[phenixbb] Custom ligand - confirming the correct scattering definition

Andy Torelli att29 at cornell.edu
Wed Nov 25 12:37:18 PST 2009

To the Phenix group:

	I've created a .cif file for a ligand that includes metal atoms.   The 
metal atoms are defined in the .cif file with their element name, but in 
actuality, they should be defined according to their oxidation state so 
that the correct scattering parameters are used during refinement.

	In CNS, this meant choosing an "atom type" that would be parsed to 
match the correct scattering definition listed in the scatter.lib file. 
  I see that phenix uses the n_gaussian table for scattering values. 
Where can I view this and the other scattering table options?  Like CNS, 
do I just need to use the name of the element with the correct 
oxidation state from the table (e.g. "Fe+2") in my .cif file to ensure 
that the correct scattering definition is used during refinement and map 

-Andy Torelli

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