Re: [PyMOL] post-processing of pdb ensemble

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.