Hi Timofey,
This wiki page is obsolete, current PyMOL includes a recent version of the VMD
plugins, and it can load xtc files (and probably trr too, but I don't have a
test file around). You need to load topology and trajectory in two steps, into
the same object. Example:
load topology.gro, so
The safest way to do that would be to convert your trajectory to a format
readably by PyMOL, with trajectory manipulation tools such as trjconv (in
GROMACS) or catdcd (you can find it in the VMD website). PyMOL recognizes
the AMBER .trj format with the "Load_traj" function, so you can use that:
ht
Dear All,
Recently I have noticed in Science and Nature paper, the author present the
helix in cartoon as thin as that observed in VMD (and even similar in
appearance). I do not know whether the author made the image by pymol or by VMD.
Is any way for pymol to make helix in carton as observe
Hi Lucile,
This picture looks unusual, can you give some details on how you created it?
E.g. is this a full-atom protein structure, or a CA-only or pseudo-atom coarse
grain model? Did you modify any settings?
The spheres look like "nb_spheres" representation, so maybe you simply need to
hide t
Is there any way to load .xtc or .trr files into PyMOL to view trajectories?
This user page on the wiki suggest the way, but it looks like it's
outdated and defunct now.
pymolwiki.org/index.php/User:Speleo3/VMD_plugins
