[phenixbb] refinement with alternative molecules?
sul2005 at med.cornell.edu
Wed Jan 27 02:50:23 PST 2010
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?
> 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
> > 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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