I am thoroughly puzzled. I am seeing so many messages in the bulletin boards with suggestions of rigid body refinement at lower than 3 Angstrom resolution datasets, especially with strict arguments of data:parameter ratio (which cannot be easily determined due to the presence of restraints). Last week, rigid body was suggested for a case of 3.3 A structure. Are there papers out there that advocate residue-by-residue rigid body refinement for >3 Angstrom structures? To me, it sounds like a recipe for clashes and bond/angle outliers (when individual coordinate refinement can be worked out with proper restraining). Any research to back this strategy up, and make it regularly applicable in the 3 to 4 Angstrom range, or an easy option in phenix.refine? (I have seen grouped B-factors tame unruly B-factor refinement, that actually works) I should say that I have never worked with DNA in crystal structures, and due to its structure, it might be better suited to parameterization that allows accurate rigid bodies. I just don't know. I would also like to point out recent work by Axel Brunger's group on low-resolution refinement (Schröder et al, Nature, 2010 and references therein). Low-resolution refinement, while not straightforward, is becoming mainstream. Engin On 4/19/10 5:21 AM, 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.
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,
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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