Headless render images of molecules with PyChimera

pychimera_screenshots.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

from __future__ import print_function
import pychimera
import os
# os.environ['CHIMERADIR'] = '/path/to/headless/chimera'
pychimera.patch_environ()
pychimera.enable_chimera()


import chimera
from chimera import runCommand
from glob import glob


def main(mask='*.pdb', output_directory='.'):
    try:
        os.mkdir(output_directory)
    except:
        pass
    filenames = sorted(glob(mask))

    for i, filename in enumerate(filenames):
        print('{}/{} Rendering {}...'.format(i+1, len(filenames), filename))
        molecules = chimera.openModels.open(filename)
        runCommand('focus')
        runCommand('copy file {}/img{:03d}.png png width 1024'.format(output_directory, i))
        chimera.closeSession()


if __name__ == '__main__':
    import sys
    main(*sys.argv[1:3])
    # Finally, run ffmpeg with something like this:
    # $> ffmpeg -i img%03d.png -c:v libx264 -pix_fmt yuv420p out.mp4