My guess is that if stereo were as easily and conveniently available as
a MacBook Pro in a coffee shop (where I'm writing this email) people
would probably use it more. That means no ginormous CTRs, no dimming
the lights, no walking over to the molecular visualization center for
checking a bit of debatable density, no glasses that make a lasting and
painful impression on the bearer's nose.
I remember that I found stereo quite useful while I had it around but
ended up migrating to the LCD screens because they strained my eyes
less. What made the transition easy were dials. Flicking the molecule
back and forth by a few degrees about a fixed axis helped me
tremendously get a realistic three-dimensional impression. I would sit
with one hand on the dials for 'virtual stereo' and the other on the
mouse for navigation, selecting, building. With the mouse only, I find
that sooner or later my molecule tumbles from its (carefully chosen)
starting position. For that reason, I'd really love to see dials
support in coot.
Two years ago (Where would we be without Google?), Paul wrote in an
email that coot supports the PowerMate (that Kevin had just bought). Is
that still true? In that case, the entire discussion above would be
moot, and I should just get a PowerMate.
Andreas
William G. Scott wrote:
On Sep 17, 2008, at 8:21 PM, Engin Ozkan wrote:
As a grad student we had access to stereo, I did not use it much. I
have to say I do not know why new students would be swayed just by
them. As a young grad student, I was amazed by chemistry in action
(and I still am), and did not need stereo to think about charge,
coordination, pi-pi packing and hydrogen bonding, and not the cool 3D
(I see the attraction to middle or high school students). Rotating
models with depth cues was sufficient.
One thing I have learned in 11 years of teaching chemistry is that no
one approach works for everyone. When it comes to spatial visualization,
this is especially the case, which is why, for example, organic
chemistry is so difficult to teach effectively (and often to learn).
Hence I think having as few limitations in place as possible is a good
thing, and having stereo hardware available to those (young or old) who
could benefit is crucial.
For me, I tend to think very abstractly, so it was quantum mechanics and
group theory that really sunk the hook into me. But my first
introduction to group theory was in my first year of college. I had just
learned organic chemistry and was fascinated by the Woodward-Hoffmann
rules and how with simply the symmetry of the orbitals alone, one could
predict with almost metaphysical certitude the outcome of a complicated
pericyclic reaction for which solving the Schrödinger equation
accurately would be completely hopeless. So I spent a very long night in
the library with a friend of mine going through every group theory book
that she and I could find. One of these had stereo glasses in the back
(along with those ubiquitous character tables) that made it possible for
me, for the first time, to really see in 3D the stereographic
projections of various point groups. It was an absolutely stunning
revelation, and probably had a lot to do with me later pursuing
crystallography. We were completely transfixed by this for hours, (which
admittedly may have had something to do with dropping acid earlier that
day), but nonetheless it was far better than simply rotating models with
depth cueing (which I since learned to do in my mind's eye).
Hardware stereo isn't for everyone, but I certainly think everyone
benefits from having it as an option on as many platforms as possible.
So keep it legal.
--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
