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. Joe 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?
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