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 9 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 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 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.
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