<snip>
> it seems that we are trying to deposit one model to satisfy two
> different purposes - one for model validation and the other for model
> interpretation (use in docking etc), and what's good for one purpose
> might not be necessarily good for the other.
</snip>
This has been discussed before on this list, but allow me to repeat it:
You would have expected that the crystallographers' aim would be to
deposit the model that maximises the product (likelihood * prior).
Clearly, this is not what we do, mainly because (a) the calculation of
likelihood is only based on a subset of the 'data' that are obtained from
an X-ray diffraction experiment (for example, we ignore diffuse scattering
as Ian pointed-out), (b) we consciously avoid 'prior' because this would
make the models 'subjective', meaning that better informed people would
deposit (for the same data) different models than the less well informed,
(c) the format of the PDB does not offer much room for 'creative
interpretations' of the electron density maps [for example, you can't have
discrete disorder on the backbone (or has this changed ?)]. I sense that
what is being deposited is not the 'best model' in any conceivable way,
but the model that 'best' accounts for the final 2mFo-DFc map within the
limitations of the program used for the final refinement.
My twocents,
Nicholas
ps. May I say parenthetically that making the deposited models dependant
on their intended usage, would possibly qualify as 'fraud' ;-)
--
Dr 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/
