[phenixbb] Custom ligand - confirming the correct scattering definition

Pavel Afonine PAfonine at lbl.gov
Wed Nov 25 13:12:17 PST 2009

Hi Andy,

currently phenix.refine will not make difference between say "Fe" and 
"Fe+2". So if you see some artifacts at mFo-DFc map around your Fe, that 
might be explained by not taking "+2" into account. Refining occupancy 
of Fe would fix the map appearance (most likely), but I would not do 
that, since it will rather hide the problem than properly address it 
(and of course it  would be misleading too).

Regarding "n_gaussian table": it is just a dynamic approximation to the 
standard scattering factor table (mostly done to optimize runtime; the 
accuracy is not compromised). For more details see:

Grosse-Kunstleve RW, Sauter NK, Adams PD:
cctbx news
Newsletter of the IUCr Commission on Crystallographic Computing 2004, 


On 11/25/09 12:37 PM, Andy Torelli wrote:
> 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 
> calculation?
> Thanks,
> -Andy Torelli
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