Hi Terry, to make sure it is recognized, look for something like this in the output phenix.refine .log file: Number of scattering types: 5 Type Number sf(0) Au 1 78.96 S 10 16.00 O 395 8.00 N 193 7.00 C 613 6.00 sf(0) = scattering factor at diffraction angle 0. Please let me know if you have questions. Pavel. On 8/24/09 7:29 PM, Terry Lang wrote:

Hey Everyone,

I am working on an xray structure that contains a ruthenium. I have been able to use elbow to create a cif file that phenix can read and refine without throwing error messages. However, there is a large amount of positive electron density after the refinement. I am looking into modeling coordinate waters, but I first wanted to check that the ruthenium is being read correctly by phenix. How do I figure out if it is properly recognized (eg correct scattering factors, bond and angle restraints, etc)?

Thanks, Terry