Re: PDB File questions also

Simon Brocklehurst (smb@bioch.ox.ac.uk)
Thu, 9 Mar 1995 14:08:16 +0000 (GMT)

Hi,
> The questions are...
>
> Where are those missing residues?
>
You're right, the PDB file is not as helpful as it might be.
The SEQRES records are for residues 10 through to the
end of the protein - the structure is for residues 17 to the
end. Thus the "missing residues" are on the N-terminal end of
the protein.

> Why does RasMol show the residues as being
> connected if there are two missing between the atom set
> of data?

If I understand you correctly, this might depend on the way that
the display program decides whether two atoms are covalently bonded or
not. IMO, programs should do this by "calculating" covalent bonds
from the relative positions of atoms (it's not a difficult computation).
However, some programs assume the connectivities from the order in
which atoms occur in the PDB file. In these cases, you can get
incorrect covalent bonds drawn both between residues, and also within
the residue itself.

-- Simon
_____________________________________________________________________________
|
| ,_ o Simon M. Brocklehurst,
| / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry,
| \>> | University of Oxford, Oxford, UK.
| \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/
|____________________________________________________________________________