Because the atoms are in the crystal, one solution is to refine them with occupancy = 1.0 and let the B factor reflect the disorder. That, to me, seems to be the approach that makes the most physical sense.
Doesn't this ignore the use of B-factor restraints in the refinement programs? Because the B-factors are in most cases refined in this way, modelling an atom in a position not supported by experimental evidence, and allowing its B-factor to inflate, will artificially inflate others in the residue as well, and correspondingly, will restrain its B-factor to a value lower than it should be. Furthermore, this practice would be expected to greatly increase user error because there is no clear indication of the atoms that were positioned arbitrarily according to non-experimental terms. Hopefully the end-user will look at the model in the context of the structure factor data, but as we know this is not always done, and even worse, can't be done where the structure factors haven't been deposited. In this worse case scenario, how can someone be sure that any surface interactions between sidechains with middle-to-high B-factor is supported at all by the electron density? Hopefully the crystallographer who models missing atoms in this way is vigilant about depositing their structure factors! I think building atoms in places not supported by the data without at least an occ=0 is the wrong approach. There are plenty of modelling programs out there that can do that for you, even humble SwissPDB viewer will arbitrarily reconstruct missing side chains and colour them differently to the rest of the protein. James -- Dr. James Irving NH&MRC C.J. Martin Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Oxford University Roosevelt Drive, Oxford OX3 7BN UK email: [EMAIL PROTECTED] phone: +44 1865 287 550
