[phenixbb] Defining planarity for Phenix.refine

Francis E Reyes Francis.Reyes at Colorado.EDU
Mon Apr 19 05:21:55 PDT 2010


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. 

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. 

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 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
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> phenixbb at phenix-online.org
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Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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