[phenixbb] Refining Anomalous Groups

Brennan Bonnet Brennan.Bonnet at lightsource.ca
Mon Nov 19 18:11:46 PST 2012

Hi All,

I am trying to use phenix.refine to refine partially occupied xenon sites using the Anomalous Groups selection under "Refinement settings".  My list of anomalous scatters initially consisted of 22 peaks as located by HySS.  Some of these were removed as they originated from S atoms from Met and Cys residues and a few others were removed after previous refinement steps due to having zero occupancy.  My remaining sites consist of my xenons (hopefully) and other metals such as Mg or Zn which are mixed in and look like partially occupied xenon sites.  My problem is that when I try to define the 11 remaining sites for the "refine anomalous groups" selection the software complains:

Invalid combination: F-obs not anomalous, but refinement of 11 f_double_prime values requested (11 scatterers): Please provide anomalous reflection data or fix all f_double_prime values (see refinement.refine.anomalous_scatterer.group input blocks)

I can't figure out exactly what I need to change to make it work and can't find a guide anywhere.  Do I need to provide additional data or is the syntax for the sites incorrect maybe?

Please help!


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