[MMTK] PDB files with modified residues like MSE (selenomethionine)

Peter mmtk at maubp.freeserve.co.uk
Fri Jan 20 20:10:52 CET 2006


 >>I'm trying to load PDB file 1PYM, but have run into a problem with
 >>modified amino acid residues, held as HETATM entries.
 >
> What I have done in the past was change HETATM to ATOM in the pdb file 
> and add MSE to the group database.  I don't remember if Se is in the 
> atom database or not.

Thanks for that.  I was hoping for a more elegant solution, as I'd also 
like to deal with PDB file 1MRO as well, which uses the following five 
modified resiudes:

HETNAM     MHS N1-METHYLATED HISTIDINE 

HETNAM     AGM 4-METHYL-ARGININE 

HETNAM     MGN 2-METHYL-GLUTAMINE 

HETNAM     GL3 THIOGLYCIN 

HETNAM     SMC S-METHYLCYSTEINE

But anyway, I think I can cope with "fixing" a couple of PDB files by hand.

Peter




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