Francis<br><br><div class="gmail_quote">On Mon, Apr 19, 2010 at 2:21 PM, Francis E Reyes <span dir="ltr"><<a href="mailto:Francis.Reyes@colorado.edu">Francis.Reyes@colorado.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Peter<br>
<br>
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.<br>
<br>
@ 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.<br>
<br></blockquote><div><br>With enough of secondary structure and NCS restraints 4A is fine for RNA� <br><br>�</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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.<br>
<br></blockquote><div> <br>refinement.geometry.restraints.edits� does not support, as far as I see, "improper" torsion angles or other way of defining planes. <br><br>Is CNS really my only option ????<br>�</div>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Just my $0.02,<br>
<br>
F<br>
<div><div></div><div class="h5"><br>
<br>
On Apr 19, 2010, at 4:23 AM, Peter Grey wrote:<br>
<br>
> Dear all,<br>
><br>
> 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.<br>
> 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.<br>
> Could you suggest how to define for �Phenix.refine this planarity ?<br>
><br>
><br>
> I am grateful for your advice,<br>
><br>
><br>
> Peter<br>
><br>
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<br>
---------------------------------------------<br>
Francis Reyes M.Sc.<br>
215 UCB<br>
University of Colorado at Boulder<br>
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8AE2 F2F4 90F7 9640 28BC �686F 78FD 6669 67BA 8D5D<br>
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