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 internally.
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.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Ralf, That worked. I forced the p222 and got this line in the file. Checking symmetry-equivalent R-free flags for consistency: OK thanks, Dave -- David N. Garboczi, PhD Phone: 301-496-4773 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 Fax: 301-402-0284 Email: [email protected] The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender's own and not expressly made on behalf of the NIAID by one of its representatives.