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AMBER Archive (2002)Subject: RE: PyMOL + AMBER Trajectories
From: DeLano, Warren (warren_at_sunesis.com)
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.
Does anyone have the following which they could share?
* A trajectory based on a non-orthogonal periodic box
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,
-- 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
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