William Reusch wrote: >Jmol Gurus (probably Bob) > >I have encountered a glitch in the lcaocartoon method for drawing hybrid >orbitals. When a sp-hybrid carbon is bonded to a sp2-hybrid carbon the >create "sp" or "-sp" command fails to draw the hybrid orbitals. The >hybrid orbitals of the sp2 carbon may be drawn as expected. Examples >are: 1-buten-3-yne (carbon 3 fails to display sp orbitals, but carbon 4 >does), allene and acrylonitrile (acetonitrile is OK). This behavior was >observed for pdb, mol and hin files. > > > OK, I found that problem. For now I think you can use "sp2" and "-sp2" to accomplish what you want to do at the sp carbon, even though it is not sp2.
In general there is another known problem, and that is that orbitals in this type of system may not be oriented the way you want. I think the only way to get around that would be to introduce some sort of capability to rotate a cartoon around an arbitrary axis. For example: lcaocartoon rotate x 10 "py" I don't know.... Bob >Bill > > >------------------------------------------------------------------------- >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 > > -- 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
