AMBER Archive (2002)

Subject: RE: PyMOL + AMBER Trajectories

From: DeLano, Warren (
Date: Tue Sep 03 2002 - 12:51:57 CDT

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?


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