Hi,
Here are two links that could give some light on the problem:
- http://www.rcsb.org/pdb/docs/format/pdbguide2.2/
PDB_format_1992.pdf : this is the "Atomic coordinate and
bibliographic entry format description - February 1992"
"For protein coordinate sets containing hydrogen atoms, the IUPAC-
IUB rules have been followed. Recommendation rule number 4.4 has been
modified as follows: When more than one hydrogen atom is bonded to a
single non-hydrogen atom, the hydrogen atom number desidnation is
given as the first character of the atom name raster tha as the las
character (e.g. Hbeta1 is denoted 1HB)"
- http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl which describes the
"Correlation of hydrogen atom naming systems" in different applications.
Concerning a questian raised by Tim concerning what is the naming
used in mmCIF, I had a look at 1L2K both in PDB and mmCIF format
(http://www.rcsb.org/pdb/cgi/explore.cgi?
job=download;pdbId=1L2K;page=0;pid=171361130167582&opt=show&format=PDB&p
re=1 and http://www.rcsb.org/pdb/cgi/explore.cgi?
job=download;pdbId=1L2K;page=0;pid=171361130167582&opt=show&format=mmCIF
&pre=1) ;
here are the records of a given H atom :
in PDB = ATOM 10 1HG1 VAL A 1 -3.462 15.657 17.717 1.00
27.83 H
in mmCIF = ATOM 10 H HG11 . VAL A 1 1 ? -3.462 15.657 17.717
1.00 27.83 ? ? ? ? ? 1 VAL A 1HG1 1
Jean
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