That's good to know! Also, molscript seems to clip atoms in an all-or-none
fashion depending on the coordinates at the center of the atom- When that
point passes through the clipping plane the atom disappears leaving a nub
like an amputated limb for the bond. And since the clipping is along Z
normal to the screen, if you make a stereo pair by rotating instead of skewing,
some atoms will be present on one side and absent on the other, which
sets off alarms in one's optical processing centers and make it painful
to view. So I guess the procedure would be to set the slab very thick
in molscript and use raster3d to do the clipping? I'll give it a try
soon.
Ed
Ethan A Merritt wrote:
On Thursday, 05 September, 2013 23:17:09 Folmer Fredslund wrote:
If you play around with the settings you can do something similar
[in pymol]
http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#cut
mvh
Folmer
For what it's worth, I note that Raster3D differs from most/all of the other
programs in that it allows you to slice through any arbitrary plane.
The plane is defined by three points (usually a choice of 3 atoms
for convenience).
Pymol and (I think) the others only allow you to clip against a plane that
is normal to the screen, tied to a single clipping value along Z.
That is, you cannot rotate the sliced object to view the same slice from
some other angle.
Ethan
2013/9/5 Ethan A Merritt <merr...@u.washington.edu>
On Thursday, 05 September, 2013 13:30:21 Arthur Glasfeld wrote:
I am hoping to create some images of protein cross-sections where the
atoms are depicted as spheres, and the spheres that are "cut" by the slab
are shown as solids with the same color as the surface. An example of what
I'm after can be found here:
people.reed.edu/~glasfeld/xsection.jpg
Does anyone know of any software that can produce similar images?
http://skuld.bmsc.washington.edu/raster3d/raster3d.html
Thanks,
Arthur Glasfeld
Reed College
Portland, OR
