IHM Meeting Summary Mar 22 2018

IHM Meeting Summary Mar 22, 2018

Attended by Ben Webb and Brinda Vallat

1. Issue 56: In the ihm_modeling_post_process category, add the following optional data items:

   • struct_assembly_id
   • dataset_group_id

   This would apply for the post-process step that uses a different sub-assembly or dataset group.

2. Issue 57: Missing residues can be identified in a straight forward way by comparing the ihm_struct_assembly table (contains the details of the entire assembly being modeled) and the tables representing the three-dimensional structure of the macromolecular assembly - atom_site, ihm_sphere_obj_site and ihm_gaussian_obj_site. Creating a separate category to identify the missing residues will be useful only if additional metadata regarding why the residues are missing is included. BW will provide a set of enumerations that provide the reasons why some regions are included in the ihm_struct_assembly table, but are missing from the modeled structure (done).

3. Issue 58: Initial set of definitions are available here.

   • Some redundancies can be removed (albeit at the cost of flexibility):
     • Scaling factor in the transformation category
     • Base plane in torus and half-torus defintions (default can be XY plane and transformation can be applied to generate other planes)
     • ihm_geometric_object_center (default can be 0,0,0 and the tranformation can be applied to move the center)
   • Are Euler angles the best way to represent rotation of 3D geometric objects, especially due to the various conventions? Also include clock-wise rotations in the set of conventions.
   • The spatial restraints table is yet to be reviewed.
   • More discussion to follow after BW generates an example.

4. The next meeting will be on Thursday, March 29th 2018, at 12:00 PM Eastern time.