[Chimera-users] Labels of Metal atoms

Tom Goddard goddard at sonic.net
Fri Feb 11 14:27:30 PST 2011

Hi Mike,

   Does the FE1 name come from a PDB or Mol2 file you opened?  If that 
name appears in the file, one obvious approach is to change the file 
replacing FE1 with Fe1.  I'm not sure if that will break code that 
expects FE1.  I don't think there are any options in Chimera to 
manipulate the case of names displayed in labels.  I believe Chimera 
just uses the capitalization of names it obtains from the file it read in.

   I guess Chimera could have some option to manipulate the case of atom 
names in labels.  But it seems very specialized.  Someone looking at a 
protein with a C-alpha atom named CA generally does not want Ca.  This 
also indicates that it isn't possible to know if an atom name refers to 
an atomic element (e.g. Fe = iron, Ca = calcium) or something else (like 


> How do I make the default label for metal atoms be upper and lower case?
> For instance in an iron compound, if I issue label ~H from the command 
> line the result will be FE1 where I prefer Fe1, etc., etc.
> This is true for all two letter atom names.
> Thanks
> Cheers,
> Mike
> <<< 
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> Dr. Michael W. Day
> Director - X-ray Crystallography Lab & Molecular Observatory
> California Institute of Technology
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