IHM Meeting Summary Apr 20 2017

IHM Meeting Summary Apr 20, 2017

Attended by BW, TG, JW and BV

1. The dictionary has been updated based on last week's discussion and the three IMP examples have also been updated accordingly. The updated Nup84, Exosome and Mediator cif files have been validated against the updated dictionary. Only Nup84 had errors:

   ERROR - In block "imp_model", mandatory item _ihm_dataset_related_db_reference.accession_code has invalid value "?" in row: _ihm_dataset_related_db_reference.id == "11"

   ERROR - In block "imp_model", mandatory item _ihm_starting_comparative_models.template_auth_asym_id has invalid value "?" in row: _ihm_starting_comparative_models.ordinal_id == "13"

   ERROR - In block "imp_model", mandatory item _ihm_starting_comparative_models.template_auth_asym_id has invalid value "?" in row: _ihm_starting_comparative_models.ordinal_id == "14"

These are due to missing information. BW will complete these fields when information is availble from the IMP modelers.

2. With the current set of updates, is _ihm_starting_model_details.starting_model_sequence_offset still relevant? Possibly, yes

3. Reference to alignment files in external format (ClustalW, PIR, FASTA): These are only provided to enable users to use the PDBx/mmCIF as a working format. The archival format for alignments will follow the MA_ALIGNMENT_DETAILS, MA_ALIGMENT and associated categories from the Model Archive dictionary and ChimeraX will be updated to support this information.

4. Requirements for ChimeraX Demo: Preferable to use the Nup84 example. The missing information in the Nup84 example include

   • multiple sequence alignments for starting comparative models (related to issue 16
   • ensemble structure models (related to issue 24
   • 2DEM information (related to issues 30 and 33)

5. Current focus is on getting more integrative model examples from non-IMP sources - recognition of the missing elephant in the room.