Angel Herraez wrote: > " Deoxy- and ribose nucleotides now have separate chemical definitions > with > the DNA forms relabeled as DA, DC, DG, DT, DI and DU. " > these are in now.
> (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. " > Since Jmol doesn't do anything more than count these for the popup menu, this should be OK. It just means that they will have their own menu item. > " • - 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) > shouldn't be an issue except for a few terminal H atoms, and I have taken care of those. > >>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. > definitely not a problem. So provided I did not mess up the numbering in my reorganization, I think we are all set. -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
