From: Axel Kohlmeyer (
Date: Sat Sep 23 2006 - 21:03:01 CDT

On Fri, 22 Sep 2006, Dr. Seth Olsen wrote:


SO> As you can see, I got very different results. The way that the camera
SO> resets upon loading the molecule makes me think that the problem is buried
SO> somewhere in how VMD resets the perspective to accomodate what has been
SO> loaded. Specifically, VMD may always draw the cylinder in the same
SO> dimensions regardless of how the view has been scaled to whatever molecule
SO> is currently loaded.

the trick is, as peter suggested, to reset
the view in between, or to add the graphics
to a given molecule. this behavior has some
advantages, e.g. if you want to add a 'label'
to the vmd display (see e.g. the colorbar plugin)
as you can predict the dimensions better
if you place this in a separate molecule and
then fix it. otherwise you'd always have to
adapt the graphics to the size of the molecule

unfortunately, it seems that the corresponding command
is only exported to the tcl scripting interface.
this is (sadly) true for a number of VMD features.
it shows that the larges number of people that write
scripts for VMD use the tcl interface (that includes
me. tcl may not be a nice as python, but i have gotten
used to tcl, and most timecritical stuff needs to
be implemented in VMD directly.

best regards,

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.