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' ;-)
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