The problem is that HETATM does NOT mean it is not an amino or nucleic acid. HETATM is used to describe "non-standard" groups, where the definition of "standard" means it is from a list of pre-determined, hard-wired residues with reserved names. It just happens that the list of selected "standard" residues are only nucleic and amino acids. This leads people to think that ATOM defines polymers and HETATM defines non-polymers, but this is wrong.
HETATM exists to allow for new "extended" types to be added to a PDB file. Because it is possible to chemically modify an amino or nucleic acid, we will always have to allow for some of these polymer types to be HET residues, even if we standardize some of the unusual amino acids. My suggestion is to make common non-polymer residues ATOM types as well, at the very least for water, which is mopre common than anything else, and would help avoid the misunderstanding that so many people have about the purpose of HETATM. Joe Krahn Phil Evans wrote: > <flame> > As an aside, does anyone understand why MSE is not an amino-acid? > Phil > </flame> > > On 30 Aug 2007, at 15:31, Clemens Vonrhein wrote: > >> If your PDB file conforms to standard >> >> http://www.wwpdb.org/documentation/format23/sect9.html#ATOM >> >> you could do >> >> % egrep "^CRYST|^SCALE|^ATOM" your.pdb > standard_residues_only.pdb >> >> You'll miss the 'non-standard' Se-MET residue 'MSE' ;-)
