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 <yu...@du.edu> 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 > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
_______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe