Re: odd display of ambpdb generated files

From: Bill Ross <>
Date: Tue 17 Apr 2001 11:20:18 -0700 (PDT)

        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
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