An advantage with stereo viewing is that you can increase the slab in
a crowed active site and still make sense of it. In my experiance,
valuable for understanding structure function relationships in
flexible proteins.
Paula Lario
On 17-Sep-08, at 8:21 PM, Engin Ozkan <[log in to unmask]> wrote:
> 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
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