Hi Prathvi,
No, there are no commands for the Modify Structure functions in Chimera.

In ChimeraX, we have tried harder to make commands for nearly everything you can do in the GUI, so if you use ChimeraX instead, take a look at the "build modify" command:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#modify>

See also the ChimeraX "open" command option "forEachFile" to run a ChimeraX command file (file.cxc) on each of many input files.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile>

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


> On Nov 3, 2022, at 5:05 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Hi Elaine,
>
> Is there a way to run the Modify Structure tool in UCSF Chimera using command line? I want to substitute a S-atom with O-atom in more than 100 structures and doing it for each structure using the GUI looks very time consuming. Please help.
>
> --
> Prathvi Singh,
> Research Fellow,
> Department of Biological Sciences & Bioengineering,
> Indian Institute of Technology, Kanpur-208016