Re: [PyMOL] rmsd sicechains super

[Tsjerk W. <ts...@gm...>]

Hi Osvaldo,

The problem can be understood from the description of 'super'.

#---------------------
PyMOL>help super

DESCRIPTION

        NOTE: This feature is experimental and unsupported.

        "super" performs a residue-based pairwise alignment followed by a
        structural superposition, and then carries out zero or more cycles
        of refinement in order to reject outliers.
#---------------------

The point is the alignment. Pymol needs the C-alphas for that. You can
achieve what you want with 'rms'.

Cheers,

Tsjerk




On Thu, Nov 28, 2013 at 5:13 PM, Osvaldo Martin <alo...@gm...>wrote:

> Hi,
>
> I am trying to use the comand cmd.super() to calculate the rmsd between
> the sidechains of two proteins using
>
> cmd.super('%s and not name ca+c+o+n' % obj0, '%s and not name ca+c+o+n' %
> obj1)
>
> And I get this error
> ExecutiveAlign: invalid selections for alignment.
>
> It seems to me that the problem is related to the exclusion of the "ca"
> atoms. because:
>
> cmd.super('%s and not name c+o+n' % obj0, '%s and not name c+o+n' % obj1)
>
> works, but
>
> cmd.super('%s and not name ca' % obj0, '%s and not name ca' % obj1)
>
> does not work.
>
>
> Osvaldo.
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.