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

Joe Krahn krahn at niehs.nih.gov
Wed Dec 5 08:04:53 PST 2007

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?

The problem with simple statistical restraints as used by CCP4 is that
they completely ignore correlations due to interactions of multiple
restraints. This is particularly bad for puckered rings like proline and
nucleic acids. Nucleic acids get around this by using a fixed sugar
pucker, which results in a lot of bad geometries for non-helical nucleic
acids (many of which make it in to the PDB).

However, if you consider the geometries "ideal value" and "ideal value
esd" as just another way to write a harmonic restraint, then it is
possible to make an improved restraint library. In this case, some
individual geometry restraints will have target values that restrain
towards non-ideal values in order to produce the correct result when all
terms are combined. The problem is that these terms will give higher
RMSD values, which would probably confuse software like REFMAC, which is
designed to tweak restraint weights based on RMSDs.

So, does phenix have any built-in restraint adjustments that is based on
current rmsds? If so, is there a way to disable it?

Joe Krahn

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