[phenixbb] base stacking

Nathaniel Echols nechols at lbl.gov
Wed Apr 10 16:27:07 PDT 2013

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

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