Thanks for the clarification.


On Thu, Nov 28, 2013 at 2:11 PM, Tsjerk Wassenaar <> wrote:
Hi Osvaldo,

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

PyMOL>help super
        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'.



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

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.


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Tsjerk A. Wassenaar, Ph.D.