Re: [PyMOL] post-processing of pdb ensemble

[Tsjerk W. <ts...@gm...>]

... of course 8-o

:p

T.
On May 25, 2016 18:32, "Thomas Holder" <tho...@sc...>
wrote:

> or simply:
>
> alter bound_combined, chain = chr(ord(chain) - 1)
>
> Cheers,
>   Thomas
>
> On 25 May 2016, at 11:06, Tsjerk Wassenaar <ts...@gm...> wrote:
>
> > Hi James,
> >
> > This should do:
> >
> > for i in range(65:78): cmd.alter("bound_combined and chain
> %s"%chr(i+1),'chain="%s"'%chr(i))
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > On Wed, May 25, 2016 at 5:00 PM, James Starlight <jms...@gm...>
> wrote:
> > More precisely I would like to know how to script in pymol the
> > following alteration fo the chains for the multi-chain pdb
> >
> >
> > PyMOL>alter (bound_combined and chain B), chain="A"
> >  Alter: modified 5157 atoms.
> > PyMOL>alter (bound_combined and chain C), chain="B"
> >  Alter: modified 2285 atoms.
> > PyMOL>alter (bound_combined and chain D), chain="C"
> >  Alter: modified 2778 atoms.
> > PyMOL>alter (bound_combined and chain E), chain="D"
> >  Alter: modified 1560 atoms.
> > PyMOL>alter (bound_combined and chain F), chain="E"
> >  Alter: modified 1114 atoms.
> > PyMOL>alter (bound_combined and chain G), chain="F"
> >  Alter: modified 950 atoms.
> > PyMOL>alter (bound_combined and chain H), chain="G"
> >  Alter: modified 895 atoms.
> > PyMOL>alter (bound_combined and chain I), chain="H"
> >  Alter: modified 843 atoms.
> > PyMOL>alter (bound_combined and chain J), chain="I"
> >  Alter: modified 806 atoms.
> > PyMOL>alter (bound_combined and chain K), chain="J"
> >  Alter: modified 574 atoms.
> > PyMOL>alter (bound_combined and chain L), chain="K"
> >  Alter: modified 501 atoms.
> > PyMOL>alter (bound_combined and chain M), chain="L"
> >  Alter: modified 511 atoms.
> > PyMOL>alter (bound_combined and chain N), chain="M"
> >  Alter: modified 433 atoms.
> >
> >
> > So each step we rename chain i to the i-1 name within given model :)
> >
> > Thanks!
> >
> > J.
> >
> > 2016-05-23 19:11 GMT+02:00 James Starlight <jms...@gm...>:
> > > Dear Pymol users!
> > >
> > > After some post-processing of MD simulation I have extracted from the
> > > traejctory several snapshots as individual pdbs which I need to
> > > 1-  to re-assign information regarding chain letters (which was lost
> > > after some operations on pdbs)  for all of those structures assuming
> > > that within each of these pdbs residues are ordered correctly e.g from
> > > (1-104 which
> > > should be chain A) than from 1-100 (it should be chain B), than 1-70
> > > (in should be chain C) etc.
> > >
> > > 2- superimpose and combine all of the pdbs within one model in
> nmr-like format.
> > >
> > > Thanks for help!
> > >
> > > James
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>