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

[Eric Pettersen]

Hi Rafi,
	ChimeraX is considerably more memory efficient that Chimera, which should make it much faster to do this processing, so the issue is whether the capabilities are available.  Adding the hydrogens is basically the same as Chimera.  Instead of having 3 different commands to save files (copy/save/write),  ChimeraX just has one: save.  So saving a Mol2 format file is just "save blah.mol2".  So the issue is adding charges.  ChimeraX's capabilities in some areas aren't as far along as Chimera's (though well past in other areas) so there is no "addcharge" command.  Nonetheless, there is add-charge capability in the Python layer, used by coulombic, and since you are writing a Python script anyway you can just use that.
	So, after adding hydrogens and before writing the Mol2 you would do this:

	from chimerax.atomic import all_residues
	from chimerax.add_charge import add_charges
	add_charges(session, all_residues(session))

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jun 6, 2022, at 5:17 PM, Rafi Brent via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users