Bob and Angel-
The minimize addHydrogens and calculate hydrogens commands seem to have a
problem with terminal alkenes. I noticed this first with transfer of
structures from JME. I now see it after a delete hydrogens followed by
either add hydrogen approaches.
The terminal alkene receives both hydrogen atoms, but they are exactly
superimposed in the molfile. A similar problem exists with a primary amine,
but the hydrogens are offset slightly in this case. Subsequent minimization
eventually gets them apart. Not so with the superimposed hydrogens on the
alkene.
Otis
--
Otis Rothenberger
http://chemagic.org
------------------------------------------------------------------------------
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
http://p.sf.net/sfu/solaris-dev2dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
