[IUCr Home Page] [CIF Home Page]
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Rigid-group identification



Dear Colleagues

The next group of proposed data names was also suggested by Gotzon, and
represents a new category designed to specify an object handled as a rigid
group of atom sites. Gotzon's accompanying commentary on this set of data
items is as follows:

 "There is also a proposal for the items defining rigid groups that should
  be included in the Core. In principle, the composition of a rigid group can
  be indicated, as a text, using _atom_site_description. The new items permit
  an operational description. The only disturbing thing is that both
  _atom_site_rigid_group_id and _atom_site_rigid_group_atom_site_label must
  be children of _atom_site_label..."

Regards
Brian

###########################
## ATOM_SITE_RIGID_GROUP ##
###########################
 
data_atom_site_rigid_group_[]
    _name                        '_atom_site_rigid_group_[]'
    _category                    category_overview
    _type                        null
    loop_ _example
          _example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
        _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

    loop_
        _atom_site_description
        _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 is a tetrahedral group formed by the atoms:
                  Se O1 O2 O3 and O1p
              O1p is related to O1 by the mirror plane perpendicular to the 
              c-axis. The coordinates given by _atom_site_fract_ correspond to 
              the centre of mass.
             ;
             SeO4 0.5  0.22346    0.41868    0.250000  ?          ?    SG   
             .
             Se   0.5  0.22216(4) 0.41861(3) 0.250000  0.00428(9) Uani S   
             .
             K1   0.5  0.1670(1)  0.08069(7) 0.250000  0.0102(2)  Uani S  
             .
             K2   0.5 -0.0013(1)  0.70766(4) 0.250000  0.0072(2)  Uani S 
             .
             O1   1.0  0.2890(3)  0.3413(2)  0.0277(3) 0.0130(6)  Uani .
             .
             O2   0.5  0.3130(4)  0.5621(2)  0.250000  0.0119(8)  Uani S
             .
             O3   0.5  0.0092(4)  0.4304(3)  0.250000  0.0164(9)  Uani S

    loop_
        _atom_site_rigid_group_id
        _atom_site_rigid_group_atom_site_label
        _atom_site_rigid_group_site_symmetry
             SeO4      Se      .
             SeO4      O1      .
             SeO4      O1      8
             SeO4      O2      .
             SeO4      O3      .
;
;
    Example 1 - extracted from the refinement listing of the incommensurate 
                phase of K~2~SeO~4~ at 113 K (unpublished).
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
    _definition
;              Data items in the ATOM_SITE_RIGID_GROUP category record
               details about the atomic composition of a rigid group. A rigid
               group is a set of atoms whose displacements with respect to 
               their initial fixed positions are determined by six parameters: 
               three translations and three rotations. Therefore the position 
               of one of the atoms is given by:

                           r~a~=p+R(r~a,i~-p)+t

               r~a~ and r~a,i~ are the actual and the initial atomic positions
               respectively, p is a reference point, where the rotation axes 
               intersect, which is normally chosen to be the rigid group centre
               of mass. The matrix R comprises not only the three rotations 
               (which could be eulerian, axial or along some selected 
               directions) but any other transformation (to a Cartesian system 
               for example) required for the calculations. t is the rigid 
               translation vector. Notice that a rigid group does not
               necessarily coincide with a molecule and therefore it need
               not possess chemical meaning.
;
  
data_atom_site_rigid_group_atom_site_label
    _name                        '_atom_site_rigid_group_atom_site_label'
    _category                    atom_site_rigid_group
    _type                        char
    _list                        yes
    _list_reference              '_atom_site_rigid_group_id'
    _list_link_parent            '_atom_site_label'
 
    _definition
;              _atom_site_rigid_group_atom_site_label is the code that 
               identifies an atom in a loop where the atoms that define a rigid
               group are being listed. This code must match the 
               _atom_site_label of the associated coordinate list and conform 
               to the rules described in _atom_site_label.
;

data_atom_site_rigid_group_id
    _name                        '_atom_site_rigid_group_id'
    _category                    atom_site_rigid_group
    _type                        char
    _list                        yes
    _list_mandatory              yes
    _list_link_parent            '_atom_site_label'
    _definition
;              A code identifying a given rigid group. This code must match the
               _atom_site_label of the associated coordinate list which contains
               the coordinates of its reference point (see the definition of 
               ATOM_SITE_RIGID_GROUP) and conform to the rules described in 
               _atom_site_label. 
;

data_atom_site_rigid_group_site_symmetry
    _name                        '_atom_site_rigid_group_site_symmetry'
    _category                    atom_site_rigid_group
    _type                        char
    _list                        yes
    _list_reference              '_atom_site_rigid_group_id'
    loop_ _example
          _example_detail        .     'no symmetry or translation to site'
                                 4     '4th symmetry operation applied'
                                 7_645 '7th symm. posn.; +a on x; -b on y'
    _definition
;              The symmetry code of each atom site as the symmetry-equivalent
               position number 'n' and the cell translation number 'klm'.
               These numbers are combined to form the code 'n klm' or n_klm.
               The character string n_klm is composed as follows:
 
               n refers to the symmetry operation that is applied to the
               coordinates stored in _atom_site_fract_x, _atom_site_fract_y
               and _atom_site_fract_z. It must match a number given in
               _symmetry_equiv_pos_site_id.
 
               k, l and m refer to the translations that are subsequently
               applied to the symmetry transformed coordinates to generate
               the atom used in calculating the bond. These translations
               (x,y,z) are related to (k,l,m) by the relations
                    k = 5 + x
                    l = 5 + y
                    m = 5 + z
               By adding 5 to the translations, the use of negative numbers
               is avoided.
; 


[Send comment to list secretary]
[Reply to list (subscribers only)]


Copyright © International Union of Crystallography

IUCr Webmaster