Ivan,
You are essentially asking for two things: the functionality of pairwise
fitting of chains/states to other chains/states; and having a menu
from which to do this. This sounded like a fun problem so I tackled the
first part. I wrote a script, autoMultiFit, and deposited it on the
PyMOLWiki,
http://pymolwiki.org/index.php/AutoMultiFit
For any homo-oligomer in N-states it'll fit any combination of
chain(s)/state(s) to other chain(s)/state(s) for some given selection.
Check out its web page for more details.
You could easily modify the code to make it return the fitted structures
and setup some consistent view, to finish your problem.
As for the latter part of the problem, if you consider all pairs of
chains and states for something as simple as a tetramer with 20 states
you're looking at 6400(=20*20*4*4) possible menu items we'd have to add
to PyMOL. So, not a good idea IMHO.
HTH,
-- Jason
Ivan Campeotto wrote:
> Dear Pymol users,
>
>
>
> I have to compare 20 different structures of the same protein, all with
> the same origin.
> The protein is a homotetramer and I am interested in comparing the
> catalytic pocket of each monomer inside a single structure and across
> the 20 structures.
> Also I would like to compare not only the same monomer across all the
> structures but also compare different monomers from different structures.
> To be more clear I would like to have the following layout in the pymol
> menu:
>
>
> Mutant1
> Catalytic pocket monomer A
> Catalytic pocket monomer B
> Catalytic pocket monomer C
> Catlytic pocket monomer D
>
> Mutant2
>
> Catalytic pocket monomer A
> Catalytic pocket monomer B
> Catalytic pocket monomer C
> Catlytic pocket monomer D
>
> and so on for all of 20, to be able to compare the catalytic pocket of
> one monomer of one structure with the monomer of another
> structure simply selecting and deselecting from the menu.
> In order to do this, I have to find a way to superimpose all the 80
> monomers on the top of each other applying the same selection and view
> of the catalytic pocket to all of them and keeping the link with the
> original pdb in a way that there is a distinction for e.g from monomer
> A of mutant 1 and monomer A of any other mutant.
> Can anyone suggest to me a way to do this without generating 80 objects
> and keeping the exact same view of the catalytic pocket for all of them?
>
> Thank you in advance,
>
>
> Ivan Campeotto
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
-- Jason
--
Jason Vertrees, PhD
(e) jason.vertr...@gmail.com
http://www.pymol.org/ -- PyMOL
http://www.pymolwiki.org/ -- PyMOLWiki
------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
