[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

Hi Andrew,

>     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.


More information about the phenixbb mailing list