VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Thu Aug 15 2002 - 16:05:55 CDT

Hi,

Sounds like a cool app! Unfortunately, it looks like the only workaround
I have at the moment for adding graphics data is to load a real molecule
instead of a 'graphics' molecule. You could create a pdb file containing
just one atom, use that to initialize the molecule, then delete the single
coordinate frame. This will certainly be fixed in a future version.

Incidentally, I would want to let you know that we are strongly considering
creating a new Python interface in which the C-level code would be
generated by SWIG from our main C++ API, and the user-level code would
be written in actual Python (though the C API could of course be accessed
directly for efficiency). I'd be interested in hearing any comments you
might have about the Python API we have now.

Cheers,

Justin
 
On Wed, Aug 14, 2002 at 11:40:31PM -0500, Pawel Kedzierski wrote:
>
> Dear VMD-team,
>
> I have just switched to the new version of VMD (1.8a21) and I
> experience some incompatibility problems. I am working on a Python
> module which, among other things, shall display electrostatic field
> on a grid. The grid should be independent of the molecular objects
> in order to dynamically change the field visualization in response to
> movement of the molecule(s).
>
> As of VMD 1.7.1, script-generated graphics was treated as a separate
> molecule having 0 atoms. Apart from a minor inconvenience of an error
> message at the time of creation:
> molecule.load('graphics', 'name')
> due to nonexistant file 'name', it used to work well. Now the same
> instruction fails completely with a ValueError. There is another
> function:
> import graphics(molid, filetype, filename)
> but the description is not very helpful, and some trial-and-error
> have not lead me to a solution.
>
> If anybody knows, how to create a standalone graphical object from
> VMD 1.8 python interpreter (or how to create cleanly an empty
> molecule, so one can append graphics to it), please let me know.
>
> Regards,
>
> Pawel Kedzierski
>
> --
>
> Pawel Kedzierski, kedziers_at_ccmsi.us
> Chemistry/CREST, Jacson State University 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys