On 31/03/2011 23:43, Zbyszek Otwinowski wrote:
Regarding the closing statement about the best solution to poorly
ordered side chains:
I described in the previous e-mail the probabilistic interpretation of
B-factors. In the case of very high uncertainty = poorly ordered side
chains, I prefer to deposit the conformer representing maximum a
posteriori, even if it does not represent all possible conformations.
Maximum a posteriori will have significant contribution from the most
probable conformation of side chain (prior knowledge) and should not
conflict with likelihood (electron density map).
Thus, in practice I model the most probable conformation as long as it
it in even very weak electron density, does not overlap significantly
with negative difference electron density and do not clash with other
residues.
If it's probability you're after, if there's no density to guide you
(very common!) you'd have to place all "likely" rotamers that don't
clash with anything, and set their occupancies to their probability (as
encoded in the rotamer library).
This is now veering into data-free protein modeling territory... wasn't
the idea to present to the downstream user an atomic representation of
what the electron density shows us?
Worse, what we're also doing is encoding multiple different things in
one place - what database people call "poorly normalised", i.e. to
understand a data field requires further parsing and if statements. In
this case: to know whether there was no density, as end-user I'd have
to have to second-guess what exactly those
high-B-factor-variable-occupancy atoms mean.
Until the PDB is expanded, the conventions need to be clear, and I
thought they were:
High B-factor ==> means atom is there but density is weak
Atom missing ==> no density to support it.
Oh well...
phx.
