Re: Visualization

From: David Case <>
Date: Thu 1 Jun 2000 06:54:39 -0700

On Wed, May 31, 2000, Garrett W Grahek wrote:

> Quick question. Is there a way to open the topology and coordinate
> files into xleap for visualization?

Use "ambpdb" (manual, p. 355) to convert topology and coordinate files to
pdb format, which can be then be loaded into LEaP.

Note that LEaP is not a particularly good visualization program, especially
for any complicated molecule. Once you have a pdb-format file, there
are lots of free and non-free alternatives availalbe for visualization
and analysis. Use the -wrap option to ambpdb to create atom names closer
to the old Brookhaven pdb standard if you plan to use a program like

...good luck....dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  WWW:                         
La Jolla CA 92037  USA            |
Received on Thu Jun 01 2000 - 06:54:39 PDT
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