Ed, > On a practical side, I now have a misleading bond_rmsd value. The > correct one can be calculated as described, but this may make geometry > weight optimization cumbersome. Do I understand correctly that an > alternative is to monitor Zbonds, with a rule that it should be around > 1.0?
No, the average value of Zbonds over the whole PDB is almost exactly 0.5 (there's no clear resolution-dependence), so that would be a good starting point. Re-refinement of ~98% of the PDB (PDB-REDO project) using weight optimisation showed a linear dependence of Zbonds on resolution in the resolution range 1 to 3 Ang.: Zbonds = 0.85 - 0.146*dmin (SD = 0.2) so e.g. <Zbonds> = 0.56 @ 2 Ang. Cheers -- Ian > And more generally, shouldn't we not look at rmsd_bonds at all and > only use Zbonds instead (which is, I assume, an average bond length > deviation to the target value ratio?) Correct. > I suspect that "acceptable" > bond_rmsd value is slightly affected by sequence. Not really, the effect of sequence on the bond lengths is insignificant in comparison with the uncertainty. Cheers -- Ian
