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

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 5 11:06:11 PST 2008

On Mar 5, 2008, at 8:28 AM, Kristina Furse wrote:

> 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.

Unless you are going to process many trajectories, the easiest  
approach I think is for you to write your Perl script to handle the  
initial zoom/rotation part, then to switch to MD Movie's per-frame  
scripting for the rest.  You don't have to use Python for the per- 
frame scripting, you can use regular Chimera commands.  As mentioned  
in the per-frame dialog, the string "<FRAME>" in commands will be  
substituted with the current frame number, so it should be easy to  
produce uniquely-named files.


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