> 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 !
What a disaster. > A last comment, in RasMol, "select LIP.1H47" is recognized. OK > I suppose that the Jmol designers didn't know this oddity of the PDB > format. That is correct. The Jmol parser did not anticipate this. I was unable to find an easy fix for the parser. You said: > 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. Q: Could one argue that this should actually be Hxx1? And that the proper syntax should be: select [LIP].H471; If so, then I may be able to fix this at a lower layer, when the .pdb file is read. I am not interested in doing this would be considered a hack, but only if people felt that it was the proper solution. Q: What does the PDB call these things in mmCif files? Q: What does the PDB call these things in their XML format? Miguel ------------------------------------------------------- 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
