Re: [PyMOL] Structural Allignment in PyMol

[Thomas H. <sp...@us...>]

Hi Syeda,

you have a lot of options in PyMOL to do this. For full-atom RMSD fit on topologically identical molecules (since it's MD, I guess this is the case), use the "fit" command:

PyMOL> fit mobile, target

Otherwise, use "align" or "super":

PyMOL> align mobile, target, cycles=0

From a python script, syntax looks like this:

from pymol import cmd
cmd.fit("mobile", "target")
cmd.align("mobile", "target", cycles=0)

http://pymolwiki.org/index.php/Fit
http://pymolwiki.org/index.php/Rms
http://pymolwiki.org/index.php/Align
http://pymolwiki.org/index.php/Super

Cheers,
  Thomas

On Oct 4, 2013, at 5:29 AM, Syeda Hira Batool <s.h...@ym...> wrote:
> Hello  I want to know how PyMol does Structural allignment. I am writing a python script to allign protein structures(from MD simulations) and eventually calculate RMSD. Please can anyone provide me a source code or  a helping material.Thanx in advance.
> 
> Hira Batool
> Student of BS-Bioinformatics
> Biosciences Department
> COMSATS Institute of Information Technology
> Islamabad, PAKISTAN