| Author |
Message |
John Keller
Unregistered guest
| | Posted on Friday, January 29, 2016 - 3:41 pm: | |
I am having trouble creating an isosurface in Jmol using a .cub file exported by MOViewer: it has lots of red and blue splotches. So I looked at the .cub file, and it contains many very large numbers like "5699" (line 6653), 202 etc etc. Normal esp values are 1 or less. The file is attached.
Why are these presumably incorrect values appearing in the exported file? (The esp surface in MOViewer itself is normal.)
Also, I imported the job into your demo server #226623, exported the ed and esp files in .cub format, and many of the same large values appear. |
John Keller
Unregistered guest
| | Posted on Sunday, January 31, 2016 - 3:54 am: | |
This problem appears with exported .cub files, but not .jvxl files. I optimized teropyrene at B3LYP/3-21G level and displayed the ESP surface. It was exported either as .cub or .jvxl, then both were displayed with Jmol 14.4 isosurface command.  |
John Keller
Unregistered guest
| | Posted on Tuesday, March 08, 2016 - 5:55 pm: | |
...BUT: saving an MO containing a node from WebMO gives only the positive half when saved in the .jvxl format. To get both halves, export the MO in .cub format, open and customize the whole MO in Jmol (isosurface.. command), then do "write isosurface MO-name.jvxl". See Robert Hanson's jmol documentation page at http://chemapps.stolaf.edu/jmol/docs/ for examples and details. |
John Keller
Unregistered guest
| | Posted on Wednesday, March 09, 2016 - 1:27 am: | |
More: The isosurface command must use the "sign" parameter to show both lobes at the same time. Then do the "write isosurface MO-name.jvxl". |
John Keller
Unregistered guest
| | Posted on Wednesday, May 04, 2016 - 3:47 pm: | |
All versions of WebMO Pro contain a bug in saving .cub files of ESP surfaces - at least for certain molecules such as H2O, tetrachloroethylene, and chloroethylene (Gaussian B3LYP/6-311++G(d,p) Opt and MO jobs). The .cub files have about half the surface correct, and the other half "piled up" when viewed with Jmol. This suggests some kind of out-of-register error in the code writing these files. On the other hand, the .jvxl files for the ESP surfaces appear correct in Jmol. |
leuenk .cub file