[phenixbb] base stacking

Ed. Pozharski epozh001 at umaryland.edu
Wed Apr 10 17:11:07 PDT 2013

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.

-------- Original message --------
From: Nathaniel Echols <nechols at lbl.gov> 
Date: 04/10/2013  7:27 PM  (GMT-05:00) 
To: PHENIX user mailing list <phenixbb at phenix-online.org> 
Subject: Re: [phenixbb] base stacking 
On Wed, Apr 10, 2013 at 4:09 PM, jp d <yoyoq at yahoo.com> wrote:
is there a way to do base stacking in phenix ?

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.

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