From e6fbeb52a4aaaf685b39d7b22948899273fff812 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Tue, 30 Jun 2026 14:01:49 +0800 Subject: [PATCH 1/6] Clarify structure_id omission in ATOM_SITES* definitions Added notes about omitting structure_id when only one _structure.id is present. --- cif_ms.dic | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/cif_ms.dic b/cif_ms.dic index 81674ef..b9545dd 100644 --- a/cif_ms.dic +++ b/cif_ms.dic @@ -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 @@ -9110,6 +9113,9 @@ save_ATOM_SITES_AXES 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 @@ -9210,6 +9216,9 @@ save_atom_sites_axes.structure_id ; A code identifying the crystallographic structure associated with the atom sites. + + This data name may be omitted if only one _structure.id is present in + the same data block. ; _name.category_id atom_sites_axes _name.object_id structure_id @@ -9313,6 +9322,9 @@ save_ATOM_SITES_MODULATION ; 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 @@ -9694,6 +9706,9 @@ save_atom_sites_modulation.structure_id ; A code identifying the crystallographic structure associated with the atom sites. + + This data name may be omitted if only one _structure.id is present + in the same data block. ; _name.category_id atom_sites_modulation _name.object_id structure_id @@ -9722,6 +9737,9 @@ save_ATOM_SITES_ORTHO The functions are constructed selecting Fourier harmonics 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 @@ -9883,6 +9901,9 @@ save_atom_sites_ortho.structure_id ; A code identifying the crystallographic structure associated with the atom sites. + + This data name may be omitted if only one _structure.id is present + in the same data block. ; _name.category_id atom_sites_ortho _name.object_id structure_id From 6b1b1ff55ab7911919becdadb7d09c7b2d64503d Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Tue, 30 Jun 2026 14:33:37 +0800 Subject: [PATCH 2/6] Fix layout --- cif_ms.dic | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/cif_ms.dic b/cif_ms.dic index b9545dd..e2f680c 100644 --- a/cif_ms.dic +++ b/cif_ms.dic @@ -71,8 +71,8 @@ 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 + + _atom_site.structure_id may be omitted if only one _structure.id is present in the same data block. ; _name.category_id ATOM @@ -9113,8 +9113,8 @@ save_ATOM_SITES_AXES 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 + + _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 @@ -9216,8 +9216,8 @@ save_atom_sites_axes.structure_id ; A code identifying the crystallographic structure associated with the atom sites. - - This data name may be omitted if only one _structure.id is present in + + This data name may be omitted if only one _structure.id is present in the same data block. ; _name.category_id atom_sites_axes @@ -9322,8 +9322,8 @@ save_ATOM_SITES_MODULATION ; 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 + + _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 @@ -9706,8 +9706,8 @@ save_atom_sites_modulation.structure_id ; A code identifying the crystallographic structure associated with the atom sites. - - This data name may be omitted if only one _structure.id is present + + This data name may be omitted if only one _structure.id is present in the same data block. ; _name.category_id atom_sites_modulation @@ -9737,8 +9737,8 @@ save_ATOM_SITES_ORTHO The functions are constructed selecting Fourier harmonics 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 + + _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). @@ -9901,8 +9901,8 @@ save_atom_sites_ortho.structure_id ; A code identifying the crystallographic structure associated with the atom sites. - - This data name may be omitted if only one _structure.id is present + + This data name may be omitted if only one _structure.id is present in the same data block. ; _name.category_id atom_sites_ortho From c67dacd58642543996680371c9290ff7e35c57eb Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Wed, 8 Jul 2026 01:02:04 +0800 Subject: [PATCH 3/6] ATOM_SITES_AXES --- cif_ms.dic | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/cif_ms.dic b/cif_ms.dic index c9729ae..180b985 100644 --- a/cif_ms.dic +++ b/cif_ms.dic @@ -9133,7 +9133,7 @@ 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 @@ -9147,13 +9147,20 @@ save_ATOM_SITES_AXES ; _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 From e582fc73dc23c22f0b8187bdac2dd7119a4ed550 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Wed, 8 Jul 2026 01:02:14 +0800 Subject: [PATCH 4/6] ATOM_SITES_MODULATION --- cif_ms.dic | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/cif_ms.dic b/cif_ms.dic index 180b985..5069ba5 100644 --- a/cif_ms.dic +++ b/cif_ms.dic @@ -9348,7 +9348,7 @@ 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 @@ -9359,12 +9359,15 @@ save_ATOM_SITES_MODULATION ; _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_ From 0af1f766a5429094c701e24e52cb5837124d5280 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Wed, 8 Jul 2026 01:02:59 +0800 Subject: [PATCH 5/6] ATOM_SITES_ORTHO --- cif_ms.dic | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/cif_ms.dic b/cif_ms.dic index 5069ba5..1956ba4 100644 --- a/cif_ms.dic +++ b/cif_ms.dic @@ -9792,13 +9792,20 @@ 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_ From df0f23eca34b1dcaf211cf8d496617a33b9a67e2 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Thu, 9 Jul 2026 20:21:35 +0800 Subject: [PATCH 6/6] upgraded structure references to 'save':structure_id_key --- cif_ms.dic | 51 +++++++++------------------------------------------ 1 file changed, 9 insertions(+), 42 deletions(-) diff --git a/cif_ms.dic b/cif_ms.dic index 1956ba4..47a29a8 100644 --- a/cif_ms.dic +++ b/cif_ms.dic @@ -9241,22 +9241,11 @@ save_ save_atom_sites_axes.structure_id _definition.id '_atom_sites_axes.structure_id' - _definition.update 2026-06-15 - _description.text -; - A code identifying the crystallographic structure associated with the - atom sites. - - This data name may be omitted if only one _structure.id is present in - the same data block. -; _name.category_id atom_sites_axes _name.object_id structure_id - _name.linked_item_id '_structure.id' - _type.purpose Link - _type.source Assigned - _type.container Single - _type.contents Word + + _import.get + [{'file':templ_attr.cif 'save':structure_id_key}] save_ @@ -9734,22 +9723,11 @@ save_ save_atom_sites_modulation.structure_id _definition.id '_atom_sites_modulation.structure_id' - _definition.update 2026-06-15 - _description.text -; - A code identifying the crystallographic structure associated with the - atom sites. - - This data name may be omitted if only one _structure.id is present - in the same data block. -; _name.category_id atom_sites_modulation _name.object_id structure_id - _name.linked_item_id '_structure.id' - _type.purpose Link - _type.source Assigned - _type.container Single - _type.contents Word + + _import.get + [{'file':templ_attr.cif 'save':structure_id_key}] save_ @@ -9931,22 +9909,11 @@ save_ save_atom_sites_ortho.structure_id _definition.id '_atom_sites_ortho.structure_id' - _definition.update 2026-06-15 - _description.text -; - A code identifying the crystallographic structure associated with the - atom sites. - - This data name may be omitted if only one _structure.id is present - in the same data block. -; _name.category_id atom_sites_ortho _name.object_id structure_id - _name.linked_item_id '_structure.id' - _type.purpose Link - _type.source Assigned - _type.container Single - _type.contents Word + + _import.get + [{'file':templ_attr.cif 'save':structure_id_key}] save_