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 > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Tsjerk Wassenaar > Sent: Wednesday, October 25, 2006 1:32 AM > To: Martin Höfling > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Support for gromacs trajectories and cube files > > 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 <martin.hoefl...@gmx.de> 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 > > > > -- > > 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 > > easier Download IBM WebSphere Application Server v.1.0.1 based on > > Apache Geronimo > > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=1216 > > 42 _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > -- > 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 > > -------------------------------------------------------------- > ----------- > 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 easier > Download IBM WebSphere Application Server v.1.0.1 based on > Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&; dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
