<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"></head><body >I wonder whether something simple like restraining a model to that of an ideal dna (a la den refinement) would do the trick with existing tools.<br><br><br>-------- Original message --------<br>From: Nathaniel Echols <nechols@lbl.gov> <br>Date: 04/10/2013 7:27 PM (GMT-05:00) <br>To: PHENIX user mailing list <phenixbb@phenix-online.org> <br>Subject: Re: [phenixbb] base stacking <br> <br><br><div dir="ltr"><div class="gmail_extra">On Wed, Apr 10, 2013 at 4:09 PM, jp d <span dir="ltr"><<a href="mailto:yoyoq@yahoo.com" target="_blank">yoyoq@yahoo.com</a>></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">
is there a way to do base stacking in phenix ?<br></blockquote><div><br></div><div style="">If you mean restraints on base stacking, no, we don't have anything like this right now. The only implementation of this anywhere, as far as I know, is the one from your (Noller) lab, but (aside from the lack of an explicit license) the fact that it's derived from CNS makes me very reluctant to even look at the code. However, if anyone has the derivation for the restraint energy function, we'd be happy to consider adding this to Phenix - we need to make a lot of changes to how we handle base-pairing anyway.</div>
<div style=""><br></div><div style="">-Nat</div></div></div></div>
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