Hi Jacob,
> Therefore, I was thinking an exposure-dependent parameter might be
> introduced into the atomic models, as an exposure-dependent occupancy of
> sorts. However, this would require refinement programs to use individual
> observations as data rather than combined reflections, effectively
> integrating scaling into refinement.
It seems to me that this approach would only be valid if the atomic (pdb)
model is a valid representation of the crystal structure irrespectively of
how much radiation damage has suffered. To put it differently, the
suggested approach would only be valid if the data collected remain
strictly isomorphous for the length of the experiment (within a scale and
overall B factor). But if the data are indeed isomorphous throughout the
data collection procedure, then the current treatment (which -through
scaling- essentially interpolates to zero radiation damage) would be
equivalent to your suggested procedure. If on the other hand, radiation
damage causes non-isomorphism (but you still deposit one atomic model),
you would be absorbing unknown model errors in yet another set of
adjustable parameters.
My twocents,
Nicholas
--
Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
