When you refine structures with disulphide bridges you often get negative difference density for the sulphurs, presumably due to the well-known radiation damage effects. The negative difference density often won't disappear with usual B-factor refinement. However, it seems to go away if you refine the occupancy of the affected sulphur atoms e.g. to 0.9 or thereabouts. Would it be acceptable to publish/deposit structures where the sulphur occupancy is less than one, given a suitable REMARK in the pdb file? Thank you.
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