Re: [PyMOL] monitor same protein conformational change with multiple trajectory files

[Thomas H. <tho...@sc...>]

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 each state is possible, but will take some time, and with the defaults you'll end up with 90000 states, which might be more than PyMOL can handle (also you'll have a 50 minute movie).

As a proof of concept, here is how you make a linear (faster than rigimol) morph with 3 interpolated states between each consecutive input state, for the first 100 of your files (yields 495 states):

from pymol import cmd
for i in range(100): cmd.load('file_{}.pdb'.format(i + 1), 'multi')
cmd.intra_fit('multi')
cmd.morph('morph', 'multi', state1=0, state2=0, refinement=0, steps=5, method='linear')

Hope that helps.

Cheers,
  Thomas


> On May 1, 2019, at 3:36 PM, David Gae <dd...@uc...> wrote:
> 
> 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...> 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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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.