[chimerax-users] using variables in command files

[Pranav Shah]

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 at 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 at 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
>