Coordinates accuracy

Ashley Deacon ash at bio.cornell.edu
Thu Feb 27 10:56:08 EST 1997


Hi,

January CCP4 Study Weekend seems to be the answer - there is also a
paper entitled "Protein precision re-examined: Luzzati plots do not
extimate final errors". He proposes models for calculating coordinate
error without running full-matrix least-squares refinement.

His poster at the IUCR in Seattle showed how well these equations
approximate the results from a full-matrix refinement.

Regards,

Ashley Deacon.






Lynn F. Ten Eyck wrote:
> 
> Vincent Escalier wrote:
> >
> > Hello,
> >
> >  I'd like to have a measure of accuracy of the coordinates in a PDB
> > file. I need a quantitative measure, and resolution doesn't make it.
> > I would need something like 'the x-coordinate of atom #1234 is
> > equal to 0.2345 +- 0.05 A '. Is it possible to have such an
> > information ?
> 
> Unfortunately this information requires a full matrix least squares
> analysis.  Some of the possibilities are given in a paper I presented
> at the January 1996 CCP4 Study Weekend; the situation is complicated
> by the fact that the normal matrices are frequently singular for
> macromolecules, but this is only a complication, not a real barrier.
> 
> Bottom line: it is not current practice.  If you specifically need the
> information for a case in which you have structure factors, you have
> some hope.
> 
> Lynn Ten Eyck
> San Diego Supercomputer Center




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