[chimerax-users] using variables in command files

[Pranav Shah]

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 at 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 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
> > --
> > Pranav Shah
> > Postdoctoral Research Fellow.
> >
> > Division of Structural Biology,
> > Wellcome Trust Centre for Human Genetics,
> > University of Oxford,
> > Roosevelt Drive, Oxford OX3 7BN,
> > UK
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>