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 !
A last comment, in RasMol, "select LIP.1H47" is recognized. I
suppose that the Jmol designers didn't know this oddity of the PDB
format.
Best regards,
Jean
Hello all
I have a PDB file in which some atoms have 4-character ID starting
with a
number; Jmol does not allow me to select them
Example:
ATOM 1 N50 LIP 1 -22.659 21.125 -23.903 .00 .0000
ATOM 2 C47 LIP 1 -21.387 21.793 -24.221 .00 .0000
ATOM 3 1H47 LIP 1 -21.046 21.461 -25.101 .00 .0000
ATOM 4 2H47 LIP 1 -21.532 22.781 -24.272 .00 .0000
ATOM 5 3H47 LIP 1 -20.717 21.592 -23.507 .00 .0000
I can select lip.c47
but not select lip.1h47, I get this error: end of expression
expected
If I try select lip.?h47, it works (but of course I get selected
more than I want)
Any clues? I have tested with 10.00.24 and 10.00.42
hi Angel,
just curious: that atom naming system is not familiar to me. is it
specific to lipids?
tim
--
Timothy Driscoll
molvisions - see. grasp. learn.
<http://www.molvisions.com/>
earth:usa:virginia:blacksburg
-------------------------------------------------------
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
