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
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