On Mon, Sep 26, 2011 at 1:53 AM, Dirk Kostrewa <[email protected]>wrote:
> when I played with H-bond restraints for secondary structures for the > refinement of a 4.3 A structure (only a few weeks before they were > introduced in phenix), I've made the following observation: at low > resolution without H-bond restraints for secondary structures, the carbonyl > groups of these secondary structures take the liberty within their globbish > electron densities to deviate from their ideal H-bond conformation, > resulting in a tight "belt" of outliers around the preferred Ramachandran > regions, with typical deviations of only a few degrees. Introducing the > additional H-bond restraints for maintaining secondary structures pulls > these outlier carbonyl groups back into the preferred Ramachandran regions. > In my case, the number of Ramachandran outliers was reduced to less than one > half! Although, these H-bond restraints do not directly include information > about allowed Ramachandran regions, the Ramachandran plot is actually > affected by these restraints. Thus, at least in my opinion, the Ramachandran > plot is then not a truly independent measure for model quality, anymore. The > same holds true for all geometrical restraints, of course. > It depends on how strictly you assess the "independence" of validation criteria. The Ramachandran plot is considered valid in most cases because refinement programs traditionally do not restrain phi and psi angles, so we need to rely on the accuracy of the data (and our placement of atoms) and various complementary geometry restraints (especially nonbonded) to keep residues in the favorable regions of the plot. There are a variety of ways to make the plot better by modification of the model and/or restraints (adding hydrogens, increasing the weight on the nonbonded restraints, secondary structure restraints, etc.), none of which are as drastic as directly restraining the model to the plot. I don't really view this as biasing the plot, for two reasons: a) the quantity being measured is independent of the quantity restrained, and b) at least in my hands, these modifications never completely fix the problem of Ramachandran outliers. (It's the loop regions that are really awful.) Anyway, I don't think anyone should feel bad about using this kind of restraint at low resolution. The caveat is that of all the specialized restraints that we (Jeff Headd and I) have been testing for low-resolution refinement (in Phenix), nothing works nearly as well in preserving good geometry, and usually improving the R-factors, as restraining model parameters to a related high-resolution structure, when one is available. Fortunately, every modern refinement program has this ability in some form, and I expect that this is going to have the most impact in improving the overall quality of low-resolution structures. -Nat
