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Added atom_sites_* structure id key #53

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e6fbeb5
Clarify structure_id omission in ATOM_SITES* definitions
rowlesmr Jun 30, 2026
6b1b1ff
Fix layout
rowlesmr Jun 30, 2026
a0214f0
Merge branch 'main' into ATOM_SITES_-structure-key
rowlesmr Jul 7, 2026
c67dacd
ATOM_SITES_AXES
rowlesmr Jul 7, 2026
e582fc7
ATOM_SITES_MODULATION
rowlesmr Jul 7, 2026
0af1f76
ATOM_SITES_ORTHO
rowlesmr Jul 7, 2026
df0f23e
upgraded structure references to 'save':structure_id_key
rowlesmr Jul 9, 2026
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70 changes: 66 additions & 4 deletions cif_ms.dic
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,9 @@ save_ATOM_SITE
used in crystallographic structure studies. Items in this
dictionary enhance those in cif_core.cif to cover modulated
structures.

_atom_site.structure_id may be omitted if only one _structure.id
is present in the same data block.
;
_name.category_id ATOM
_name.object_id ATOM_SITE
Expand Down Expand Up @@ -9130,24 +9133,34 @@ save_ATOM_SITES_AXES
_definition.id ATOM_SITES_AXES
_definition.scope Category
_definition.class Loop
_definition.update 2024-08-09
_definition.update 2026-06-15
_description.text
;
Data items in the ATOM_SITES_AXES category record
details about the transformation matrices that define the
displacements and rotations of atoms and rigid groups. Details
for individual atom sites are described by data items in
the ATOM_SITE_DISPLACE_ and ATOM_SITE_ROT_ categories.

_atom_sites_axes.structure_id may be omitted if only one
_structure.id is present in the same data block.
;
_name.category_id CIF_MS_HEAD
_name.object_id ATOM_SITES_AXES
_category_key.name '_atom_sites_axes.matrix_seq_id'

loop_
_category_key.name
'_atom_sites_axes.matrix_seq_id'
'_atom_sites_axes.structure_id'

_description_example.case
;
#\#CIF_2.0

# - - - - data truncated for brevity - - - -

_structure.id "4,4'-Dichlorobiphenyl Sulfone"

loop_
_atom_sites_axes.matrix_seq_id
_atom_sites_axes.matrix
Expand Down Expand Up @@ -9225,6 +9238,17 @@ save_atom_sites_axes.matrix_seq_id

save_

save_atom_sites_axes.structure_id

_definition.id '_atom_sites_axes.structure_id'
_name.category_id atom_sites_axes
_name.object_id structure_id

_import.get
[{'file':templ_attr.cif 'save':structure_id_key}]

save_

save_atom_sites_axes.transf_description

_definition.id '_atom_sites_axes.transf_description'
Expand Down Expand Up @@ -9313,20 +9337,26 @@ save_ATOM_SITES_MODULATION
_definition.id ATOM_SITES_MODULATION
_definition.scope Category
_definition.class Set
_definition.update 2025-06-04
_definition.update 2026-06-15
_description.text
;
Data items in the ATOM_SITES_MODULATION category record details
common to the modulation of atom sites in a modulated structure.

_atom_sites_modulation.structure_id may be omitted if only one
_structure.id is present in the same data block.
;
_name.category_id CIF_MS_HEAD
_name.object_id ATOM_SITES_MODULATION
_category_key.name '_atom_sites_modulation.structure_id'
_description_example.case
;
#\#CIF_2.0

# - - - - data truncated for brevity - - - -

_structure.id Fe(NCS)~2~

_cell.modulation_dimension 1

loop_
Expand Down Expand Up @@ -9690,6 +9720,17 @@ save_atom_sites_modulation.global_phase_t_9

save_

save_atom_sites_modulation.structure_id

_definition.id '_atom_sites_modulation.structure_id'
_name.category_id atom_sites_modulation
_name.object_id structure_id

_import.get
[{'file':templ_attr.cif 'save':structure_id_key}]

save_

save_ATOM_SITES_ORTHO

_definition.id ATOM_SITES_ORTHO
Expand All @@ -9708,6 +9749,9 @@ save_ATOM_SITES_ORTHO
until a desired degree of orthogonality and completeness is
reached (see _atom_site_occ_crenel.ortho_eps).

_atom_sites_ortho.structure_id may be omitted if only one
_structure.id is present in the same data block.

References: Petricek, V., Van Der Lee & Evain, M. (1995).
Acta Cryst. A51, 529-535. DOI 10.1107/S0108767395000365
On the Use of Crenel Functions for Occupationally Modulated
Expand All @@ -9726,13 +9770,20 @@ save_ATOM_SITES_ORTHO
;
_name.category_id CIF_MS_HEAD
_name.object_id ATOM_SITES_ORTHO
_category_key.name '_atom_sites_ortho.func_id'

loop_
_category_key.name
'_atom_sites_ortho.func_id'
'_atom_sites_ortho.structure_id'

_description_example.case
;
#\#CIF_2.0

# - - - - data truncated for brevity - - - -

_structure.id "\d~1~-CoZn~7.8~"

_cell.modulation_dimension 1

loop_
Expand Down Expand Up @@ -9855,6 +9906,17 @@ save_atom_sites_ortho.func_id

save_

save_atom_sites_ortho.structure_id

_definition.id '_atom_sites_ortho.structure_id'
_name.category_id atom_sites_ortho
_name.object_id structure_id

_import.get
[{'file':templ_attr.cif 'save':structure_id_key}]

save_

save_atom_sites_ortho.wave_vector_seq_id_list

_definition.id '_atom_sites_ortho.wave_vector_seq_id_list'
Expand Down
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