Timothy Driscoll wrote:
On Oct 23, 2005, at 4:41 , Jan wrote:
...
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.
this only describes the need to distinguish HG from Hg while nothing of
right justification of element symbols on column 14 is written in Part
63/68 ATOM/HETATM, but there is
* Appendix 3: Atom Names
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_76.html
13 - 14 Chemical symbol - right justified, except for hydrogen atoms
you are right, how to do this, by overflow must be guessed from:
* PDB Change Advisory Notice July 9, 1999
http://www.rcsb.org/pdb/lists/pdb-l/199907/msg00013.html
3. Amino acid hydrogen atom nomenclature
We propose to label amino acid hydrogen atoms according to the
IUPAC recommendations described in reference [3]. The specific list
of atom names to be used is included at the end of this document.
We will continue to follow existing PDB conventions on the alignment
of the atom name within the 4 char atom name field (i.e. the H in a
hydrogen atom label is placed in column 2 of the atom name field).
but is shown in examples:
* there is a table showing the Correlation of hydrogen atom naming systems
http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl
Regards, Jan
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.
-------------------------------------------------------
This SF.Net email is sponsored by the JBoss Inc.
Get Certified Today * Register for a JBoss Training Course
Free Certification Exam for All Training Attendees Through End of 2005
Visit http://www.jboss.com/services/certification for more information
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
