[Chimera-users] Mol2 Trajectory Reader?

Eric Pettersen pett at cgl.ucsf.edu
Thu Jan 6 15:55:37 PST 2005

Hi Joshua,
	Given that what you really want to do is assemble a movie of your 
conformations rather than actually analyze them as a trajectory, what 
we've decided to do is write an extension that will allow you to record 
whatever is going on in Chimera as a series of frames (it will have a 
"Start" and a "Stop" button) and will assemble those frames into an 
mpeg.  It will optionally allow you to keep the frames in case you want 
to assemble them into a format that is harder for us to support across 
all platforms (e.g. Quicktime), and may also support generating an 
animated GIF.
	A preliminary version will probably be done in a couple of weeks and 
we could send that to you if you want to be a guinea pig.  Otherwise, 
it will be in the next release, which will probably be April or so.


On Dec 25, 2004, at 8:15 PM, S Joshua Swamidass wrote:

> Good point.
> I didn't notice the move menu. The ultimate goal of all this for me is
> to literally make some movies, either with screen shots in sequence or
> ideally if chimera can output an avi automatically. So i guess,
> viewdock should work IF there is a way to capture all the images to
> disk rather than just play them to the screen.
> S Joshua Swamidass
> On Sat, 25 Dec 2004 09:29:55 -0800, Eric Pettersen <pett at cgl.ucsf.edu> 
> wrote:
>> Hi Joshua,
>>        Implementing the Mol2 trajectory format looks perfectly doable 
>> with
>> the data file you provided.  Before proceeding with the work, I guess 
>> I
>> have a question as to why you want to use the molecular-dynamics Movie
>> tool on the file rather than ViewDock tool.  You do know that the
>> ViewDock tool has a "Movie" menu
>> (http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/
>> viewdock/viewdock.html#movmenu) that allows you to step through docked
>> conformers one by one?  I guess I'm trying to determine if I should
>> really be adding this fomat to the Movie tool or if we should somehow
>> be improving the capabilities of ViewDock instead.
>> --Eric

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