Thank you so much for your immediate assistance.

Hi Minsong, In general, I agree 100% with Tom Goddard. It is very convenient to use the ChimeraX menu and click icons and then easily see in the Log the commands that were used. However, currently ChimeraX does not have the ability to write DMS. I believe it does have all the other steps that you mentioned in your first message, as ChimeraX commands: open, select, delete, save, surface, dockprep, close <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> Another advantage of ChimeraX is that you can do some simple looping to execute the same ChimeraX command file on multiple input files without having to use python code. See the "forEachFile" option of the "open" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> If in the future you have ChimeraX questions, we recommend using this address: chimerax-users@cgl.ucsf.edu <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 15, 2023, at 10:16 AM, Tom Goddard via Chimera-dev <chimera-dev@cgl.ucsf.edu> wrote:

You would be better off using ChimeraX instead of the old Chimera program which we stopped developing many years ago. In ChimeraX the menu entry and buttons you click log equivalent commands so you can see the equivalent command easily. Chimera does not do that so it is harder to figure out the commands.

Tom

...

From: Elaine Meng via Chimera-dev <chimera-dev@cgl.ucsf.edu> Subject: Re: [chimera-dev] Queries about operational command of chimera Date: May 14, 2023 at 9:37:35 AM PDT

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!

###################################

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

###################################

Sincerely, Mingsong Wu