On Mon, Apr 19, 2010 at 11:56 AM, Francis E Reyes <span dir="ltr">&lt;<a href="mailto:Francis.Reyes@colorado.edu">Francis.Reyes@colorado.edu</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div style="word-wrap:break-word"><div>Now let&#39;s talk about flexibility during refinement. Without restraining the bases with some kind of strict geometry weight, or in the case of the OP, specifically restraining <b>coplanar</b> <b>base pairing for canonical watson crick pairing</b>, depending on the quality of the phases, I&#39;ve seen phenix.refine and refmac pull bases that we know to be base paired in an A-form helix out of the &#39;coplanar base pair&#39; orientation. If I were solving an RNA from scratch, I&#39;d know apriori that this is a true base pair, and it&#39;s almost offensive that a refinement program would say otherwise. It&#39;s not drastic, but any RNA/DNA structural biologist will look at your structure and clearly see that there&#39;s something wrong with the geometry.   While it maybe a minor nuisance to correct this manually, I can only wonder how it affects the refinement.</div>
</div></blockquote><div><br></div><div>Okay; it probably isn&#39;t very difficult to add base pair restraints to Phenix, we&#39;re just not quite sure how to make a general solution (which would support planarity restraints in addition to H-bonds).  The main bottlenecks right now are a) figuring out a convenient reduced representation for base pairs, and b) identifying base pairs in a model.  Aren&#39;t non-WC base pairs going to be very important in large RNA structures?  Are there (free, open-source) tools that will generate a listing of *all* base pairs found in a model, not just the canonical ones?  (Actually, a simple and more-or-less machine-readable listing of the bonds formed by each base pair type would be close enough.)</div>
<div><br></div><div>-Nat</div></div>