Hi Alastair,

same chain ID + same residue number + different altlocs

will make phenix.refine to couple involved residues. Residues (residue names) can be different.

For examples, see pages 38-39 here:
http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf

and also
http://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement

Pavel

On 8/2/14, 8:36 AM, Alastair Fyfe wrote:

I also ran into this recently and was puzzled about the correct PDB encoding. Using the same residue number with differing altloc, atom name and element fields seems straightforward but what should the residue name be ? In my experience not all PDB-processing software is happy with different residue names for the same residue number. Is there definitive PDB documentation for this case?
thanks,
Alastair

On 08/02/2014 08:12 AM, Pavel Afonine wrote:
On 8/2/14, 5:36 AM, Elke De Zitter wrote:

you should make sure the summation of their occupancies equals 1.

While this might help refinement convergence, in general this is not necessarily because phenix.refine will constrain coupled occupancies to add up to 1.

Pavel
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