Re: [PyMOL] post-processing of pdb ensemble

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

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
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.