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I'm with the group that believes side chains should be in the model since they're definitely in the crystal and taking up space. Whether one allows the B's to go very large or sets the occupancies to 0 is a matter of taste.
To reply to the argument that non-crystallographers will take these positions as valid when they're not, the same is true for side chains held in place by crystal contacts. These positions are well defined and all would agree that the atoms should be in the crystallographic model, yet their positions probably do not hold real information for those looking for clues to function.
OTOH, I have seen folks totally confused while looking at a structure because they can't find an interesting arginine in the pdb file (because it looks like an alanine).
Sue Roberts Department of Biochemistry & Molecular Biophysics University of Arizona [EMAIL PROTECTED] 520 621-8171
