IHM Meeting Summary Sep 14 2017

IHM Meeting Summary Sep 14, 2017

Attended by Ben Webb, Tom Goddard, David Castillo, John Westbrook and Brinda Vallat

1. Representing hierarchy of structural components (issue 40):

   This has been incorporated using IHM_STRUCT_ASSEMBLY_CLASS, IHM_STRUCT_ASSEMBLY_CLASS_LIST and _ihm_struct_assembly.parent_assembly_id in the updated dictionary. David will create an example that represents the hierarchy using these data categories and data items and Tom will help visualize the hierarchy using ChimeraX.

2. Discussion on coloring distance restraints derived from chemical crosslinks:

   • Coloring based on restraint type would be useful.
   • Coloring based on satisfaction and/or violation of distance restraints may be enhanced with better gradation rather than the current green and red lines.
   • Definitions may be required for representing both upper and lower bounds in a distance restraint (David to verify and email). Currently only a distance threshold is defined (_ihm_cross_link_restraint.distance_threshold).

3. Broader discussion on what the project needs in the long term:

   (i) Funding

   (ii) More structures in PDB-Dev

   (iii) Better visualization of multi-state models (exosome example) and hierarchies of structural assemblies (example from David awaited)

   (iv) Data harvesting tools capable of collecting data from different sources (experimental and computational) in different formats (csv, tsv, excel, plain text, json, hdf5 etc.) and converting these to PDBx/mmCIF extension format. ChimeraX is interested in providing this capability. It would be useful if the visualization tool also provides the capability to write data in IHM format. The main challenge is in capturing the detailed relationships between data items in different categories that may originate from different sources (eg: mapping starting homology model templates and alignments to the molecular system). These data harvesting tools will enable the end user to create the files in the correct format for deposition to PDB-Dev and will address point (ii) above.