IHM Meeting Summary Feb 23 2017

IHM Meeting Summary Feb 23, 2017

Attended by BW, TG, OS, JW and BV

1. Introductions

   The IHM dictionary extension is being developed collaboratively to enable the archival of integrative/hybrid models of macromolecular assemblies. These structural models can be multi-scale, multi-state or time-ordered ensembles and are built using restraints derived from a variety of experiments. Our efforts are focused on capturing the details of these complex integrative models and associated methods in an extension dictionary that is compliant with the PDBx/mmCIF dictionary.

2. Updates since last meeting

   • IHM extension dictionary and documentation have been updated to address issue 2, issue 6 and issue 14.
   • Next steps: BW will adopt these in IMP to produce examples (Nup84, mediator and exosome) that incorporate these changes and TG will adopt these in ChimeraX. BV will address issue 8 and provide a high level overview of the dictionary.

3. Further discussion on specific issues at the Github repository

   • Issue 3: Using file extensions to differentiate IHM files from mmcif files were discussed. It is perhaps better to separate content specification (cif, mmcif, ihm) from the parsing syntax (cif) and not overload the file extension to handle both. Examples of XML, RDF and HDF5 files were discussed.
   • Issue 7: Pros and cons of using the ihm_starting_model_coord category to capture the starting structural models were discussed. While it is very useful for the archive to have the starting models defined in the same data file as the resulting integrative model, software developers prefer the starting models to be separate and follow the PDBx/mmCIF data model. Suggestion: Starting model files compliant with the PDBx/mmCIF dictionary can be made mandatory at deposition (either deposited in the PDB or the Model Archive or linked via a DOI) so that these are available for all I/H models and can be used by Chimera and other visualization software. The ihm_starting_model_coord category is an archive requirement and can be populated by the archive from these external objects. Outstanding issue (to be discussed at the next meeting): How to handle starting models with minor modifications such as changing MSE to MET?
   • Issue 19: We will include the IHM extension dictionary at the wwPDB mmCIF resource site.
   • Issue 21: Need a new data item (either free text or enumerated list) to clarify what each "state" in multi-state modeling is. It may also be possible to generalize the ihm_time_ordered_ensemble category to capture a set of I/H models ordered in a generic manner (to be discussed further at the next meeting).
   • We also discussed the use of restraints derived from FRET experiments in integrative modeling and how to capture this information in the IHM dictionary extension.

4. The meeting had to end abruptly due to audio issues with Skype. We will reschedule these monthly meetings at a more convenient time and discuss this offline via email.