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Entity detection in trajectories with protein-ligand complexes #533

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rabiakhd opened this issue Jun 28, 2024 · 1 comment
Open

Entity detection in trajectories with protein-ligand complexes #533

rabiakhd opened this issue Jun 28, 2024 · 1 comment

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@rabiakhd
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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
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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?

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@BradyAJohnston @rabiakhd