[chimerax-users] Analysis of the protein-ligand interactions using ViewDock

[Enrico Martinez]

Dear ChimeraX users!

I would like to use ChimeraX to calculate protein-ligand contacts
established in docking calculations for the ensemble of the docking
solutions (88 conformations of the ligand saved in multi-model
format). Basically using the GUI of the UCSF Chimera previously I
could do the following routine for the analysis of docking results:
1. Open the protein PDB
2. Use the Surface/Binding Analysis > ViewDock tool to open the docking poses
3. Using the Model Panel, select all docking poses
4. Use the Surface/Binding Analysis >  FindHBond tool to locate all
H-bonds. Make sure to check "Only find H-bonds with at least 1 end
selected". You can check "write information to file" to save the
H-bonds.

May I adapt this protocol with the ChimeraX to perform such computing
in batch (no-gui mode)? What should be the differences in the commands
between Chimera and ChimeraX ( I've already seen that ViewDock is
available in the ChimeraX as well...)
Many thanks in advance!
Cheers
Enrico