[Chimera-users] How to run a script in ChimeraX

[Elaine Meng]

Hi Shanti,
Yes, you can run a script by simply opening the script file, as long as the commands or code in it are written correctly for that program. If you are trying to write a script with commands but you are not very experienced with the program, you should first test the commands interactively (by entering them into the command line) in the graphical user interface of the program to make sure they are correct.

Some other tips 
- a command script should be a plain text file
- Chimera and ChimeraX are two different programs; a script for one will not work in the other
- make sure you have a reasonably new version of the program (P.S. there is also a chimerax-users at cgl.ucsf.edu mailing list if you want to ask specifically about ChimeraX)
- if you want help when something doesn't work, you will need to describe exactly what you did and what happened, and possibly also include your structure data ... "does not work" is not enough information

If Chimera, then you need Chimera commands.  Usually filename ends in .cmd or .com
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile>

If ChimeraX, then you need ChimeraX commands.  Usually filename ends in .cxc
<https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files>

For either program, you could also write scripts in python code, or save and restore session files, but again, a script or session for Chimera would only work in Chimera, and one for ChimeraX would only work in ChimeraX.

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

> On Mar 30, 2022, at 5:00 PM, Shanti Pal Gangwar via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi
> I am trying to run a script in chimeraX but it did not work. I even downloaded the example files and that also did not work. I wonder if a script can be run in ChimeraX as we do in PyMol.
> Any help would be appreciated.
> Thank you
> Shanti Pal