From: Axel Kohlmeyer (
Date: Wed Oct 04 2006 - 08:26:45 CDT

On 10/3/06, Dr. Seth Olsen <> wrote:
> Hi VMDers,
> There may be a problem with the cube file viewing capacity of the new VMD
> distribution. I was having trouble viewing some cube files containing
> orbitals and densities, so I decided to try some old files and an old
> script which had previously worked fine. The result was garbage (I've
> attached a screenshot). Since the same script and cube files worked in my

hi seth,

script? are you talking about a saved state file?
vmd handles cube files out of the box.

can you please upload your files to the public VMD biocore project.
this way john and i can easily have a look at it. the cube file reader
does work very hard to handle all kinds of weird cube files (many programs
do not write correct cube files, as many authors mistake the instructions
for entering a grid manually in the gaussian manual for a description of
the format...).

> last vmd distribution ( 1.8.4, I think), the problem must be with the change
> in vmd version. Is there any other information about a possible problem?

no. i've been looking at a large number of cube files and they all worked.

> I've double checked by running the cube through other visualization
> utilities and they don't seem to have a problem.

this may or may not indicate a problem. see above. for a visualization program
like VMD it is always difficult to deal with formats, that many codes
write slightly
different. additionally, with the increased use of VMD for analysis it
is getting
even more difficult. for visualization a guess is better than nothing, but for
analysis it can be desasterous and we as of now don't have any indicator for
how trustworthy certain information is.

that being said, it is always good that people report problems with newer
versions of VMD instead of reverting to the old version, so people have a
chance to investigate, and correct potential errors or improve heuristics.

> Cheers,
> Seth
> --
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> Dr Seth Olsen, PhD
> Postdoctoral Fellow, Biomolecular Modeling Group
> Centre for Computational Molecular Science
> Australian Institute for Bioengineering and Nanotechnology (Bldg. 75)
> The University of Queensland
> Qld 4072, Brisbane, Australia
> tel (617) 3346 3976
> fax (617) 33654623
> email:
> Web:
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> The opinions expressed here are my own and do not reflect the positions of
> the University of Queensland.

Axel Kohlmeyer
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.