Bill,
Fit is an extremely finicky command...it only works when the two
objects have matched identifiers for each atom to be superimposed (name,
resi, resn, chain, segi, alt). Align won't help you because you're using
RNA. So you'll need to use pair_fit, which requires that you specify a set
of paired atoms in each structure. Fortunately, you no longer have to
specify each pair separately, so long as the ordering is the same in each
selection (almost always true).
pair_fit ( trna10 and resid 10:15 and name P ), ( ref4 and resid 10:15 and
name P )
should do the trick.
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> William Scott
> Sent: Saturday, June 19, 2004 10:53 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] superposition of two molecules
>
> This is driving me nuts. I am trying to superimpose two
> RNA molecules:
>
>
> PyMOL>load trna10.pdb
> ....
> Executive: object "trna10" created.
> PyMOL>load ref4.pdb
> ....
> Executive: object "ref4" created.
> PyMOL>color blue
> Executive: Colored 2668 atoms.
> PyMOL>color yellow, ( trna10 and resid 10:15 and name P )
> Executive: Colored 6 atoms.
> PyMOL>color red, ( ref4 and resid 10:15 and name P )
> Executive: Colored 6 atoms.
>
> All of the above works without incident, so the atom
> selection syntax must be ok.
>
> Then I want to fit the two sets of colored phosphorus atoms,
> selecting with the same syntax:
>
>
> PyMOL>fit ( trna10 and resid 10:15 and name P ), ( ref4 and resid
> 10:15 and name P )
> ExecutiveRMS-Error: No atoms selected.
>
> same error if I replace fit with rms
>
> What am I doing wrong?
>
>
>
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