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
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