Re: [ccp4bb] Popularity of Stereo graphics in crystallography
I haven't used stereo since the last millenium - I don't miss it. You don't really need it and it's not worth the expense/hassle to set up. In my opinion it's just something to impress visitors! Dave --- Dr. David M. Lawson Biological Chemistry Dept., John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Fax: +44-(0)1603-450018 Email: [EMAIL PROTECTED] Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Roger Rowlett Sent: 20 June 2007 20:27 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Popularity of Stereo graphics in crystallography I've found that many of my undergraduates like the stereo capability, although I personally rarely use it. So I guess it's worth the pain of getting the stereo hardware to play nice with the OS and specialized applications. We put the cheapest stereo-ready cards available at the time(Quadro 980XGL) in our Linux workstations, along with NuVision 60GX glasses, and none of the workstations cost more than $2000 to build. If you don't need stereo, clearly almost any reasonable PC will do. Even the lowliest of Nvidia or ATI graphics cards are more than ample for running O, Coot, Pymol, etc. Cheers, ___ Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Santarsiero, Bernard D. Sent: Wednesday, June 20, 2007 1:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Popularity of Stereo graphics in crystallography I agree with Kevin. We have stereo on about half of our workstations, and no one has used them in about three years. We typically use O. Also, we have three large servers which are relatively fast. So the main purpose of a workstation is building, not computing here. That way you can easily work on multiple structures on a workstation at the same time, while you're refining and building them. We have a few people that use PC's and Coot as well. Bernie On Wed, June 20, 2007 11:45 am, P Hubbard wrote: Hi, Thanks for the e-mail. The current results of the survey would certainly put you in the minority! Stereo graphics are not dead after all. I have used systems with and without stereo graphics. I personally prefer them, and think they are great for helping newbies refine, and for non-structural biologists and students to look at molecular architecture. It seems a lot of other people, for whatever reason, like them too. Paul From: Kevin Cowtan [EMAIL PROTECTED] Reply-To: Kevin Cowtan [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 17:27:04 +0100 More likely the issue is that some of us do not find stereo to be necessary of beneficial for crystallographic model building. In which case, given the power of modern PCs and graphics cards, a basic off-the-shelf PC costing $1000/£500 is completely adaquate for typical structure solution and model building problems. I use coot a lot and I haven't even bothered installing the graphics drivers for my graphics card. All the 3D stuff gets gone in software, and most of the graphics hardware sits around doing nothing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those listed on www.stereo3d.com). However, the price of peripherals like a 3D LCD monitor are prohibitively expensive (and the quality of the images is supposed to be poor). Do you know of a relatively inexpensive way of displaying 3D images on PCs? Any other comments would be greatly appreciated. Paul _ Get a preview of Live Earth, the hottest event this summer - only on MSN http://liveearth.msn.com?source=msntaglineliveearthhm
Re: [ccp4bb] Popularity of Stereo graphics in crystallography
I have found stereo essential for building low resolution structures where data beyond 3.3A is not available, I must also say that I have found it unnecessary for any structures which there is data (with decent phases) to 3A and beyond. The question is, is it worth spending a substantial amount of money for that one project out of 50 (for example) which will need a stereo workstation to build? My gut instinct would be yes - but only if you can. Mike Michael Latchem, Post Doctoral Research Associate Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom Tel: +44 (0)1235 778643 -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of david lawson (JIC) Sent: 21 June 2007 09:12 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Popularity of Stereo graphics in crystallography I haven't used stereo since the last millenium - I don't miss it. You don't really need it and it's not worth the expense/hassle to set up. In my opinion it's just something to impress visitors! Dave --- Dr. David M. Lawson Biological Chemistry Dept., John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Fax: +44-(0)1603-450018 Email: [EMAIL PROTECTED] Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Roger Rowlett Sent: 20 June 2007 20:27 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Popularity of Stereo graphics in crystallography I've