[phenixbb] Custom ligand - confirming the correct scattering definition
PAfonine at lbl.gov
Wed Nov 25 13:12:17 PST 2009
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:
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
> -Andy Torelli
> phenixbb mailing list
> phenixbb at phenix-online.org
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