[phenixbb] Defining planarity for Phenix.refine

[Peter Grey]

Francis

On Mon, Apr 19, 2010 at 2:21 PM, Francis E Reyes <Francis.Reyes at colorado.edu
> wrote:

> Peter
>
> Restraining RNA base pairs is a debated topic. Some say that you shouldn't
> do this and let the X-ray data speak for itself. Some say defining these
> base pairs should allow the refinement to converge and not distort the rna
> bases too much.
>
> @ 4A, you're asking for a lot if you're refining with individual_sites. You
> may want to stay with rigid body refinement with group adp /tls until you've
> nearly completed the model and then use individual_sites.
>
>
With enough of secondary structure and NCS restraints 4A is fine for RNA



> While I don't think phenix.refine takes base pairing restraints
> specifically, one option is to heavily restricting wxc_scale to a small
> value. Another option is to select your atoms such that A-form helices are
> not refined with individual_sites and place them precisely with COOT.
> Another option is to use refinement.geometry_restraints.edits option of
> phenix.refine. Another option is to switch to CNS in which you can restrain
> the base pairing in the way you suggest.
>
>
refinement.geometry.restraints.edits  does not support, as far as I see,
"improper" torsion angles or other way of defining planes.

Is CNS really my only option ????


> Just my $0.02,
>
> F
>
>
> On Apr 19, 2010, at 4:23 AM, Peter Grey wrote:
>
> > Dear all,
> >
> > I have an RNA/Protein big complex at low resolution (roughly 4A). I would
> like to have the base pairs in the RNA as close as possible to ideal base
> pairs.
> > I added restraints for distances between base pair hydrogen-bonding atoms
> but this is not enough to ensure that the bases will be  in the same plane.
> > Could you suggest how to define for  Phenix.refine this planarity ?
> >
> >
> > I am grateful for your advice,
> >
> >
> > Peter
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100419/f9e53c31/attachment-0003.htm>