Dear Steve,
despite your survey/perception, bottom line is, comes paper writing
time, nothing beats stereo viewing of the molecules or the packing of
them in the crystal lattice: facts become apparent that are otherwise
easily overseen in two dimensions!
Stereo-free macromolecular crystallography? Not really a good practice/idea!
Jeroen.
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.
>
--
Dr. Jeroen R. Mesters
Gruppenleiter Strukturelle Neurobiologie und Kristallogenese
Institut für Biochemie, Universität zu Lübeck
Zentrum für Medizinische Struktur- und Zellbiologie
Ratzeburger Allee 160, D-23538 Lübeck
Tel: +49-451-5004070, Fax: +49-451-5004068
Http://www.biochem.uni-luebeck.de
Http://www.iobcr.org
Http://www.selfish-brain.org
Http://www.opticryst.org
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me (Macbeth)
--
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