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. --Eric 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@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