Appendix F: Handling special position atoms and ions

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• The non-bonded contact term of the TNT geometry function ignored any interaction between an atom and any of its symmetry copies. This is correct for single atoms in special positions, but leads to odd results for larger groups: protein side-chains could interpenetrate, and sulfate ions would be pushed from special positions and axes. To avoid this, it was necessary manually to create EXCLUDE cards.
• The July 2009 release introduced a distance cutoff of 0.5 Å. This means that an atom must be within 0.5 Å of its symmetry copy to be regarded as special. This distance can be adjusted with the -special_dist command line argument: for instance -special_dist 1.5 would treat any atom within 1.5 Å of its symmetry copies 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.
• The November 2011 introduced the ability to manually setup utility distance restraints to prevent atoms drifting from special positions or axes. For further details see Appendix D: Using utility distance restraints across a cell symmetry operation (for special positions).
• It is planned to further improve the treatment of atoms at special positions in a future release. In particular, automated adjustment of occupancies and distance restraints to symmetry copies would be desirable.