[phenixbb] Defining planarity for Phenix.refine
eozkan at stanford.edu
Mon Apr 19 08:50:28 PDT 2010
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
On 4/19/10 5:21 AM, Francis E Reyes wrote:
> 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,
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
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