From ed3dc188ce7e4d242c85b7ab9bc34fcc7f8baeb2 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Wed, 13 Dec 2023 18:03:16 +0100
Subject: [PATCH] doc: SCHWED-6088 add note on data items requirements
Make it clear we require author residue numbers and insertion codes for
waters and ligands. This is due to a limitation (flaw?) of the format.
And yes, waters may include H atoms so this is not easily worked around.
---
modules/io/doc/mmcif.rst | 15 +++++++++++++++
1 file changed, 15 insertions(+)
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 6fd699772..53880c2dd 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -89,8 +89,23 @@ Notes:
* ``atom_site.auth_asym_id``: ``residue.GetStringProp("pdb_auth_chain_name")``
* ``atom_site.auth_seq_id``: ``residue.GetStringProp("pdb_auth_resnum")``
* ``atom_site.pdbx_PDB_ins_code``: ``residue.GetStringProp("pdb_auth_ins_code")``
+
+ The last two items might be missing (not empty) if the ``atom_site.auth_seq_id``
+ or ``atom_site.pdbx_PDB_ins_code`` are not present in the mmCIF file.
* Missing values in the aforementioned data items will be denoted as ``.`` or
``?``.
+* Author residue numbers (``atom_site.auth_seq_id``) and insertion codes
+ (``atom_site.pdbx_PDB_ins_code``) are optional according to the mmCIF
+ dictionary. The data items (whole columns) can be omitted in structures where
+ the "new" residue numbers (``atom_site.label_seq_id``) are defined (to valid
+ values). This is usually the case for polymer chains. However non-polymer and
+ water chains do not have valid "new" residue numbers. In structures
+ containing such missing data, OST requires the presence of both "old" residue
+ numbers and insertion codes in order to identify and build residues properly.
+ It is a known limitation of the mmCIF format to allow ambiguous identifiers
+ for waters (and ligands to some extent) and so we have to require these
+ additional identifiers.
+
Info Classes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
--
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