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missing link between `_ihm_sphere_obj_site` and `_ihm_model_representation_details`

Open aozalevsky opened this issue 7 months ago • 3 comments

In the scenario when a residue is represented on multiple scales simultaneously:

  1. martini-like (multiple beads per residue, by-feature)
  2. Ca (on bead per residue, 'by-residue`)

It's impossible to distinguish beads corresponding to those levels.

Part of the problem is that each bead maps only to chain + residue numbers. Thus, both martini-like and Ca bead maps to the same residue. By linking _ihm_sphere_obj_site -> _ihm_model_representation_details we can explicitly specify groups of beads, even if they correspond to the sub-residue levels.

Another side of this issue is that a bead resolution (like X residues per bead, or X beads per residue), which is a property of representation, can't be accessed from the _ihm_model_representation_details alone. In current examples, for instance, NPC (PDBDEV_00000012) one record from _ihm_model_representation_details :

15 1 2 Nup85 B 40 sphere . flexible by-feature 5

corresponds to a collection of 5 beads with different resolutions (from 6 to 10 residues per bead):

661 2 1 10 B 384.656 -36.334 194.513 5.750 . 1                                                                                                                                                                                                                                                                                
662 2 11 20 B 393.670 -56.265 193.917 5.750 . 1                                                                                                                                                                                                                                                                               
663 2 21 30 B 382.286 -63.889 194.476 5.750 . 1                                                                                                                                                                                                                                                                               
664 2 31 40 B 371.511 -70.143 196.024 5.750 . 1                                                                                                                                                                                                                                                                               
665 2 41 46 B 358.367 -59.733 188.068 4.931 . 1 

Thus, one has to read the table with actual coordinates to get accurate sizes (which are properties of representation).

aozalevsky avatar Jul 03 '24 22:07 aozalevsky