[phenixbb] refinement with alternative molecules?

Pavel Afonine PAfonine at lbl.gov
Mon Jan 25 21:39:48 PST 2010

Hi Su-Chang,

yes, you can do it in phenix.refine and it is very easy. Make sure both 
molecules have the same chain id, and assign each molecule a different 
altLoc identifier, like A and B. Then everything else will be done 
automatically next time you feed such PDB model into phenix.refine.

Please let me know if you need any help with this, have any questions or 
need an example.

Good luck,

On 1/25/10 7:09 PM, Su-Chang Lin wrote:
> Hi, 
>     Recently I got a crystal structure of a multiple-molecules protein complex. 
> There are many protein subunits with the same fold. From the likelihood-weighted 
> maps by Phenix, I can see two different subunits occupy the same 
> position. (So I can put the model of either subunit in the same 
> densities, but some loop regions and the C-terminal tail look 
> different. ).
> I know Phenix can do occupancy refinement with a residue that has N 
> alternative conformations. My question is can Phenix do occupancy 
> refinement with alternative molecules?  
> The RMSD for two subunits is about 1.3 angstrom. The sequence 
> identity is about 30%. 
> Thank you very much!
> Su-Chang Lin, Ph.D., Postdoc Associate
> Department of Biochemistry
> Weill Medical College, Cornell University
> Whitney Building, room W-212
> 1300 York Avenue, New York, NY 10021
> 212-746-6458
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