Very well phrased Steve, and I do agree - however stereo is helpful
e.g. looking at binding pockets etc.
I think it depends very much on your workflow what you are actually
doing if you really need lots of stereo. In my case I run everything
on my MacbookPro but I occasionally walk over to our stereo linux box
to visualize things in stereo. How often does this happen is the
question - I'd say 2-5% of my model building / analysis time. And a
workaround e.g. at home is crosseyed in Pymol it's weird but it works
- at least for me.
I'd love to have the option to use stereo on Leopard or hopefully Snow
Leopard.
Jürgen
On 17 Sep 2008, at 08:02, Steve Lane wrote:
> Warren et al.:
>
> The following is based largely on a survey conducted here about 6
> months
> ago (the survey questions are at the bottom of this msg).
>
> Among the "older" generation of PIs, there is a strong perception that
> stereo and SGI dials are very important to users. This perception
> is not
> at all borne out among users themselves (20+ grad students and
> postdocs,
> plus one or two junior faculty) - no one uses the dials (see below for
> why), and stereo is used very infrequently to never.
>
> The consensus among the users regarding stereo seems to be some
> version
> of the following: if it's available, I might use it occasionally for a
> particularly difficult part of a molecule, but not otherwise; if it's
> not available, that's fine. Reasons for not using it seem to be based
> primarily on: inconvenience (we use StereoGraphics glasses and
> emitters -
> in spite of having many pairs available, and efforts by the admins
> here
> to keep them functional, it can be difficult for a user to find a pair
> that works, either because of dead batteries or because they're just
> broken); discomfort (wearing the glasses themselves is a pain, people
> complain of headaches, and the ambient lighting situation can make
> using
> them difficult under some circumstances and cause eye strain); and
> lack
> of need.
>
> No one uses the dials because no one in our environment is building
> with
> O, and this is the only piece of software we have that supports the
> dials
> (we have a Linux-only environment). *Everyone* here builds with Coot.
> I believe (based on somewhat anecdotal evidence) that if Coot
> supported
> the dials people would use them more, but they seem quite happy
> without
> them; they are certainly not enough reason for people to learn to
> use O
> (or go back to using it).
>
> The above "perception vs reality" dichotomy seems to stem largely
> from a
> generation gap: users who learned to build using SGIs running O are
> firm
> believers in the need for stereo and dials (even though, for the most
> part, they are no longer actively building); users who learned to
> build
> on Linux boxes using Coot simply don't see the need, for the most
> part.
> Note that these are, for the most part, users who have never used O,
> but who *do* actively build, spending hours and days at a time sitting
> in front of the workstation doing so.
>
> In addition, many/most users these days do alot of their building
> using their own laptops (many/most of which are Macs running OS X),
> often but not always in conjunction with an external flat panel
> display.
> When doing so, they don't use stereo or dials, and again, this doesn't
> seem to be a huge loss to them, especially given the convenience of
> being
> able to work where they want (i.e. at home, in coffee shops &
> libraries,
> outdoors, etc.)
>
> Users also like to be able to sit in front of a flat-panel display
> to do
> their work. This seems to be a combination of two factors: the extra
> space available on the work surface that isn't taken up by a huge CRT;
> and the absence of the huge, heavy, space-hogging CRT sitting in
> front of
> them all day (i.e. a psychological "lightness" provided by a flat-
> panel
> display - this seems hard to quantify, but I experienced it myself
> when
> switching from a CRT to a flat-panel, and others I have talked to have
> reported similar feelings). Obviously, if a reasonably-priced flat-
> panel
> stereo solution were to become available this would influence
> decisions
> about stereo.
>
> I've included our survey questions below my .sig - please feel free to
> use or adapt them as you like.
>
> --
> Steve Lane
> System, Network and Security Administrator
> Doudna Lab
> Biomolecular Structure and Mechanism Group
> UC Berkeley
>
> ==================================
>
> Greetings. This is a semi-informal survey of recent crystallography
> workstation users. Please take a minute to respond. Your answers
> will
> help us improve the crystallography computing environment.
>
>
> 1) Have you recently (past few months) used a crystallography
> workstation
> for molecular model building and/or visualization? YES NO
>
> Answer:
>
>
> 2) If yes to (1), which model building software did you use (list all
> that apply)? COOT O <OTHER - please specify>
>
> Answer:
>
>
> 3) When model building, do you use the dial box?
> ALWAYS OFTEN SOMETIMES RARELY NEVER
>
> Answer:
>
>
> 4) When model building, do you use 3D stereo visualization (i.e.
> stereo
> glasses)? ALWAYS OFTEN SOMETIMES RARELY NEVER
>
> Answer:
>
>
> 5) If yes to (1), which molecular visualization software did you use
> (list
> all that apply)? COOT O CHIMERA PYMOL <OTHER - please specify>
>
> Answer:
>
>
> 6) When visualizing molecular models, do you use the dial box?
> ALWAYS OFTEN SOMETIMES RARELY NEVER
>
> Answer:
>
>
> 7) When visualizing molecular models, do you use 3D stereo
> visualization
> (i.e. stereo glasses)? ALWAYS OFTEN SOMETIMES RARELY NEVER
>
> Answer:
>
>
> 8) Is there any software you would like to have available in the
> computing environment to assist you in molecular model building
> and/or
> visualization that is not currently available?
>
> Answer:
>
>
> Thank you for your time.
-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
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