Hi Martin,
As far as I know there is no such plugin yet for gromacs trajectories.
But you can convert the gromacs trajectory to a multimodel .pdb file
using gromacs utility trjconv and load that in pymol. Alternatively,
you could take up the effort of writing a plugin and have a look at
the way Amber trajectories are loaded in PyMOL. This would make many
people, including me, quite happy.
As for the volumetric data, I don't know which format you have in
mind, but it should be possible to convert it to an XPLOR/CNS map and
load it into Pymol, or write a plugin to read it in.
By the way, would you mind sharing a copy of the python-gmx connection with me?
Cheers,
Tsjerk
On 10/25/06, Martin Höfling <[email protected]> wrote:
Hi everybody,
Does somebody of you know if gromacs trajectories (xtc or trr) are supported
by some plugin? Same thing with volumetric data in cube files?
I am using gromacs trajectories from python already by using the gromacs
c-libraries via ctypes. This is not truely platform independant or at least
not independant from external (gromacs) code.
So in case I have to write the stuff on my own, is a plugin or a patch for
pymol the best choice?
Regards
Martin
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
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+31 50 363 4336
