Dear Mingsong Wu, Sorry, we do not have resources to figure out the exact command scripts for everybody's project, but here is the general process. (1) figure out Chimera commands for those menu actions. You will probably have to spend some time trying each one to get it right. More details below. (2) then put all those Chimera commands into a Python script for looping as described here <https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> Here are the commands you will want to look at: open, select, delete, write, surface, addh, addcharge, close Help pages for all of these commands are linked here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> However, there are no commands for some of the Dock Prep options, and there is no command for Write DMS. You didn't say which specific options you are using in each of those tools, but if you give all those details, somebody else may be able to provide Python code (I don't know Python). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 12, 2023, at 6:17 PM, 吴明松 via Chimera-dev <chimera-dev@cgl.ucsf.edu> wrote:
Dear Chimera developer,
I would like to perform the same operation on multiple files and I know that this can be done using a loop. However, I am not sure how to write the corresponding command or script. Therefore, could you please help me by writing a script that can perform the following operation? I have installed the 64-bit version of Chimera Headless Linux on my Windows subsystem.
Thank you very much for your help!
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operation:
File-> open -> abc.pdb
Select-> structure->ligand
Actions-> delete
File->save PDB->rec_noH.PDB
Actions->Surface->show
Tools ->structure editing->write dms->rec.ms
Actions->Surface->hide
Tools ->structure editing->Dock prep->rec_charged.mol2 ##select the parameter of Unspecified(determined by method)
File-> open -> abc.pdb
Select-> structure->ligand
Select-> invert (all models)
Actions-> delete
File->save mol2->ligand_site.mol2
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Sincerely, Mingsong Wu
mingsong_wu@foxmail.com _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev