[Chimera-users] Batch mode for Chimera

Eric Pettersen pett at cgl.ucsf.edu
Wed Aug 30 13:54:11 PDT 2017

Hi James,
	First, if you want to save images without showing the Chimera GUI then you have to use the “headless” version of Chimera, available on the download page.  To do the other things you want, just put the equivalent commands in a file that ends in “.cmd” and just add that file to your invocation of Chimera, e.g.:

	chimera $pdb script.cmd

The easiest way to handle the image file name is probably to used a fixed name in the Chimera “copy” command, and then in your bash script move that file to the final name you want.  Also, "preset” is the command to apply presets — “help preset” in Chimera for more info.

Hope this helps.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Aug 30, 2017, at 8:40 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> Dear Chimera Users!
> My simple bash script loops the folder with the pdbs and open it in Chimera
> for pdb in ${output}/xtc_proc/*.pdb ; do
> name=$(basename "$pdb")
> echo "I am sending ${name} to Chimera!"
> chimera $pdb
> done
> My question - can I use with chimera some batch file which will
> apply the following commands to each of the loaded pdbs without
> opening of Chimera GUI:
> 1- Apply "publications-2" preset
> 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb
> according to b-factor provided in the pdb file
> 3- make a screen-shot of the colored cartoon figure in the selected
> output folder.
> I thanks so much for the example of batch file and the syntax accepted
> by chimera from the linux shell.
> James
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