[chimera-dev] python script for ligand preparation

[Elaine Meng]

Hi Gayatri,
There is a Dock Prep tool that does all this.  Menu: Tools... Structure Editing... Dock Prep
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html>

If you mean that you have too many files to do individually with the graphical interface, however, you may need to figure out how do it with Chimera commands instead. See commands "open" to open the ligand file, "addh" to add hydrogens,  "addcharge" to assign partial charges (and maybe other commands depending on what you mean by prepare) and"write" to save Mol2.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> 

You should first try entering those individual commands in the Command Line one by one to figure out exactly what options you want for each ligand.  After you know what commands and options you want to use for each ligand, then you can put a python script around it to loop through multiple files as described here
<https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 20, 2022, at 4:37 AM, ngayatri via Chimera-dev <chimera-dev at cgl.ucsf.edu> wrote:
> 
> Dear Chimera Team,
> I am trying to prepare separate ligand file and saving it in the .mol2 file. So if you could help with script or the approach would be grateful. 
> Thank You
> Regards
> Gayatri