IHM Meeting Summary Nov 15 2018

IHM Meeting Summary Nov 15, 2018

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

1. Incorporating support for the IHM-dictionary within HADDOCK using the python-ihm library is in progress. Support has been included for ligands and modified residues.

2. Issue 76: Issue created to address inclusion of multiple extension dictionaries in the audit_conform category.

3. Issue 38: Including definitions for chemical descriptors (SMILE strings, INCHI keys etc.) of crosslinking agents will require modification of the crosslinking restraint categories that are used extensively in the existing structures in PDB-Dev. This will be addressed after
   Issue 76 regarding audit_conform is addressed.

4. Deposition of genome structures require a different mechanism of handling ensembles. Currently, a limited set of representatives are included in the IHM data file and the ensemble is referenced as an external file (may be in DCD format). Additionally, the localization density of the ensemble may be provided using ihm_gaussian_object_ensemble or as an external file. However, for genome structures, picking a limited set of representatives is arbitrary because the structure corresponds to the entire ensemble. The full ensemble should either be contained within the IHM data file or referenced as an external file. Whichever method is chosen, consideration should be given to file size as well as ease and speed of data retrieval (especially for visualization).

5. Work is in progress to organize an IHM workshop during the 2019 Biophysical society meeting at Baltimore.

6. No meeting on November 22nd (Thanksgiving holiday in the US). Next meeting is on Thursday, November 29th at 9AM PT / 12PM ET / 6PM CEST.