Appendix F: Handling special position atoms and ions

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• There is a distance cutoff of 0.5 Å so that an atom must be within 0.5 Å of another atom within the same residue (by symmetry) to be regarded as special. This distance can be adjusted with the -special_dist command line argument: for instance -special_dist 1.5 would then treat any atom within 1.5 Å as special.
• All contacts between any atoms from a residue containing a special atom are ignored.
• A WARNING is produced if the occupancy of any atom regarded as special is 1.0.