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Ironically as this stereo discussion ensues, it seems NVidia is pushing 3d glasses once again (http://tech.slashdot.org/tech/08/09/17/1530202.shtml ) . Those 120Hz LCD's are welcome reprieve from the bulky SGI monitors in our x-ray core now. More on topic, however, as a 'newer' generation (4th year grad) and after building several structures, I have no problem with not having stereo. One particular case it might be helpful in my experience is building into experimental density maps (the worse the map the more helpful the stereo). However, with automated building programs available (even secondary structure building is quite good), I find this to be a non issue anymore. As for normal building, at least in coot, a simple movement of the model/monomer into the density (using simple translations) and then real space refine usually takes care of the job. More of my opinion, I use software that I can run on minimal hardware / low cost (it surprises me how much the Quad FX card for a Mac Pro costs!). My 0.02 FR On Sep 17, 2008, at 9:21 PM, Engin Ozkan 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