[phenixbb] picking rfree

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Feb 7 12:24:44 PST 2008

Hi Dave,

> I am working with a dataset that I believe to be P21 even though the 
> beta angle is 89.9.  I picked the rfree set with phenix and expected 
> it to pick the set in the orthorhombic set, because 
> use_lattice_symmetry= True is the default.
> But the log file did not reflect that phenix recognized the almost 
> orthorhombic symmetry.

Yes, that's (unfortunately) true. The whole calculation is done in
a black box which doesn't report back the lattice symmetry it used

> I'd like to know if it did pick the rfree set 
> in the higher symmetry or not.

An indirect way to find out is to force the higher symmetry.
phenix.refine will merge the R-free set and complain if
symmetry-equivalent flags are incompatible.

To do this:

  phenix.refine your.mtz your.pdb --space-group=p222 --unit-cell="21.937 4.866 23.476 90 90 90" refinement.input.symmetry_safety_check=warning

It will be best to use the correct a,b,c unit cell parameters instead
of the dummy values.

If something is wrong you will see a message like this:

Checking symmetry-equivalent R-free flags for consistency:
Sorry: Incompatible symmetry-equivalent R-free flags: incompatible flags for hkl = (1, 0, 5)

If it runs beyond the point of analyzing the input "X-ray data"
the flags are what you are hoping for.


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