[phenixbb] Defining planarity for Phenix.refine
petgxray at gmail.com
Mon Apr 19 06:30:55 PDT 2010
On Mon, Apr 19, 2010 at 2:21 PM, Francis E Reyes <Francis.Reyes at colorado.edu
> 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,
> 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
> > 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
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> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
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