Thanks for the clarification.
Osvaldo.
On Thu, Nov 28, 2013 at 2:11 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> 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
