Very much appreciate your finding that, Xavier. We did a lot of testing of that, but it's still possible that there is a bug there. I will definitely look into it immediately.
By the way, you can deliver those cube files as JVXL format surfaces with very little files space if you want to. http://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf Xavier Prat-Resina wrote: > Jmol developers, > > it's seems that Jmol is not able to display the right shape of > some Molecular Orbitals when the data is read form Gaussian outputs > (not cube files). > This anomaly can already be seen in > http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm > when it loads "water-G03W.out" and the 6th MO has the wrong shape. > > I tested it myself comparing it with cube files > (for water, the discrepancy starts at MO=6) > http://144.92.39.89/xavier/mo/index.html > (for ethyne the very first MO is not symmetric) > http://144.92.39.89/xavier/mo/ethyne.html > > It seems to me that Jmol has problems with the d functions, > labeled in Gaussian as XX, YY, ZZ, XY, XZ, YZ (just a guess). > For water or ethyne this basis set is used with keywords like 6-31g(d) > For third or higher row elements, these d functions are always > included (with the exception of sto-3g basis) > I tested this for Br: > http://144.92.39.89/xavier/mo/brf5.html > > I've been looking at the source code but I have no clue where the > problem is. > I would be willing to do it myself if I get a hint :) > Is there any standard/XML format for molecular properties such > as vibrations, molecular orbitals etc? This would save Jmol a lot > of trouble when reading formatted files. > > Thanks for your help > > > Xavier > > -- > Xavier Prat-Resina > Research Associate > Journal of Chemical Education and University of Wisconsin > 209 N. Brooks St. Madison, WI 53715-1116 > > Tel: 608 8901702 // Fax: 608 2627145 > e-mail: xavier.prat.resina + gmail.com <http://gmail.com>; skype: > xavierprat > http://x.prat.resina.googlepages.com > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-developers mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- 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: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
