Garib, indeed - I tested 5.6.077 and the bond_rmsd is down to 0.006 as it should. Thanks,
Ed. On Thu, 2010-10-14 at 22:04 +0100, Garib N Murshudov wrote: > 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 -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
