[phenixbb] refine occupancies for MET/MSE double conformations

Pavel Afonine pafonine at lbl.gov
Tue Nov 11 23:25:32 PST 2008

Hi Jonathan,

currently it's not possible (if I correctly understand what you are 
trying to do), but it will be available (hopefully) in the next version.


On 11/11/2008 3:13 AM, Jonathan Elegheert wrote:
> 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
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>>> phenixbb at phenix-online.org
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