[phenixbb] Can geometry restraints include non-ideal target values?

Joe Krahn krahn at niehs.nih.gov
Fri Dec 7 09:46:30 PST 2007

However, they all use hard-wired sugar puckers. PHENIX is currently
essentially the same as REFMAC. They do better than CNS only because the
restraint energies are reduced. Although they won't pull atoms
completely out of the density, they still produce bad geometries when
the actual sugar puckers differ. I just created a C2'-endo patch for
PHENIX, which was needed to avoid getting several strained angles.


William Scott wrote:
> I have used 3 programs to refine RNA structures recently: CNS, Refmac and
> Phenix.
> Of these, only CNS has the temerity to enforce what it thinks is a correct
> sugar pucker to the extent that it will pull atoms out of the electron
> density. Refmac and Phenix both do a much better job of refining
> non-canonical sugar puckers in RNA in my experience.
> Joe Krahn wrote:
>> I see that phenix is using the same kind of simplistic statistical
>> restraints as CCP4. Are there plans to improve the geometry restraints
>> once the rest of phenix is stable?
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list