[Chimera-users] Using ChimeraX in no-gui mode

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 15 11:59:31 PDT 2019

Hi James,
There is a different email address for asking ChimeraX questions (CC’d here).

Yes, you can script imaging in ChimeraX with nogui if you are using Linux and start with the “nogui” and “offscreen” options on the system command line (they have dash-dash in front but my Mail keeps editing it to a long hyphen instead). 

 In ChimeraX the command script filenames end in .cxc

The commands may be different than in Chimera.  Open is with “open”  save is with “save” and there is no publication preset but you can change to white background and show silhouettes with the “set” command.  See the individual command help pages

making images

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 15, 2019, at 2:14 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> Dear Chimera users!
> Would be possible to use new ChimeraX for execution of some simple
> scripts for structure visualisation and imaging via no-gui mode?
> I am using bash script to loop over pdbs and would like to
> 1) open each pdb which contains b-factors info in chimeraX
> 2) apply preset publication
> 3) colour the pdb using "color byattribute bfactor palette rainbow ave residue"
> 4) save high quality image at the selected directory using chimera render
> Would it be possible to do these things directly from linux terminal
> providing each time pdb and some script file with the list of the
> applied commands?
> chimerax-daily ${pdb} ${script}
> Thank you in advance!

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