[Chimera-users] MD trajectory play by commandline

inhee park ipark.c at gmail.com
Mon Jan 13 17:18:46 PST 2014

Dear Chimera developers and users:

I am using Chimera (production version 1.8 (build 38824) 2013-06-07
21:09:20 UTC).

I wanted to process MD trajectories to extract their detailed H-bond
To do so, I would like to process by script with Hbond.py file.
$ chimera --script Hbond.py

from chimera import runCommand

# pr trajectory movie
with open("metafile", 'w') as m:
    meta_input = """amber
    print >> m, meta_input
runCommand("open movie:metafile")
runCommand("alias ^myhb hbond relax true savefile hbond.$1")
runCommand("perframe myhb")
runCommand("coordset #0 1,1000,10; wait 100")

As I have many MD trajectories to be processed, I was looking for a
in lieu of actually clicking buttons in MD movie GUI to play.
I thought that "coordset #0 1,10000,10; wait 100" may operate like
starting the MD movie to load frame 1 to 1000 at every 100 interval.
But resulting saved H-bond files contain same information all about the
first frame
(because graphically displayed was the first frame without any update
unless clicking the button in MD movie GUI).

Is there a way to achieve an automatic play via commandline?

Thank you,
  inhee park
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