Dear Jacob
If you do want brainless and are not fastidious, you can fake a
similar solid-looking cutaway surface using Rasmol
display your coordinates in rasmol
Centre on an atom you wish to see lying in the cutaway surface by typing
set picking centre
and clicking on it.
Make a space filling representation with
cpk (or cpk 600 if you want the spheres bigger and overlapping)
and finally do
slab 50 (or slab 55)
to cut away the front part of the molecule. You can then use rasmol's
simple commands to modify the colours and represntation of different
parts of the structure
OK, not a real vdW surface, no electrostatics, no finesse, but
possibly OK for a seminar if not a publication, and certainly br/
painless
best wishes
Pete
Pete Artymiuk
University of Sheffield
On 14 Mar 2009, at 02:25, Ethan A Merritt wrote:
On Friday 13 March 2009, Jacob Wong wrote:
Dear all,
http://www.nature.com/nature/journal/v458/n7234/fig_tab/nature07819_F3.html
Just came across this figure Fig. 3b) and would like to know what
is the
general and easiest way to make things like this, as a "non-
brainer". Thank
you, -Jacob
I don't know of any way to not engage a brain in the process,
but that particular figure could be made by
1) create electrostatic coloured surface in GRASP or MSMS or ....
2) export surface as a file and convert it to Raster3D
3) define a bounding plane (some point on the plane + a surface
normal)
4) render the surface in Raster3D, clipped by the bounding plane
Example: top figure in
http://skuld.bmsc.washington.edu/raster3d/examples/examples.html
I have been slowly working to put together a less brain-involving
pathway, ideally involving some smallish number of mouse clicks in
Coot or PyMol or ccp4mg that feed the information to Raster3D for
rendering.
But nothing is currently in place that would allow a label
"no actual brains were consumed in producing this figure".
Ethan
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
