Thank you, Bruno and Tsjerk. I found both approaches work very well.
Eric
Frankly, with Pymol, people don't as far as I know. What I usually do
is
determine for the first frame of the individual pdb files (obtained
with
trjconv -sep) the orientation, viewing point and appearance. This I
save
in a .pml script. Then with a bit of python code, looping over the
frames, calling them, processing the script, raytrace, write the image
and delete the object again. It's at present the best I can think of.
It
appears that Dino is capable of processing a gromacs trajectory and
outputting raytraced frames, but I haven't felt like starting at the
bottom of that learning curve...
To help out a bit, the loop code could look like this:
for i in range(nr_of_frames):
cmd.load('frame_' + repr(i) '.pdb', 'prot')
cmd.do('@script.pml')
cmd.delete('prot')
Everything to go in script.pml could ofcourse also be explicitly given
in the loop...
Hope it helps,
Tsjerk
