Dear all,
following this discussion and enjoying AGAIN 3D on a Mac - at least
in Pymol -, I'd like to add my two cent opinion.
Whether or not stereo is important in research might be a matter of
debate, true! But, we are focussing on membrane proteins and normally
these structures are at medium resolution. Here, stereo is absolutely
a plus and no depth-cue or whatsoever is an alternative. This is why
we still keep some old SGI somehow running, although everything else
is done on the Mac. But I agree that this might be a personal taste or
age-question. Although I do not think that I am really that old - no
offense to anybody out there :-)
However, I like to add another flavor to the discussion. Have you ever
seen the eyes of students when they see their first 3D structure of a
protein? It happened to me today that I showed a stereo representation
of a protein to an "old" emeritus professor in pymol. And suddenly he
understood the enzyme, he was working on for a really long time. True,
he is not a student anymore but this example was an eye-opener for me.
Thus, research is one thing and a lot of personal taste is involved,
but do students not deserve the best we can offer? And 3D beamers are
one thing, but stereo is for sure a must! The alternative is to switch
to LInux, true again, but at least at German universities we hardly
have the man power to keep up and running X-ray generators, computers,
protein purification, etc. I am not complaining here, I simply like to
make the point that Apple might miss a big opportunity in not fixing
stereo in Leopard.
Cheers
Lutz
Am 17.09.2008 um 20:14 schrieb Nathaniel Echols:
I find that depth-cue/fog is a sufficient cue for me to determine the
"3-dimensionality" of what I am viewing on my 2-dimensional monitor,
and I find that most 3D systems tend to give me a headache long before
I would get one without them.
Even when the depth-cue/fog isn't enough, simply rotating the view
slightly with the mouse often makes the 3D arrangement very
obvious. For those of us who drink too much coffee, this is already
a constant process. When I've tried to use 3D stereo in the past, I
found myself reflexively spinning the molecules around anyway. Fake
3D is no substitute for multiple perspectives, IMHO. (And I can't
even interpret the cross-eyed stereo images in older crystallography
papers.)
Since I was one of Steve's survey-takers, I can confirm that this is
almost entirely a generational difference (and . One factor he
left out is that those of us who came of age (technologically
speaking) in an era of ubiquitous bright, high-contrast (and
increasingly massive) LCD screens can't bear to look at a CRT
display any more. Using a Linux workstation with a CRT increasingly
feels like stepping back in time; imagine how much worse this felt
around 2004, before we got rid of the Octanes. Thanks to other
software and hardware improvements, many of us aren't used to
routinely building entire models from scratch either, so in theory
we don't have to spend as much time squinting at electron density.
(Disclaimer: I don't work on RNA or nucleosomes or low-resolution
structures, so I'm spoiled.) Even the P.I.s who swear by stereo for
building usually end up doing much of the paper preparation on their
Macs anyway.
I haven't seen any evidence to support the idea that stereo is
"necessary" (the way use of R-free is necessary) for good
crystallography or paper-writing except as a matter of personal
preference. I'm also inclined to think that the superiority of the
Mac vs. Linux in nearly every other aspect - and the convenience of
laptops, of course - more than compensates for the lack of stereo.
I do think we'd benefit from better input devices - I like the
Griffin Powermate, but it's too simple to be a complete solution.
If Apple ever introduces tablets or iMacs with iPhone-like multi-
touch screens, I'll be in heaven.
-Nat
