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Mischa Machius wrote:
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.
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....
If you can not see the atom in the electron density map, what sense does it make to report coordinates in a PDB file ?
-- Marc SCHILTZ http://lcr.epfl.ch
