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