Entity detection in trajectories with protein-ligand complexes

[rabiakhd]

Blender 4.1 Molecular Nodes 4.1.4 Windows 11

MD simulation software: Schrodinger Maestro Trajectory conversion form .cms to .dcd using VMD

topology and trajectory files: [https://miami.box.com/s/mdwiau38bho3dv635flszy3169602l9a]

The ligand and solvent are grouped together and identified as one chain on MD import Automatic ligand detection from protein-ligand complexes inside trajectories will be awesome.

[BradyAJohnston]

This seems to be more an issue the topology. Looking at the data you sent, there are only two chains identified in the topology to begin with.

>>> np.unique(universe.atoms.chainIDs)
array(['A', 'X'], dtype=object)

There is potential to improve the ligand detection though - how would you extract ligand information from this trajectory currently?