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*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)**Reply-To*:*coredmg@iucr.org*

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7 1/2+x,1/2-y,z 8 x,y,1/2-z # # The following loop is much as Gotzon gave it except that the # _*_group_description has been replaced by _atom_site_rigid_group_id # (child of _rigid_group_id), and I have deleted the coordinates # of the atoms in the group since these are defined in the #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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