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
sed 's/END/ENDMDL/g' $z > $z.r
{ echo 'MODEL'; cat $z.r; } >$z.new
rm $z.r
done
cat *.new > all.pdb
rm *.new
---------------------
I am sure there are many ways to do this inside pymol as well. you might want
to look up https://pymolwiki.org/index.php/Main_Page
hope this helps,
David
> On Apr 30, 2019, at 5:57 PM, Yu Qi <[email protected]> wrote:
>
> 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 CAMPARI and
> have gotten back 3000 trajectory (pdb) files, my question is: how do I use
> PyMOL to make a movie by using those trajectory files? Basically, I want to
> know how to visualize how the protein moved from the first pdb file to the
> second, then to the third, etc.
>
> I tried morphing two pdb files with one step from file_1.pdb to file_2.pdb, I
> aligned them first, then morphed them. I'm not sure how to go from there
> because I had a result file with 2 states and 2 frames, then when I tried to
> morph the result file with file_3.pdb, it did not work as I expected.
>
> please let me know if you have questions, and I really appreciate the help.
>
> Thank you for the help,
> Yu
>
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