From: Axel Kohlmeyer (
Date: Thu Oct 05 2006 - 10:51:17 CDT

On Thu, 5 Oct 2006, Dr. Seth Olsen wrote:

SO> Hi Axel,


first off, please don't sent files as large as yours to
any mailing list, there are a ton of people out there
reading mail with a slow link and for them a 9MB mail
is a serious chunk and can cost them a lot of time and
money. the really recommended way is to register for a
biocore account and join the vmd public project and then
upload your data to the biofs (and send an e-mail about
this to the list).

SO> The script I mentioned was one that I whipped up to read in the cube file in
SO> question and do the surfaces the way I wanted them. I have attached it ('
SO>') with a cube file that it will read in (filename is coded in
SO> the script), and a jpeg file which shows what I got out of it when I did the
SO> 'gopython' thing. Any insight is greatly appreciated.

i don't have any problems with your visualizing your input and it
looks perfectly ok on my machine, so there could be a problem with
your video driver.

furthermore, there is no need to load the same file 3 times to get
3 representations. you can add multiple representations to a single
molecule (or data set).

i'm attaching a corresponding tcl script (i find doing this in tcl
more convenient, but that is probably a matter of taste). to make
sure that this is really driver problem (and not a python problem),
please load the script with vmd -e isosurf.vmd and compare. thank.


SO> Cheers,
SO> Seth

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.