Hi Lenka and Mat, Unfortunately, Amber ".nc" (NetCDF) files are currently not supported. Can you convert the file to one of the supported formats, like ".crd"?
We can probably add NetCDF support to the next release. It's included in the VMD molfile plugins, and only excluded in PyMOL to avoid the dependency on the libnetcdf library. I can also give you instruction how to compile PyMOL from source and patch in a modified version of the molfile plugins, but it's a bit of work and requires some understanding of how to build software. Cheers, Thomas > On Jul 23, 2018, at 3:27 PM, Stejskal, Lenka <lenka.stejskal...@ucl.ac.uk> > wrote: > > Hi Mat, > > I have of course read that but I am still unable to load the trajectory. I > was looking for an actual successful example not just a guide. > > Thanks > > Lenka > From: Mateusz Bieniek <bieniek...@gmail.com> > Sent: 23 July 2018 14:04:22 > To: Stejskal, Lenka > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Amber .nc > > Hi Lenka, > > Let me first state that the command "help load_traj" points to the webpage > which in turns says that the .nc format is supported by pymol. > > I come from the gromacs background. Once you load the topology/state of your > system (in my case .gro or .pdb), then use "load_traj", ie > load_traj trajectory.nc > > There are other options for this command (start, end, shift, etc). > > Hope this helps, Mat > > On Mon, Jul 23, 2018 at 11:42 AM Stejskal, Lenka > <lenka.stejskal...@ucl.ac.uk> wrote: > Dear Pymol users, > > Can somebody advise how I can open amber trajectory file in .nc format? > > Thank you > > Lenka -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
