Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Lijun Liu liulj {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-09-18

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Date: 2008-09-18

Subject: Re: Progresss with Stereo 3D under Mac OS X Leopard
From: Lutz Schmitt lschmitt {- at -} EM {- dot -} UNI-FRANKFURT {- dot -} DE
Date: 2008-09-18

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

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Classic density map drawing!
From: Lijun Liu liulj {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-09-18

Next message:
Subject: Re: Progresss with Stereo 3D under Mac OS X Leopard
From: Scott Pegan pegan {- at -} UIC {- dot -} EDU
Date: 2008-09-18