[phenixbb] picking rfree

David Garboczi dgarboczi at niaid.nih.gov
Thu Feb 7 13:02:50 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" 
>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
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: dgarboczi at niaid.nih.gov

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.

More information about the phenixbb mailing list