On Mon, Apr 19, 2010 at 2:21 PM, Francis E Reyes
<Francis.Reyes@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
>
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---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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