Richard is quite right in his assessment that the main problem here is
the column in which the atom name starts. Most PDB entries
that include protons have the majority of atom names starting
in the 14th column, with names such as HG21 altered to 1HG2
and started in the 13th column. This avoids the atom name and
residue name running into one another, and is what insightII
expects. To keep space between the atom and residue names
the ambpdb code elects to start all atom names in the 13th column.
Actually, the PDB standard assigns the 13th column to be only
occupied by a 2nd (wrapped) number on a hydrogen - the 14th is
supposed to be the beginning of the element. If it isn't an H
with the extra digit (HC12), there shouldn't be anything in 13.
The atom name can extend to the residue # in the standard.
Of course programs do what programmers find reasonable & convenient,
and the standard is only a contributing factor.
Bill Ross
Received on Tue Apr 17 2001 - 11:20:18 PDT
