Hi Yunfeng Hu,
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
Yunfeng Hu wrote:
Hi, I wonder if people can give a summary of how pymol makes movies
out of gromacs trr (or xtc) files without having to use all the
individual frame pdb files. Thanks!
Eric
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