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

Joe Krahn krahn at niehs.nih.gov
Fri Dec 7 09:38:02 PST 2007

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.


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