Thanks, Ian, this is excellent. It appears that depending on the
sequence the "ideal target rmsd" may vary from 0.018 for a poly-H to
0.024 for a poly-P. Except for some really short sequences, in PDB the
variation is generally between 0.021-0.022, indeed undetectable.
On Fri, 2010-10-15 at 10:26 +0100, Ian Tickle wrote:
> Ed,
>
> > 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?
>
> No, the average value of Zbonds over the whole PDB is almost exactly
> 0.5 (there's no clear resolution-dependence), so that would be a good
> starting point. Re-refinement of ~98% of the PDB (PDB-REDO project)
> using weight optimisation showed a linear dependence of Zbonds on
> resolution in the resolution range 1 to 3 Ang.:
>
> Zbonds = 0.85 - 0.146*dmin (SD = 0.2)
>
> so e.g. <Zbonds> = 0.56 @ 2 Ang.
>
> Cheers
>
> -- Ian
>
> > 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?)
>
> Correct.
>
> > I suspect that "acceptable"
> > bond_rmsd value is slightly affected by sequence.
>
> Not really, the effect of sequence on the bond lengths is
> insignificant in comparison with the uncertainty.
>
> Cheers
>
> -- Ian
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
