In my experience, the reference structure restraint in phenix (or LSSR in buster) works quite well at holding the model together in poor molecular replacement phases (rfree in the 40s) or low resolution experimental phases (4A or worse). I used to be a fan of CNS's base pair restraint but found it was very limited to canonical base stacking. On the other hand, finding a reasonable structure in the pdb and using it as a reference model allowed for much more flexibility. F On Apr 10, 2013, at 5:11 PM, Ed. Pozharski wrote:

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 Date: 04/10/2013 7:27 PM (GMT-05:00) To: PHENIX user mailing list Subject: Re: [phenixbb] base stacking

On Wed, Apr 10, 2013 at 4:09 PM, jp d 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.

-Nat _______________________________________________ phenixbb mailing list phenixbb@phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

--------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder