On 23/11/10 17:00, Mark Abraham wrote:
If you only want a snapshot, then simply write a single chosen frame to
a .gro or .pdb using trjconv. Load only that into VMD, and it won't
generate PBC-crossing bonds.
If you want a movie, then there I seem to recall that there is a VMD
option to generate bonds for each frame, and not to use those from the
first frame. Ask their mailing list. Such bonds will not traverse the
PBC, obviously. There is no general solution for bonds visualized on a
single set of coordinates, however - over a trajectory, either molecules
appear to diffuse out of the box, or appear to break.
For PyMol, here is the solution:
http://www.mail-archive.com/pymol-us...@lists.sourceforge.net/msg07721.html
thanks for pointing!
m.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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