[chimerax-users] using variables in command files

[Pranav Shah]

Awesome, thanks!

On Sat, 25 Jun 2022 at 00:45, Tom Goddard <goddard at sonic.net> wrote:

> Hi Pranav,
>
>   I improved the ChimeraX runscript command so it can pass arguments to a
> ChimeraX command file (.cxc suffix) replacing $1, $2, $3 ... in the
> commands with the given arguments.  This will be in tomorrow's daily
> builds.  For example,
>
>         run radcolor.cxc mymap.mrc mymap.png
>
> where the radcolor.cxc text file contains
>
> # Color map radially and save an image
> open $1
> color radial palette rainbow
> save $2 height 512 width 512 transparentBackground true
>
> Thanks suggesting the idea.
>
>         Tom
>
>
> > On Jun 24, 2022, at 12:09 PM, Tom Goddard via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> 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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> >>
> >
> >
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> >
>
> --
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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