On Tuesday 14 September 2010 12:44:37 pm Pavel Afonine wrote:
> Hi Ethan,
>
> > I do not favor depositing riding hydrogen coordinates for
> > the same reason that I do not like the recent PDB preference
> > for depositing ANISOU records for structures that have been
> > refined with TLS.
> >
> > In both cases the enumeration of these many thousands of
> > parameter values gives the strong, but false, impression that
> > they have been individually modeled. They have not.
>
> following this logic one could say that the individual x,y,z coordinates
> listed in ATOM records for a structure refined at very low resolution
> using rigid-body refinement only (or torsion angle Simulated Annealing
> only) also may make a false impression that these coordinates were
> refined individually.
I agree with this, at least for the case of true rigid-body.
But you would still need to describe somehow the coordinates of all the
atoms in your rigid model. If it came straight out of the PDB, then
in principle it would suffice to give the PDB+CHAIN code and the
rotation/translate matrix. But if any adjustments were made, which
is I think typical if only to correct for sequence differences,then as a
practical matter you still need to provide the true starting coordinates.
And at that point you might as well provide the ending coordinates instead,
since it's the same amount of information.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
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