pymol-users

[PyMOL] Support for gromacs trajectories and cube files

[Martin <mar...@gm...>]

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

-- 
Wenn Kritik nicht kritisch ist, ist sie zu kritisieren.
(Nico Hoffmann in dtj)

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
>
> --
> Wenn Kritik nicht kritisch ist, ist sie zu kritisieren.
> (Nico Hoffmann in dtj)
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job ea=
sier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronim=
o
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


--=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

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

[DeLano S. <de...@de...>]

Hi Folks,

Support for reading TRR, TRJ, and XTC is present in the open-source code
(-D_PYMOL_VMD_PLUGINS with source code from the contrib/uiuc directory =
--
must modify setup.py), and the capability is present in our latest
precompiled beta builds.

You just need a PDB which exactly matches the trajectory.

Cheers,

DeLano Scientific LLC
Email Support Services=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of Tsjerk Wassenaar
> Sent: Wednesday, October 25, 2006 1:32 AM
> To: Martin H=F6fling
> Cc: pym...@li...
> Subject: Re: [PyMOL] Support for gromacs trajectories and cube files
>=20
> Hi Martin,
>=20
> As far as I know there is no such plugin yet for gromacs trajectories.
> But you can convert the gromacs trajectory to a multimodel=20
> .pdb file using gromacs utility trjconv and load that in=20
> pymol. Alternatively, you could take up the effort of writing=20
> a plugin and have a look at the way Amber trajectories are=20
> loaded in PyMOL. This would make many people, including me,=20
> quite happy.
>=20
> As for the volumetric data, I don't know which format you=20
> have in mind, but it should be possible to convert it to an=20
> XPLOR/CNS map and load it into Pymol, or write a plugin to read it in.
>=20
> By the way, would you mind sharing a copy of the python-gmx=20
> connection with me?
>=20
> Cheers,
>=20
> Tsjerk
>=20
>=20
> On 10/25/06, Martin H=F6fling <mar...@gm...> wrote:
> > Hi everybody,
> >
> > Does somebody of you know if gromacs trajectories (xtc or trr) are=20
> > supported by some plugin? Same thing with volumetric data=20
> in cube files?
> > I am using gromacs trajectories from python already by using the=20
> > gromacs c-libraries via ctypes. This is not truely platform=20
> > independant or at least not independant from external=20
> (gromacs) code.
> > So in case I have to write the stuff on my own, is a plugin=20
> or a patch=20
> > for pymol the best choice?
> >
> > Regards
> >         Martin
> >
> > --
> > Wenn Kritik nicht kritisch ist, ist sie zu kritisieren.
> > (Nico Hoffmann in dtj)
> >
> >=20
> ----------------------------------------------------------------------
> > --- Using Tomcat but need to do more? Need to support web services,=20
> > security?
> > Get stuff done quickly with pre-integrated technology to=20
> make your job=20
> > easier Download IBM WebSphere Application Server v.1.0.1 based on=20
> > Apache Geronimo
> >=20
> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
1216
> > 42 _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>=20
>=20
> --
> Tsjerk A. Wassenaar, Ph.D.
> Groningen Biomolecular Sciences and Biotechnology Institute=20
> (GBB) Dept. of Biophysical Chemistry University of Groningen=20
> Nijenborgh 4 9747AG Groningen, The Netherlands
> +31 50 363 4336
>=20
> --------------------------------------------------------------
> -----------
> Using Tomcat but need to do more? Need to support web=20
> services, security?
> Get stuff done quickly with pre-integrated technology to make=20
> your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on=20
> Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&
dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

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

[Martin <mar...@gm...>]

=2E..got the svn code compiled with -D VMD...
If i load a PDB, then load a topology and then try to load a trajectory=20
via "load" loading the trajectory fails, complaining like this:

CmdLoad: "/home/martin/workspace/testdata/ProtOut.pdb" loaded as "ProtOut".
PyMOL>load /home/martin/workspace/testdata/topol.tpr
CmdLoad: "/home/martin/workspace/testdata/topol.tpr" loaded as "topol.tpr".
PyMOL>load /home/martin/workspace/testdata/ProteinTraj.xtc

Best wishes,
	Martin
=2D-=20
Meinungsfreiheit hei=DFt nicht, dass ich mir jeden Schei=DF anh=F6ren muss.
(Tobias Erle in bln.misc)

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

[DeLano S. <de...@de...>]

Hi Martin,

> ...got the svn code compiled with -D VMD...

Great!=20

> CmdLoad: "/home/martin/workspace/testdata/ProtOut.pdb" loaded=20
> as "ProtOut".
> PyMOL>load /home/martin/workspace/testdata/topol.tpr
> CmdLoad: "/home/martin/workspace/testdata/topol.tpr" loaded=20
> as "topol.tpr".
> PyMOL>load /home/martin/workspace/testdata/ProteinTraj.xtc

Skip the tpr -- PYMOL can't read that at all. Try

load ProtOut.pdb, your-object-name
load ProteinTraj.xtc, your-object-name

where your-object-name is the same object.

Cheers,

DeLano Scientific LLC
Email Support Services=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of Martin H=F6fling
> Sent: Friday, October 27, 2006 2:20 PM
> To: pym...@li...
> Subject: Re: [PyMOL] Support for gromacs trajectories and cube files
>=20
> ...got the svn code compiled with -D VMD...
> If i load a PDB, then load a topology and then try to load a=20
> trajectory via "load" loading the trajectory fails,=20
> complaining like this:
>=20
> CmdLoad: "/home/martin/workspace/testdata/ProtOut.pdb" loaded=20
> as "ProtOut".
> PyMOL>load /home/martin/workspace/testdata/topol.tpr
> CmdLoad: "/home/martin/workspace/testdata/topol.tpr" loaded=20
> as "topol.tpr".
> PyMOL>load /home/martin/workspace/testdata/ProteinTraj.xtc
>=20
> Best wishes,
> 	Martin
> --
> Meinungsfreiheit hei=DFt nicht, dass ich mir jeden Schei=DF anh=F6ren =
muss.
> (Tobias Erle in bln.misc)
>=20
> --------------------------------------------------------------
> -----------
> Using Tomcat but need to do more? Need to support web=20
> services, security?
> Get stuff done quickly with pre-integrated technology to make=20
> your job easier Download IBM WebSphere Application Server=20
> v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20