From another member of the new generation...
I could not agree more with Scott. Stereo is not essential, my lab of
thirteen crystallographers does not even have the capability, and noone
has ever asked for it (including our older PI). And I have refined and
built in one year one 3.9 A and one 3.8 A model, and someone else just
built a 3.5A de novo phased model on a small Mac screen with coot (I
think that was heroic). We have to do without stereo, but only if there
was an easy way to set it up and use it, I would have it. And we should
have it (hear that Apple). It's just not worth the lack of freedom and
limitations right now.
As a grad student we had access to stereo, I did not use it much. I
have to say I do not know why new students would be swayed just by
them. As a young grad student, I was amazed by chemistry in action
(and I still am), and did not need stereo to think about charge,
coordination, pi-pi packing and hydrogen bonding, and not the cool 3D (I
see the attraction to middle or high school students). Rotating models
with depth cues was sufficient.
Engin
Scott Pegan wrote:
Just to put my two cents in on this as I would fall into that new
generation so to speak:
I started out with the SGI and linux systems with stereo, O, and dials
about eight years ago. Never used the dials and rarely seen anyone
else use them. Over the past few years I have transition to coot, pc,
and now have a MAC. The freedom of not having a bulky system that I
have to build on is a huge plus for many of the reasons you described.
However, My colleagues and I I DO WANT STEREO. I have nearly
perfected building without IT not out of choice but mostly out of lack
of one. I feel as many of my colleagues do, that if we had the stereo
option on our flat panels we most undoubtedly would use it. We just
don't those type of options right know. As a result, I wholeheartedly
support anyone trying to get us this added capability.
Scott
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)
--
--
Scott D. Pegan, Ph.D.
Senior Research Specialist
Center for Pharmaceutical
Biotechnology
University of Illinois at Chicago
