[phenixbb] refinement with alternative molecules?

Pavel Afonine PAfonine at lbl.gov
Mon Jan 25 22:21:03 PST 2010

I just made up an example of how you can do it. The input/output files 
are here:


The command is in "run" file. Of course you can run any other your 
custom command.


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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