[chimerax-users] Analog of Chimera "addcharges" command in ChimeraX

[Rafi Brent]

To whom it may concern,
   I have about 20,000 pdb files to which I'd like to add Hydrogens, add
partial charges, and convert to the mol2 format using either Chimera or
ChimeraX. I have not had much success with Chimera, as the process slows
down quite drastically over time when run through the GUI, and when I run
Chimera from the terminal (using chimera --nogui  python_script.py), I run
into errors with ANTECHAMBER that do not occur when my script is run
through the GUI. I'll write to the Chimera support email with more details,
and I'd appreciate any advice if you have any, but based on these errors
I'm thinking that there is likely a better way to perform this task using
ChimeraX. I noticed that the "addcharges" command no longer exists in
ChimeraX, and the "write" command which I was using to convert to mol2
files in Chimera appears to have been replaced as well. Because of this,
any recommendations about how to run my operation using the closest analogs
to the original Chimera methods would be greatly appreciated. Thanks so
much for any advice you may have.

Sincerely,
Rafi Brent
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