Hi Yu and David,
I like to throw in one of the many ways to do this inside PyMOL :-)
from pymol import cmd
# load 3000 files into the "multi" object
for i in range(3000): cmd.load('file_{}.pdb'.format(i + 1), 'multi')
# if you want, fit to the first state
cmd.intra_fit('multi')
Morphing between
Dear Yu,
Try this bash script and then run "pymol all.pdb” in your PDB directory. this
might help you view your files as a trajectory.
for i in {1..3000}
do
# change frame_$i.pdb to your file name. for example mine is frame_1.pdb
[ -f "frame_$i.pdb" ]
z=frame_$i.pdb
Some background: I'm an undergraduate student and am doing research with my
professor about modeling protein conformational changes. I am new to this field
and and am actively learning how to use command lines, python and other
relative tools. I have simulated how the protein will walk with
