[phenixbb] about low resolution refinement
pafonine at lbl.gov
Sun Oct 10 16:48:57 PDT 2010
> I am refining a low resolution data. According to sigma vs.
> resolution, my resolution is 4.7A.
not sure what is "sigma vs. resolution" but hope you made the right
> Because there are four identical molecular per asymetric unit, I can
> use positional refinement. There are about 65% alpha-helices in the
> structure, so I want to use secondary structure restrain. Does phenix
> has this restrain in the refinement?
Sorry for missing documentation on this subject.
First of all, get the latest version of PHENIX (the one you have is very
Then (once you have the latest), yes, you can use secondary structure
phenix.refine model.pdb data.hkl main.secondary_structure_restraints=true
so phenix.refine automatically determines secondary structure and
applies the restrains. Note, GIGO principle applies, that is if your
input model is distorted then it's unlikely that the procedure will
figure out the secondary structure correctly.
To make it a less black-box, you can run
phenix.secondary_structure_restraints model.pdb > ss_restraints.params
and then check (and edit if necessary) the ss_restraints.params file,
and then run phenix.refine as following:
phenix.refine model.pdb data.hkl
I hope Nat comments more if I missed something.
Let me know if you have any other questions.
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