[chimerax-users] using variables in command files

[Pranav Shah]

HI Elaine, sorry to write to you privately. Writing for the sake of
reducing the spam in other peoples inboxes. Can I ask how I could then
use the foreach command to color the map value using values from
another map? It seems forachfile has a very limited capacity to handle
more complex workflows and I might have to turn to writing stuff up in
python using the chimerax api.
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 5:02 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> Yes, sorry about that, my example was wrong and should not have had the "open" command inside the cxc file.
>
> Glad you figured it out.
> Best,
> Elaine
>
> > On Jun 24, 2022, at 8:56 AM, Pranav Shah via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> >
> > 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 at 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 $file.png
> >> transparentBackground true
> >>
> >> Looking at the log, ChimeraX appears to be running two open commands
> >> for some reason. In the first instance it opens the map as expected
> >> but then stops executing a second open with the aforementioned error.
> >> Not sure why it needs to run open twice.
> >>
> >> Not sure where I am going wrong.
> >> Best,
> >> Pranav
> >> --
> >> Pranav Shah
> >> Postdoctoral Research Fellow.
> >>
> >> Division of Structural Biology,
> >> Wellcome Trust Centre for Human Genetics,
> >> University of Oxford,
> >> Roosevelt Drive, Oxford OX3 7BN,
> >> UK
> >>
> >> On Fri, Jun 24, 2022 at 4:18 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >>>
> >>> Hi Pranav,
> >>> For something like this I believe you would instead use the "foreach" option of the "open" command to open the ChimeraX command file, which could contain "$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
> >>>
> >
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