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 <[email protected]> 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
------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk
_______________________________________________
PyMOL-users mailing list ([email protected])
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/[email protected]
