Francis
On Mon, Apr 19, 2010 at 2:21 PM, Francis E Reyes 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 gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D _______________________________________________
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