I am using Pymol to visualize a "pseudo polymer" generated by some
brownian dynamics code. We take the coordinate files generated by our
simulation and convert them into a PDB file using the hetatm
representation and having explicit connections defined with conect. For
example:
HETATM 1 P UNK A 2.637 1.188 0.470
HETATM 2 C UNK A 2.883 0.865 0.178
HETATM 3 N UNK A 3.176 0.740 0.564
.
.
.
.
CONECT 1 2
CONECT 2 1 3 4
CONECT 3 2
I also have the associated HETNAM and FORMUL header lines, but this
doesn't seem to make any difference.
Pymol displays the individual files in the trajectory fine, but when we
go to load in a trajectory of structures to view as a movie, the
connectivity gets weird after only a couple of frames. Random atoms are
attached to each other. Another strange behavior is that after 72
frames of the movie it regains the correct bonding for one frame and
then dies again. For long trajectories, in other word, frames 1,2,74,
146, 218, etc are ok. However there are only 61 atoms in each file, so
I don't see an obvious reason for this cycle.
If anyone wants a zipped archive of some of the pdb files to play
around with, please email me. Any suggestions would be most
appreciated.
Joshua Adelman
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Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://www.ocf.berkeley.edu/~jadelman
Berkeley, CA 94720 USA [email protected]
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