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
