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.
Hi, Recently I got a crystal structure of a multiple-molecules
There are many protein subunits with the same fold. From the
On 1/25/10 7:09 PM, Su-Chang Lin wrote: protein complex. 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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