Ah! OK i see where I was going wrong. essentially there is no need to include an open command in the command file because that is implicit in the open call to the command file in the GUI. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Fri, Jun 24, 2022 at 4:50 PM Pranav Shah <p.shah.lab@gmail.com> wrote:
Thanks for that pointer Elaine. I have a question- (a) <file> has no suffix error - I am running the program as described in the help page. Essentially, open test.cxc foreach myfile.* My script has the following three lines in it open $file color radial #1 palette rainbow
save $file.png transparentBackground true
Looking at the log, ChimeraX appears to be running two open commands for some reason. In the first instance it opens the map as expected but then stops executing a second open with the aforementioned error. Not sure why it needs to run open twice.
Not sure where I am going wrong. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Fri, Jun 24, 2022 at 4:18 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, For something like this I believe you would instead use the "foreach" option of the "open" command to open the ChimeraX command file, which could contain "$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