[phenixbb] How to resolve "Conflicting scattering type symbols" error

Andrew T. Torelli att29 at cornell.edu
Tue Dec 21 08:19:32 PST 2010

Hi Ralf,

	I believe correcting the spacing as you suggested did the trick.  May I suggest changing the error message output slightly to read something like:

	Actual symbol: 		"  F" (from pdb element column)
	Expected/New symbol:	" FE" (with residue name SF4)

By including actual white spaces within quotations the error message will clue the user in to the fact that the spacing is off in their .pdb file (as it was for me).  Maybe you could also include an explicit reminder that the spacing is critical and should be checked.  Also, the Actual/Expected terminology seems more logical to me than Initial/New.  Just a friendly suggestion.

Thanks for your help and have a nice holiday,
-Andy Torelli

-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Ralf W. Grosse-Kunstleve
Sent: Monday, December 20, 2010 6:38 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] How to resolve "Conflicting scattering type symbols" error

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.

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