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If this approach was pushed to the extreme, it would imply that
bulk solvent atoms should also be explicitly included in the PDB
file, because, clearly "the atoms are in the crystal", e.g. refine
hundreds of bulk solvent atoms with occupancy = 1.0 and let the B
factor reflect the disorder....
The difference between the disordered water molecules you mentioned
and disordered lysine side chain atoms is that the lysine side chain
atoms are covalently connected to the rest of the protein. If C-beta
is well defined, we have a pretty good idea about where C-gamma is
and so on. Contour the 2Fo-Fc map at 0.3 sigma and you will likely
see some density. Whether this is noise or signal is a matter of
discussion (ask people in Tom Alber's lab), but at least refinement
programs have something to base their B values on.
Likewise, the argument that disordered atoms will inflate the B
factors of the ordered atoms (like James Irving mentioned) is valid
the other way around too: an ordered C-beta will keep the B factor
for C-gamma at bay, and so on. If the B factor is meant to reflect
degree of disorder, then a mutual effect is completely desirable.
However, we all know that B factors are not perfect, either.
If you can not see the atom in the electron density map, what sense
does it make to report coordinates in a PDB file ?
For those who advocate omitting covalently attached atoms from the
model, I would like to ask for objective, agreed-upon criteria that
clearly tell me when I should omit an atom and when not.
I agree with Dirk in that there probably is no completely
satisfactory solution. In any case, whatever we decide to do about
'invisible' atoms, I think we should not dumb down our models because
we fear someone else might not fully understand them. With 'dumbing
down', I mean omitting useful information.
Best - MM
------------------------------------------------------------------------
--------
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
