Re: [PyMOL] RMSD between two structures

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

Hi Martin,

is it the transform=0 argument what you are looking for?

http://pymolwiki.org/index.php/Align#PYMOL_API

x = cmd.align('foo', 'bar', transform=0)
print 'RMSD:', x[0]

About the "some kind of refinement": There are arguments "cutoff" and 
"cycles" that control this behaviour.

Cheers,
   Thomas

On 11/11/2011 02:46 PM, Martin Hediger wrote:
> Dear List.
> When aligning two structures using the PyMOL align command, one gets a
> final RMS value indicating some kind of "convergence" i would say. Can I
> somehow access the function for calculating this value directly from the
> pymol prompt without aligning?
>
> Thanks for hints
> Martin

-- 
Thomas Holder
MPI for Developmental Biology