On Oct 23, 2005, at 4:41 , Jan wrote:
Miguel wrote:
Hello,
The notation 1Hxx is unfortunately standard in all the PDB files
reporting the coordinates of Hydrogens and it corresponds to Hxx1 in
standard IUPAC notation. It comes from the fact that initially in
the PDB format 3 char slots were reserved for the atom names : it
was
enough for the X-Ray diffraction models, the methodology does not
allow to determine the position of Hydrogens. But when the
structures with Hydrogens come out, there was no place for 4 chars
atom names. The solution that have been adopted : place the forth
character before the first ! A very "interesting" solution for all
the designers of PDB parsers !
It's written in the PDB Format Guide, Part 63 about the ATOM
record, cited at this list several times:
- Hydrogen naming sometimes conflicts with IUPAC conventions. For
example, a hydrogen named HG11 in columns 13 - 16 is differentiated
from a mercury atom by the element symbol in columns 77 - 78.
Columns 13 - 16 present a unique name for each atom.
it is part of the PDB format like altLoc which is e.g. *;A in
RasMolScript
hi Jan,
the paragraph that you quote is about differentiating a gamma H from
a mercury (Hg), but I don't see how it applies here.
I read the pdb doc several times after Jean's original post, but I
could find nothing about naming hydrogen atoms with the fourth char
moved to the first spot. (nor did I find anything about less than
four chars for atoms names, but I assume Jean was talking about a
time that predates the current pdb spec). hence my question about
whether there is a "special" doc listing these other solutions.
if someone knows of such a doc, I am sure it would be a great help to
Jmol when it comes to file parsing.
regards,
tim
--
Timothy Driscoll
molvisions - see. grasp. learn.
<http://www.molvisions.com/>
earth:usa:virginia:blacksburg
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