[chimerax-users] Command line utility for .cmap

[Tom Goddard]

Hi Daniel,

  In theory you should be open your MRC files as a series with ChimeraX command "open map*.mrc vseries true".  But the vseries option is currently broken as described in bug report

	https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3519#comment:7 <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3519#comment:7>

Probably Eric will fix that in a day or two.

  If you still prefer making the cmap file, ChimeraX is the only thing that writes those files, cmap stands for Chimera map, and I think you could run chimerax like "chimerax --nogui --exit --cmd "open maps*.mrc ; save map.cmap models #1-100" using the "--cmd" option described in the docs

	https://www.rbvi.ucsf.edu/chimerax/docs/user/options.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/options.html>

to run a command (here two commands separated by semicolon) instead of starting the ChimeraX GUI.  Worked when I tried it.  The "100" can be larger than the number of models without causing any errors so you don't need to know exactly how many maps you are saving.

	Tom


> On Jul 15, 2020, at 12:14 PM, Daniel Asarnow <asarnow at msg.ucsf.edu> wrote:
> 
> Hi all,
> I have only been able to load volume series data using the .cmap format (using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop.
> 
> Best,
> -da
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