IHM Meeting Summary Jun 15 2017

IHM Meeting Summary Jun 15, 2017

Attended by BW, JW and BV

1. BW to send the list of subscribers in the ihm-repval (ihm-repval@salilab.org) email list (done).

2. BV to follow up with Juergen Koefinger and Mike Goodstadt (done).

3. BV will work on the EAGER final report, due on 06/30/2017.

4. BV will validate the new multi-state exosome mmCIF file (done). No errors.

5. Issue 19: The IHM extension can be added to the wwPDB mmCIF webpage. BV to send JW the link to the dictionary (done).

6. Issue 37: It is more useful to refer to the aligned and transformed ensemble structures (instead of randomly oriented ones that are generated directly by IMP) in the mmCIF file. Once TG provides the transformed files, BW will update the files on zenodo and the references within the mmCIF files.

7. Issue 9, follow up on email discussion on describing multiple states: The exosome example contains two states: a nuclear-localized state and a cytoplasm-localized state i.e., complex ABCD and ABCE. Chains A, B and C are common in both states, and chain D and E exclusive to one of two states.
   The question is whether the mmCIF definitions should describe the same entities in multiple states as different chains or not.

   • The multiple copies of the same entity in the two states (as in exosome) can all have different asym_ids (ABCD, EFGH where A=E, B=F, C=G and D & H are different)
   • Or they can have the same asym_ids in multiple states (ABCD and ABCE) and described as separate structure assemblies in ihm_struct_assembly.

   The modeling assumes the ABC subunits as the same in both states (same representation, same starting models, same sequence, same subset of crosslinks). Therefore, it is better to keep the multi-state definitions in the mmCIF file consistent with the modeling and use the second option above.