[phenixbb] refine occupancies for MET/MSE double conformations

Jonathan Elegheert jonathan.elegheert at ugent.be
Tue Nov 11 03:13:39 PST 2008


Hi Pavel,

Actually, I have 2 practical problems (see attachment) which I haven't 
been able to deal with so far using phenix.refine (latest version).

Ligand A shows 2 stacking modes (A1 and A2) above an FMN cofactor. The 
A2 conformation also overlaps partially with another partially occupied 
ligand B. How do I couple the occupancy refinements of these 
interrelated ligands? Until now, I solved it by refining the occupancy 
as if ligand A has 3 modes; A1, A2 and A3 (= B). Otherwise, ligand B is 
always pushed out of its density due to the anti-bumping restraints. 
This is high res data (~1.5 A), so pretty decisive about atomic positions.

The same question goes for the coupling of conformation C1 of an Ile 
residue and water D on one hand, and conformation C2 of that Ile on the 
other hand.

Thus far I've only been able to define these relations in SHELXL, but 
it's not entirely clear to me how to do this in phenix.refine (which I 
prefer for this dataset).

Many thanks in advance,

Jonathan Elegheert
PhD Student
L-ProBE, Ghent University
Belgium

Pavel Afonine wrote:
> Ralf,
>
> it's not that uncommon. See for example:
> http://www.rcsb.org/pdb/files/1ejg.pdb
>
> Also, you may want to couple partially occupied residue's side chain 
> with partially occupied water.
>
> Pavel.
>
>
> On 11/4/2008 9:36 AM, Ralf W. Grosse-Kunstleve wrote:
>> Hi Tassos,
>>
>>   
>>> However, I want to refine my MET residues in double conformations, one
>>> as MET (AMET) and the other one as MSE (BMSE) with each 0.5 occupancy
>>> to start with.
>>>     
>>
>> In addition to what Pavel wrote: I just tried out the AMET BMSE mix
>> without giving any manual atom selections, and it works fine for me.
>> (P.S.: I'm thrilled to see this use of the
>> multiple-conformers-with-mixed-residue-names feature,
>> since it was a lot of work.)
>>
>> Ralf
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>   
> ------------------------------------------------------------------------
>
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