From: Axel Kohlmeyer (
Date: Sun May 16 2004 - 14:03:11 CDT

hello everybody on VMD-L,

there are currently two visualization problems for which i'd
like to find a better/cleaner solution. after banging my head
against the wall for quite some time, i thought that perhaps
the 'brain-pool' on VMD-L can provide some helpful suggestions.

problem 1:

check out

while this already works very nicely for creating animations from a script,
with a reasonably fast and large machine you can even work interactively.
in that case it would be nice to find a way, that changes in the Isosurface
representation are not overwritten every time a new frame is shown. this
would speed up the tuning of the parameters immensely, especially when using
multiple isosurface representations and/or volumeslices.

problem 2:

check out

the challenge is, that i want to create a 3d 'rubbersheet' from within
VMD without using an external program (which has to be re-compiled and
installed at the proper place for each platform). since this is used in
an introductory MD exercise package for undergraduate students, i would
like to reduce the external dependencies as far as possible. also, the
way the cubefile/isosurface is used to emulate the rubbersheet, is somewhat
inelegant (to say the least). perhaps someone has a few ideas on how
to create a smooth 'rubbersheet' with VMD graphics primitives directly
from the protein backbone angle data.

...and it would be über-super-prima-cool, if the height of the peaks
could be color coded, but that is not really required.

with the best wishes for the new week,
        axel kohlmeyer.

Axel Kohlmeyer       e-mail:
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum
If you make something idiot-proof, the universe creates a better idiot.