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.:

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.

Eric Pettersen

UCSF Computer Graphics Lab

On Aug 30, 2017, at 8:40 AM, James Starlight <jmsstarlight@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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