[Chimera-users] Batch mode for Chimera

James Starlight jmsstarlight at gmail.com
Wed Aug 30 08:40:03 PDT 2017


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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