[phenixbb] rotamers

Antony Oliver Antony.Oliver at sussex.ac.uk
Sat Mar 26 03:06:47 PDT 2011

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
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
>>> The policy is just a preference not an enforced change to the

>>> 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


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

email: antony.oliver at sussex.ac.uk
tel (office): 01273 678349
tel (lab): 01273 677512

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