Re: [PyMOL] post-processing of pdb ensemble

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