[phenixbb] Two ions at same position

Pavel Afonine pafonine at lbl.gov
Sat Aug 2 08:41:50 PDT 2014


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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>
>
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