[phenixbb] refinement with alternative molecules?

[Su-Chang Lin]

Hi Ravel,
Thank you for the example.  I am using phenix.refine 1.6.  I tried to do occupancy refinement for the alternative molecules with ALTID. At the same time, I also want to use NCS restraints in refinement.
 
But I got the same problem as Joe Krahn had on Wed Sep 23 12:04:31 PDT 2009:
He said: "When NCS restraints contain a residue with alternate conformations, that 
residue gets excluded from all equivalences, even if the selections 
contain ALTID to avoid the redundant atoms."

The error message I got is "Sorry: NCS restraints selections do not produce any pairs of matching atoms".

I tried different residue numbers for the alternative molecules, still got the same error message.

Turning on find_automatically for ncs gave me the same error message.

Is it possible that phenix.refine thought that the residues/atoms with ALTID are different from they should be?  

Thanks,
Su-Chang 


> I just made up an example of how you can do it. The input/output files 
> 
> are here:
> 
>  http://cci.lbl.gov/~afonine/example_111/
> 
> The command is in "run" file. Of course you can run any other your 
> custom command.
> 
> Pavel.
> 
> 
> 
> 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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> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> >   
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