Re: [PyMOL] RMSD between two structures

Is the RMS the same as RMSD? PyMOL writes "RMS" when using align.
Martin





Am 11.11.11 14:59, schrieb Thomas Holder:
> 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
>