Dear all, I have had some personal off-line communication with the PDB about the current policy on zero-occupancy atoms. I thought it would be useful to disseminate the information to the wider community... I have just taken the key points and listed them below...(hopefully without changing the intended meaning!)
The PDB deprecates the use of zero occupancy atoms - but they are certainly allowed - they are annotated in remark 475 if present. The preferred action is for them to be removed and then the missing atoms are documented in remark 470. At no point should this be imposed on the authors - it is by agreement. The policy is just a preference not an enforced change to the coordinates.
you can check the policies at the wwPDB http://www.wwpdb.org/procedure.html search for the section Zero occupancy residues (REMARK 475) and atoms (REMARK 480) which indicates that zero occupancy atoms are allowed in the format.
I keenly await the (hopefully) consensus opinion on what we, as crystallographers, should do with residues with poor or absent side-chain density. Tony. -- Dr Antony W. Oliver Senior Research Fellow Cancer Research UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton BN1 9QR email: [email protected] tel (office): 01273 678349 tel (lab): 01273 677512