Comments (3)
While separation of content and format are important considerations adopting naming
conventions, overloading the file name extension to carry both of these details is not path that we would prefer to follow. We would prefer to follow to follow a convention where the file extension
identifies the parsing syntax, and then separately specify the content specification (e.g. supporting dictionary/schema). For example, in file released by PDB in recent years, audit records are provided in the mmCIF files and schema records in PDBML files to identify content specifications.
As a practical alternative to using the file extension to convey content details, we would prefer to
use a combination internal audit records and standard file naming templates to convey this
information. For example, accession-code-ihm.cif ) .
from ihmcif.
Related discussion in Chimera issue 16277.
from ihmcif.
One proposal from last week's Skype meeting was to use the extension .ihm.cif
for these files. This allows for packages such as ChimeraX to recognize the files as using the IHM dictionary based purely on the file extension, while at the same time allowing non-IHM software (such as legacy Chimera) to visualize at least the atomic information in the file.
from ihmcif.
Related Issues (20)
- Add AlphaFoldDB to the list of databases HOT 3
- the data category 'ihm_ordered_ensemble' is misleading
- Add generic restraints
- Depositor-reported cross-linking satisfaction rates
- Dictionary update for Input dataset groups - Add modeling option for application
- Item type for `_ihm_dataset_related_db_reference.accession_code`
- Extend IHMCIF to add model_id to existing PDBx/mmCIF tables
- Updated descriptions of model related categories
- Allow for optional asym_id in tables where information can be the same across different instances of the same entity
- Allow for segments of branched entities to be defined and used in related categories
- Review parent-child relationships in ihm_starting_model_coord
- Add "starting model" to the enumeration list for `_ihm_dataset_group.application`
- Address redundant parent-child relationships in atom_site category
- Update CX-MS to Crosslinking-MS in the dictionary
- Expand ihm_cross_link_list table
- Rename `ihm_ensemble_info` category HOT 3
- Use cases of `multi-residue` `_ihm_model_representation_details.model_granularity`
- missing link between `_ihm_sphere_obj_site` and `_ihm_model_representation_details` HOT 3
- Remediation of jPOST IDs with ProteomeExchange
- Update all PDB-Dev references to PDB-IHM
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