[Chimera-users] Step through trajectory from command line?

Kristina Furse kfurse at nd.edu
Wed Mar 5 08:28:19 PST 2008

> 	There is no command for advancing trajectory frames.  Perhaps you
> can detail the scenario that you need this for and why the per-frame
> scripting of the MD Movie tool doesn't cover your needs.  Are you
> trying to completely automate the production of a movie from a
> trajectory or some such?


> 	Even if there were a command to advance the trajectory, how would
> you know when to stop?  There are no "flow control" statements (if
> statements/for loops/functions) in the Chimera command language.  I
> think you will have to use Python scripting for completely automating
> trajectory-related scripting.  I can provide assistance there.

You are correct in your assessment--I don't know Python, but I do know Perl so I
just wanted to use Perl to produce a line by line Chimera script that would do
some zooms and rotations, writing POV files (actually x3d files that I'll
translate into POV files in a later step), then flow straight into an MD movie,
writing POV files for each frame. No worries--I'm sure I can figure out how to
do a per-frame Python script that will write an x3d file with a unique name for
each trajectory frame. It just made more sense to me the other way around.


Kristina Furse
Postdoctoral Research Associate
262 Stepan Chemistry Hall
Notre Dame, IN 46556

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