[phenixbb] picking rfree
dgarboczi at niaid.nih.gov
Thu Feb 7 13:02:50 PST 2008
>> 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"
>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.
>phenixbb mailing list
>phenixbb at phenix-online.org
That worked. I forced the p222 and got this line in the file.
Checking symmetry-equivalent R-free flags for consistency: OK
David N. Garboczi, PhD
Investigator, Structural Biology Section (SBS)
Laboratory of Immunogenetics (LIG)
National Institute of Allergy and Infectious Diseases (NIAID)
National Institutes of Health (NIH)
Twinbrook 2/Room 110
12441 Parklawn Drive
Rockville, Maryland 20852-1742
Email: dgarboczi at niaid.nih.gov
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