Next: Determination of Standard Values Up: Knowledge-Based B-Factor Restraints for Previous: Existing Methods and Limitations
Next: Determination
of Standard Values Up: Knowledge-Based
B-Factor Restraints for Previous: Existing
Methods and Limitations
It is proposed that the B-factors of macromolecular models be restrained by
where 
and 
are the current B-factors of the two bonded atoms, 1 and 2. 
is the expected increase in B-factor when moving from atom 1 to atom 2.
is a measure of the confidence of
. The parameters of the model are adjusted to minimize this function, while
simultaneously minimizing the residual in the diffraction data restraints.
One cannot have a separate
for each bond in the molecule, one would not know what value to use in
each instance. The bonds must be categorized in some fashion to reduce
the number of standard values required. In this work a systematic study
was not performed to determine an optimal parameterization. Instead the
method used in the TNT refinement package for the description of stereochemistry
was chosen. In this scheme all the bonds in the main chain are considered
to be in the same class while the bonds in the side chains are classified
by the amino acid type.