Thanks to those of you who have responded to my request for Amber trajectories. They've been quite helping in teaching PyMOL how to read both Amber6 and Amber7 prmtop & trajectory files. Based on my tests, it looks like PyMOL can give up to 100-frames a second playback even on very large systems (10k+ atoms). The longest trajectory I've tested is 2350 frames, without a hiccup.
However, I'm still looking for a few more examples to test before releasing the new version.
Does anyone have the following which they could share?
* A trajectory based on a non-orthogonal periodic box
* A trajectory based on a truncated octahedron in a non-orthogonal periodic box (if such a beast exists...)
Also, I've got a question about centering: Sometimes the interesting molecule in a trajectory will straddle the periodic boundary, creating a trajectory which is difficult to visualize. Would it be useful for PyMOL to be able to optionally center an atom selection in the periodic cell at load time?
Cheers,
Warren
--
mailto:warren_at_sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 FAX:(650)-266-3501
Received on Tue Sep 03 2002 - 10:51:57 PDT
