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Re: Rigid-group identification

  • To: Multiple recipients of list <coredmg@iucr.org>
  • Subject: Re: Rigid-group identification
  • From: "I. David Brown" <idbrown@mcmail.cis.mcmaster.ca>
  • Date: Thu, 10 May 2001 19:58:09 +0100 (BST)

Comments on Rigid Groups
------------------------
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# I have tried to get around the problem of having two different _id's 
# having the same parent.  This requires using a more logical description
# of the rigid groups.  I have sketched out a possible arrangement
# in terms of Gotzon's example where I have replaced the 
# _atom_site_rigid_group loop by two new loops, one (_rigid_group)
# describing the properties of the whole group and the other 
# (_rigid_group_atoms) describing the atoms that form the rigid group.  
# I am not familiar with the way in which rigid groups are handled 
# in refinements, so what I propose here may not make
# sense in practical applications.
#

        _symmetry_space_group_name_H-M            'P n a m'

    loop_
        _symmetry_equiv_pos_site_id
        _symmetry_equiv_pos_as_xyz
                           1               x,y,z
                           2               1/2+x,1/2-y,1/2-z
                           3               1/2-x,1/2+y,-z
                           4               -x,-y,1/2+z
                           5               -x,-y,-z
                           6               1/2-x,1/2+y,1/2+z
                           7               1/2+x,1/2-y,z
                           8               x,y,1/2-z

#
# The following loop is much as Gotzon gave it except that the
# _*_group_description has been replaced by _atom_site_rigid_group_id
# (child of _rigid_group_id), and I have deleted the coordinates
# of the atoms in the group since these are defined in the
# _rigid_group_atoms list.  They could optionally also be included here,
# depending on the way in which the CIF is to be used.  
# Any coordinates shown in this loop are derived from those in
# the _rigid_group_atoms list which remain the primary
# coordinates.  I have also corrected the occupancies which are now 
# all set to 1.0.  In Gotzon's example the occupancies were 
# incorrectly given as
# site_multiplicity/general_position_multiplicity - a common mistake. 
# There is a different item for this information. 
# The refinement flag has been set to G for atoms in the rigid group.
#

    loop_
        _atom_site_group_id
        _atom_site_label
        _atom_site_occupancy
        _atom_site_fract_x
        _atom_site_fract_y
        _atom_site_fract_z
        _atom_site_U_iso_or_equiv
        _atom_site_thermal_displace_type
        _atom_site_refinement_flags
         SeO4    Se   1.0  .          .          .         .          Uani G 
         .       K1   1.0  0.1670(1)  0.08069(7) 0.250000  0.0102(2)  Uani S  
         .       K2   1.0 -0.0013(1)  0.70766(4) 0.250000  0.0072(2)  Uani S 
         SeO4    O1   1.0  .          .          .         .          Uani G
         SeO4    O2   1.0  .          .          .         .          Uani G
         SeO4    O3   1.0  .          .          .         .          Uani G

#
# The following loop gives information about the rigid group as a whole. 
# It is the parameters in this loop that I assume are refined. 
# I have shown the fractional coordinates of the center of the group
# but I have not included the rotation matrix (or equivalent) which
# also needs to be given.  This matrix (which can be defined if
# this arrangement of CIF items is acceptable) relates the axis system
# used to define the rigid group to the crystal axis system.
#

    loop_
        _rigid_group_id
        _rigid_group_center_fract_x
        _rigid_group_center_fract_y
        _rigid_group_center_fract_z
         SeO4   0.22346    0.41868    0.25

#
# The following loop describes the rigid group itself.  _*_rigid_group_id
# is a child of _rigid_group_id and _*_atom_site_label is a child of
# _atom_site_label.  The coordinates of the atoms that compose
# the rigid group are given in their own coordinate system and
# in this example are expressed in terms of spherical coordinates,
# though we should also define cartesian coordinates so the user has a
# choice.  The purpose of this loop is to make the definition of the
# group clear to the user.  Of course this loop need not appear if it is
# not thought to be necessary, provided that the coordinates of all
# atoms are given in the _atom_site loop.  I have only shown isotropic Us,
# I am not sure how the anisotropic Us are defined.  If in terms of
# the crystal coordinates, they should appear in an _atom_site_aniso loop.
#

    loop_
        _rigid_group_atoms_rigid_group_id
        _rigid_group_atoms_atom_site_label
        _rigid_group_atoms_site_symmetry
        _rigid_group_atoms_coord_radial
        _rigid_group_atoms_coord_theta
        _rigid_group_atoms_coord_phi
        _rigid_group_atoms_Uiso_or_equiv
             SeO4      Se      .    0       0      0    0.00428(9)
             SeO4      O1      .    1.84    109    120  0.0130(6)
             SeO4      O1      8    1.84    109    240  0.0130(6)
             SeO4      O2      .    1.84    0      0    0.0119(8)
             SeO4      O3      .    1.84    109    0    0.0164(9)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -


				David



*****************************************************
Dr.I.David Brown,  Professor Emeritus
Brockhouse Institute for Materials Research, 
McMaster University, Hamilton, Ontario, Canada
Tel: 1-(905)-525-9140 ext 24710
Fax: 1-(905)-521-2773
idbrown@mcmaster.ca
*****************************************************

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