Re: [PyMOL] Support for gromacs trajectories and cube files

[Tsjerk W. <ts...@gm...>]

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 H=F6fling <mar...@gm...> wrote:
> Hi everybody,
>
> Does somebody of you know if gromacs trajectories (xtc or trr) are suppor=
ted
> 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 lea=
st
> not independant from external (gromacs) code.
> So in case I have to write the stuff on my own, is a plugin or a patch fo=
r
> pymol the best choice?
>
> Regards
>         Martin
>
> --
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--=20
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336