Re: [PyMOL] monitor same protein conformational change with multiple trajectory files
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
>
> ___
> 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
>
___
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
[PyMOL] Space group Symmetry operators
PyMOL uses some preprogrammed space group operators to generate symmetry-related molecules. These molecules are numbered _010, _020, _030. I need to know which operators these correspond to for space group 18, P21212. Does anyone know where this can be found? There are different orders of the operators depending on what book one consults. Thanks, Mark ___ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III sa...@umich.edu +1 (734) 764-3353 mobile: (734) 276-6505 ___ 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
Re: [PyMOL] Space group Symmetry operators
Hi Mark, The first two digits of the code correspond to the zero-based index of the symmetry operators list found here: https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/xray.py#L95 The following three digit pairs correspond to the X, Y, Z unit cell offsets along that axis. Jarrett J. On Wed, May 1, 2019 at 1:07 PM Mark Saper wrote: > PyMOL uses some preprogrammed space group operators to generate > symmetry-related molecules. These molecules are numbered > _010, _020, _030. I need to know which operators these > correspond to for space group 18, P21212. > > Does anyone know where this can be found? There are different orders of > the operators depending on what book one consults. > > Thanks, > Mark > ___ > Mark A. Saper, Ph.D. > Associate Professor of Biological Chemistry, U-M Medical School > Room 3220B, MSRB III sa...@umich.edu +1 (734) 764-3353 mobile: (734) > 276-6505 > > ___ > 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 -- Jarrett Johnson PyMOL Developer Schrödinger, Inc. ___ 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
