Following my previous message:
> > "H5T", // 45 - 5' terminus hydrogen which replaces P + O1P + O2P
> > "O5T", // 46 - 5' terminus oxygen which replaces P + O1P + O2P
"Terminal protons should be labeled HO5' and HO3' instead of H5T and
H3T."
Looks like a sound opinion, it's a wwPDB discussion list:
http://wwpdb-remediation.rutgers.edu/mail-archive/msg00014.html
Haven't found anthing about O5T. Maybe just plain O5 prime ?
Another good source of info, finally:
http://www.wwpdb.org/documentation/format3.1-20070719.pdf
on page 22 (last):
"[new names acc. to IUPAC]
with the exception of the well-established
convention for Cterminal atoms OXT and HXT
"
"
Deoxy- and ribose nucleotides now have separate chemical definitions with
the DNA forms relabeled as DA, DC, DG, DT, DI and DU. "
(This we already knew.)
"Modified nucleotides formerly identified as using the “plus-nucleotide”
syntax (e.g. +C, +G) have been relabeled with the particular 3-letter code
corresponding to the full chemical description of the modified nucleotide.
"
(Bob, this may also affect Jmol; I seem to remember that +C etc. are used in
JmolConstants.java)
"
• -
Atom names begin with their element symbol.
-•
Heavy atom names follow the traditional PDB justification rules in
which the atom element symbol is right justified in the second
character position of the 4-character atom name. 4-character
names for atoms with 1-character element symbols have been
compressed to 3 characters.
-•
Hydrogen atoms names all begin with “H” and are not subject to the
justification rule.
"
(not sure if this justification stuff affects Jmol)
>From reading this, I understand that some trouble we have had occasionally with hydrogen
atom names that had numbers before the H (and were fixed on the go by Bob) will no longer
appear.
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