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IHM Meeting Summary Mar 8 2018

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brindakv edited this page Mar 8, 2018 · 2 revisions

IHM Meeting Summary Mar 8, 2018

Attended by Ben Webb, Tom Goddard, Mikael Trellet and Brinda Vallat

  1. The new repository with python code adapted from IMP supports the IHM dictionary and has classes that are not IMP dependent. Other classes are under development. MT and TG may be able to use these to incorporate support for the IHM dictionary in HADDOCK and ChimeraX respectively. Any exisiting ChimeraX IHM code that is relevant may be added to this repository.

  2. Issue 58: BV will address this issue based on information regarding solid geometry primitives provided here and here. The aim is to be as generic as possible.

  3. NPC structure may be released soon. SAS data has been added in the recent update. Other related structures such as Nup133 are still in progress. We are waiting for data from SJ.

  4. We had an extensive discussion about how to enhance the impact of the IHM dictionary and PDB-Dev.

    • Provide software tools that will read and write IHM dictionary compliant data files (see point 1 above).
    • Adopt PDBx/mmCIF (and the IHM extension) as the internal working format in modeling software such as IMP and HADDOCK. In IMP, visualization of intermediate results and use of integrative models as starting structural models are the driving force to adopt the IHM dictionary as the internal working format. HADDOCK can accept mmCIF files as input, however it converts these into PDB files (with ATOM records) for internal use. There is a large energy barrier that makes it difficult to shift from the convenient PDB format to the PDBx/mmCIF format.
    • Get more straightforward examples into PDB-Dev quickly. This would increase the value and contents of PDB-Dev. These would mainly involve modeling examples that do not require extensive additions to the dictionary.

  5. More discussions are required to figure out the best way to capture metadata and provenance information regarding the spatial restraints used in the modeling. Should this carried out before modeling or after modeling but before deposition?

  6. The next meeting will be on Thursday, March 15th 2018, at 12:00 PM Eastern time.

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