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)
--
