Skip to content

IHM Meeting Summary Oct 19 2017

Jump to bottom Edit New page
brindakv edited this page Oct 19, 2017 · 1 revision

IHM Meeting Summary Oct 19, 2017

Attended by Ben Webb, Tom Goddard, David Castillo, Lukas Hoenig, Mikael Trellet, John Westbrook and Brinda Vallat

  1. Dictionary validation tool needs to be updated to work for concatenated dictionary extensions. In the interim, the sdb files can be provided on GitHub.

  2. Heterogeneous models: Visualization software such as Chimera and pymol assume that different models within an entry are homogeneous with the same set of atoms in each model, provided in the atom_site category. This assumption breaks for I/H models, where the models within an entry can be heterogeneous (mapped to the ihm_struct_assembly category).

  3. The following issues need to be addressed in the HSA structures:

    • The three domains modeled separately should be three different entries.
    • The ProteomeXchange accession code should be added to the data file.
    • The predicted contacts data could be uploaded to Zenodo and linked via a DOI.
    • It is not possible to interpret residue-based crosslinking restraints in an atomistic model. Atom ids should be included in the ihm_cross_link_restraint table (_ihm_cross_link_restraint.atom_id_1 and _ihm_cross_link_restraint.atom_id_2).
    • _ihm_cross_link_restraint.group_id should refer to _ihm_cross_link_list.id.

  4. ChimeraX updates:

    • Update to match the latest dictionary (will fix Nup84, Mediator and Exosome visualization)
    • Support for atomistic I/H models that contain atom_site category (will support visualization of diubiqutin and HSA structures)
    • Visualization of structural hierarchies (TADs)
    • Visualization of multi-state models (Exosome)

  5. Issue 46: Different kinds of experiments provide information on residues that are at the interface of two chains. HADDOCK encodes this information as a set of ambiguous distance restraints between the interface residue and a set of residues from the other chain. Mikael will provide detailed examples of how these are implemented in HADDOCK (including upper or lower distance bounds, uncertainties, ambiguities, fraction of restraints used in the modeling etc) so that they can be defined in the dictionary.

  6. Issue 47: Distance restraints can be obtained from different experiments. These may be represented as residue-residue contacts or atomic distances or distance between coarse-grained spheres or blobs or centers of mass from a set of atoms. Mikael will provide an enumerated list of anchor points that are likely to be used for defining distance restraints in modeling. These can then be incorporated into the dictionary.

  7. Next meeting is scheduled for Wednesday, October 25th at 12:00 PM Eastern time.

Add a custom footer
Clone this wiki locally