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Rigid-group identification
- To: Multiple recipients of list <coredmg@iucr.org>
- Subject: Rigid-group identification
- From: Brian McMahon <bm@iucr.org>
- Date: Wed, 9 May 2001 10:03:43 +0100 (BST)
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.
;
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