPGUI Screen snapshot">
     85The "Modify Atom" button ("Modify Atoms" when multiple atoms are
     86  selected) provides access to additional options that can
     87  transform or modify the selected atom(s) from the phase panel 
     88<A href="expgui.html#mouseactions">(see Mouse Actions</A> for
     89  information on selecting atoms); this opens the menu window shown to
     90  the right.
     91Note that changes are made to the coordinates when the buttons on this
     92  window (such as
     93"Transform Coordinates", "Set Occupancies",...) are pressed.
     94<P><B>Modify Coordinates:</B>
     95  This is used
     96to transform the coordinates coordinates of the selected atoms using a
     97set of  transformation relationships.
     99<P><B>Reset Multiplicities:</B>
     100 When atom positions are edited in EXPGUI, they may be moved off from
     101  or onto special positions in the cell, changing the site
     102  multiplicity -- but this will not be reflected in the phase
     103  display. When atoms are subsequently refined, GENLES will update the
     104  multiplcities. Pressing the  "Reset Multiplicities" button cases
     105  this to be done right away (I think this may not work if there are no
     106  histograms present).
     108<P><B>Xform Origin 1 to Origin 2:</B> This button is only available for those
    101109orthorhombic, tetragonal and cubic space groups that are listed in the
    102110International Tables with two origin settings. (These space groups have
    106114of symmetry. GSAS only uses the origin 2 settings.)
    107115If coordinates have been entered in the origin 1 setting, they may be
    108 transformed to the origin 2 setting using this button.
     116transformed to the origin 2 setting using this button. It is important
     117  to select all atoms in the asymmetric unit before using this button.
     119  <P><B>Modify Occupancies:</B>
     120 This allows the occupancy to be set for one or more atoms. It is
     121  most convenient for when many atoms will have their occupancy
     122  changed at one time.
     124<P><B>Modify Displacement Parameters:</B>
     125  This allows one to set Uiso (or Uequiv) values for the selected
     126  atoms (<B>Set U</B>). To change the flag that determines if the
     127  selected atom(s) are represented as Isotropic or Anisotropic, press
     128  the <B>Set Isotropic</B> or <B>Set Anisotropic</B> buttons.
     130<P><B>Erase Atoms:</B>
     131  The "Erase Atoms" removes the selected atoms from the phase. I
     132  usually set the occupancy to 0. instead.
     134<P><B>Fix Atom Coordinates:</B>
     135When an atom is refined in GSAS, only the coordinates that are not
     136defined by site symmetry are refined. However, in some space groups,
     137it is necessary to not refine additional coordinates. The most common
     138example are polar space groups (P1, P2, P2<sub>1</sub>, C2,  P4, P4<sub>1</sub>, P
     1394<sub>2</sub>, P4<sub>3</sub>, I4, I4<sub>1</sub>, P3, P3<sub>1</sub>, P3<sub>2</sub>, R3, P6, P6<sub>1</sub>, P6<sub>5</sub>, P6<sub>2</sub>, P6<sub>4</sub> and
     140P6<sub>3</sub> - from
     141<a href="http://www.ruppweb.org/Xray/comp/space_instr.htm"> Bernard Rupp's
     142web site, http://www.ruppweb.org/Xray/comp/space_instr.htm</A>) where
     143one or more coordinates of the origin are not defined by symmetry. In
     144these space groups an appropriate number of coordinates must be fixed
     145to define the origin. As an example, in P1, one x, one y and one z
     146coordinate must not be refined; in space group P2<sub>1</sub>, the
     1472<sub>1</sub> screw axis defines the origin at (0,0,z) so one z
     148coordinate cannot be varied.
     150Occasionally, while symmetry may allow
     151atom coordinates to be varied, a crystallographer may choose to
     152simplify or constrain the representation to fix the atom in a
     153particular location and not refine with all allowed degrees of freedom.
     155<IMG SRC="new.gif" alt="New!">
     156 The "Fix Atom Coordinates" buttons allows a flag to be set (or
     157cleared) for an atom
     158to prevent refinement of selected coordinates, even when the X
     159refinement flag is set. Note the addition of an "F" for the x and z
     160coordinates of the first atom as shown in the phase panel, above. This
     161indicates that x & z have been fixed. When the atom position is
     162varied, only y will be optimized.
    110164<br clear=all>
    250 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    251 <font size=-1><? lastmod(); ?> </font>
    252 <br>$Revision$ $Date$
Note: See TracChangeset for help on using the changeset viewer.