Hi Ed refmac 5.6 should not have this problem. Yes, you are right. It should be considered as a bug. I think I have fixed it. Could you please try 5.6version from:
www.ysbl.york.ac.uk/refmac/latest_refmac.html You need to take experimental version (it should be stable enough, although I update it more often than older versions). In this version to make external restraints as covalent bonds you need to specify type 1 (type 0 means dictionary values will be overwritten and type 2 is external restraints for non-covalent bonds) I hope it helps regards Garib On 14 Oct 2010, at 21:51, Ed Pozharski wrote: > It appears that external restraints are included in bond_rmsd > calculation. When they are used to restrain the hydrogen bonds to > maintain the Watson-Crick pairing in a 3A resolution structure of a > protein-DNA complex, the bond_rmsd is inflated about 5 times. To verify > this, the refmac run was done with external restraints removed and zero > refinement cycles. With external restraints I get 0.028A, without - > 0.006A. > > This is with v.5.5.0109. I assume this may be classified as a bug - > there is no limitation to using external restraints only for the > covalent bonds, thus they should not be included in bond_rmsd > calculation. > > 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? 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?) I suspect that "acceptable" > bond_rmsd value is slightly affected by sequence. > > Ed. > > -- > "I'd jump in myself, if I weren't so good at whistling." > Julian, King of Lemurs
