[phenixbb] Two ions at same position
pafonine at lbl.gov
Sat Aug 2 08:41:50 PDT 2014
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:
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?
> 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.
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