Ralf W. Grosse-Kunstleve wrote:
Hi Joe, Our group (Berkeley) is working with the Richardsons to analyze RNA sugar puckers and adjust the restraints for the 2' and 3' states. This should become available relatively soon. Ralf
OK, but is there a plan to create restraints that correctly restrain towards any sugar pucker without needing to apply hard-wired conformation patches? I suspect not, because this is not possible with the simple statistical approach used by the current monomer libraries. If the 5-membered ring angle and dihedral restraints are defined such that they are somewhat "strained", then it is possible to end up with energy minima that automatically match the actual puckers. But, implicitly "strained" restraints mean that their target values are intentionally NOT the ideal values. A similar problem occurs with proline puckers. To illustrate the problem, if you look at angle distributions of low-resolution structures refined with REFMAC, you will find that some angle distributions do not match the ideal distributions that the ideal values were derived from. This happens because some values are correlated, but simple individual "ideal value" statistics ignore the correlations. Joe