Hi Pranav, For something like this I believe you would instead use the "foreach" option of the "open" command to open the ChimeraX command file, which could contain "$file" meaning the base name (before suffix) of the input files. This also allows specifying multiple input files to loop through in one "open" command, as explained here <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> Your command file would contain something like open $file color radial palette rainbow save $file.png height 512 width 512 transparentBackground True ...i.e. there is only one substitution string $file (you can't have a different $outfile), but in the example above if you opened 2gbp.pdb, the saved image would then be named 2gbp.png. If you opened infile.mrc, then the saved image would be named infile.png. 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 24, 2022, at 5:57 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team, Is it possible for one to declare a variable in a command file that can then be passed to via the chimeraX command line interface. A minimal example of something I would like to do is - command.cxc open $file color radial palette rainbow save $outfile.png height 512 width 512 transparentBackground True
In the chimeraX command line window I would then like to run open command.cxc infile.mrc outfile.png Best, Pranav