Tiancen Hu wrote:
> Dear all,
>
> Some problems occurred when coot was dealing with the element symbol
> (columns 77-78) for two Mn2+ ions in the PDB file. Here is the description:
>
> Coot version: 5.0.2, Mac OS X
> Problem trigger:
> 1) I used Phenix to refine the structure. The element symbols for the
> two Mn2+ ions were "Mn" in the generated PDB file.
> 2) I used PDBSET to rename some chains (not affecting the metal ions).
> The element symbols for the two ions became blank.
> 3) I opened coot to real space fine part of the "PDBSETted" coordinate,
> and saved a new PDB. The element symbols now became "M", which could not
> be recognized by Phenix.refine and caused an error when I tried to
> generate metal restraints. After I manually changed the "M" to "Mn",
> phenix.refine performed well.
>
> Is this a bug, or did I do something improperly?
At a guess: "Mn" is not a valid element symbol, so PDBSET reset it to
blank. I am surprised that you find that Coot converts " " to " M" when
the atom is "MN " (if indeed that is what is happening). Coot
certainly does not do that for me - it converts the element to "MN" as
it should.
Paul.
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