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; skype: xavierprat
http://x.prat.resina.googlepages.com