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 <aloctavo...@gmail.com>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.
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
> Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Tsjerk A. Wassenaar, Ph.D.
------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
