VMD-L Mailing List

From: Dr. Seth Olsen (seth.olsen_at_gmail.com)
Date: Thu Oct 05 2006 - 03:32:34 CDT

Hi Axel,

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

Cheers,

Seth

On 10/4/06, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
>
> On 10/3/06, Dr. Seth Olsen <seth.olsen_at_gmail.com> 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.
>
> thanks,
> axel.
> >
> > Cheers,
> >
> > Seth
> >
> > --
> > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> >
> > 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: s.olsen1_at_uq.edu.au
> > Web: www.ccms.uq.edu.au
> >
> > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> > The opinions expressed here are my own and do not reflect the positions
> of
> > the University of Queensland.
> >
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> 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.
> 

-- 
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
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: s.olsen1_at_uq.edu.au
Web: www.ccms.uq.edu.au
ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
The opinions expressed here are my own and do not reflect the positions of
the University of Queensland.

cube-test.jpg