Yeah, it would be really nice to be able to pass multiple commands to a script. I did think about putting together an alias with multiple lines, but thought it would be too unwieldy. Writing a python script ended up being the most efficient. Having said that, how does one get a voxelsize from a map? I tried to use mrcfile which I know is installed but ChimeraX doesnt appear to be able to load it. 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 8:09 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Pranav,
Currently ChimeraX does not have a way to substitute argument values into a *.cxc file except for the open command "foreach" option which allows substituting the file name in for $file. For simple series of commands you could define an alias, for example,
alias radcolor open $1 ; color radial palette rainbow ; save $2 height 512 width 512 transparentBackground true
This defines the radcolor command that you can use like
radcolor mymap.mrc image.png
Here's the documentation for the "alias" command
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/alias.html
The other mechanism for handing arguments to a script is the "runscript" command which passes arguments to Python scripts only. I could imagine runscript being enhanced so that it works with a *.cxc command script and substitutes arguments in for $1, $2, $3, ... occurring in the script.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/runscript.html
Tom
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 -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users