[phenixbb] How to resolve "Conflicting scattering type symbols" error
Ralf W. Grosse-Kunstleve
rwgk at yahoo.com
Mon Dec 20 15:38:29 PST 2010
> Initial symbol: "F" (from pdb element column)
> New symbol: "FE" (with residue name SF4)
> I've changed the element column in my .pdb file from "F" to "FE", but
> that did not help
Did you shift the "F" one column to the left in the PDB file when
adding the "E"? The correct positioning is critical.
> On a related note, are there now more options for explicitly defining
> the oxidation state of metal atoms in custom ligand/prosthetic groups (i.e.
> so the correct scattering factors are used)?
Yes, that should work now. Just add the charge after the element name
in the PDB file. You can check in the phenix.refine output. Look for
the output like this:
Number of scattering types: 4
Type Number sf(0) Gaussians
O2- 1 9.97 2
O 20 7.97 2
N 12 6.97 2
C 33 5.97 2
sf(0) = scattering factor at diffraction angle 0.
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