Doug,
As far as I know there isn't any resource online, so I'll try to
answer your questions here:
PyMOL does not automatically align structures.
intra_fit is presumably the command you're looking for to do this, since
you're placing models are in one object.
intra_fit name ca, 1
would for example align all of the models to the first model using
alpha-carbon coordinates.
intra_fit resi 10-15, 1
would align all models to the coordinates of atoms in residues 10-15.
As far as RMS statistics go, PyMOL may be the best tool for this yet,
since it doesn't current have the ability to generate statistics for the
ensemble.
What statistics in particular would you like it to provide?
Also note that if you have you ensemble in a multiple-model pdb file
(with MODEL and ENDMDL records), you can just load it in one command
load ens.pdb
Cheers,
Warren
--
mailto:war...@delanoscientific.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 Douglas Kojetin
> Sent: Monday, January 26, 2004 11:22 AM
> To: pymol
> Subject: [PyMOL] nmr ensemble alignment
>
> Hi All-
>
> Will reading in a structural ensemble
>
> load pdb01.pdb, ens
> load pdb02.pdb, ens
> ...
>
> ... automagically align the structures? If not, do I need to run
> another command, such as ' intra_fit (name ca) ' ? Or should I use
> normal 'fit'?
>
> Also, what is the best method for determining the RMS of the ensemble?
> There are a few commands in the reference manual (rms, rms_cur,
> intra_rms, intra_rms_cur), and I'm confused as to which is best for
> structural ensembles.
>
> Or, to save typing, is there a current web resource for using PyMOL
> with NMR models (with hints, scripts, etc.)? One thing I /miss/ from
> MOLMOL is the 'sausage' display -- has anyone implemented this in
PyMOL
> yet?
>
> Thanks,
> Doug
>
>
>
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