found that many of my undergraduates like the stereo capability, although I personally rarely use it. So I guess it's worth the pain of getting the stereo hardware to play nice with the OS and specialized applications. We put the cheapest stereo-ready cards available at the time(Quadro 980XGL) in our Linux workstations, along with NuVision 60GX glasses, and none of the workstations cost more than $2000 to build. If you don't need stereo, clearly almost any reasonable PC will do. Even the lowliest of Nvidia or ATI graphics cards are more than ample for running O, Coot, Pymol, etc. Cheers, ___ Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Santarsiero, Bernard D. Sent: Wednesday, June 20, 2007 1:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Popularity of Stereo graphics in crystallography I agree with Kevin. We have stereo on about half of our workstations, and no one has used them in about three years. We typically use O. Also, we have three large servers which are relatively fast. So the main purpose of a workstation is building, not computing here. That way you can easily work on multiple structures on a workstation at the same time, while you're refining and building them. We have a few people that use PC's and Coot as well. Bernie On Wed, June 20, 2007 11:45 am, P Hubbard wrote: Hi, Thanks for the e-mail. The current results of the survey would certainly put you in the minority! Stereo graphics are not dead after all. I have used systems with and without stereo graphics. I personally prefer them, and think they are great for helping newbies refine, and for non-structural biologists and students to look at molecular architecture. It seems a lot of other people, for whatever reason, like them too. Paul From: Kevin Cowtan [EMAIL PROTECTED] Reply-To: Kevin Cowtan [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 17:27:04 +0100 More likely the issue is that some of us do not find stereo to be necessary of beneficial for crystallographic model building. In which case, given the power of modern PCs and graphics cards, a basic off-the-shelf PC costing $1000/£500 is completely adaquate for typical structure solution and model building problems. I use coot a lot and I haven't even bothered installing the graphics drivers for my graphics card. All the 3D stuff gets gone in software, and most of the graphics hardware sits around doing nothing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those
Re: [ccp4bb] Popularity of Stereo graphics in crystallography
It seems not so long ago that people were interested not only in stereo graphics, but also in research into interactive gloves etc. for maximal virtual reality in manipulating protein structures, feeling forces, etc. To simulate depth by rendering solvent accessible surfaces with shadows and reflections is fine for understanding those surfaces, and rotations of stick representations of bonds is OK if the zoom is large. But best understanding of structures, comparisons, dynamics, must come with maximal use of the brain's natural abilities, including stereo vision. I am sure that the computer gaming world will make virtual reality widely affordable for protein structure research in a few years. Rick - The Norwegian Structural Biology Centre Department of Chemistry University of Tromsø 9037 Tromsø, Norway - Hi, Thanks for the e-mail. The current results of the survey would certainly put you in the minority! Stereo graphics are not dead after all. I have used systems with and without stereo graphics. I personally prefer them, and think they are great for helping newbies refine, and for non-structural biologists and students to look at molecular architecture. It seems a lot of other people, for whatever reason, like them too. Paul From: Kevin Cowtan [EMAIL PROTECTED] Reply-To: Kevin Cowtan [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 17:27:04 +0100 More likely the issue is that some of us do not find stereo to be necessary of beneficial for crystallographic model building. In which case, given the power of modern PCs and graphics cards, a basic off-the-shelf PC costing $1000/500 is completely adaquate for typical structure solution and model building problems. I use coot a lot and I haven't even bothered installing the graphics drivers for my graphics card. All the 3D stuff gets gone in software, and most of the graphics hardware sits around doing nothing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those listed on www.stereo3d.com). However, the price of peripherals like a 3D LCD monitor are prohibitively expensive (and the quality of the images is supposed to be poor). Do you know of a relatively inexpensive way of displaying 3D images on PCs? Any other comments would be greatly appreciated. Paul _ Get a preview of Live Earth, the hottest event this summer - only on MSN http://liveearth.msn.com?source=msntaglineliveearthhm --
Re: [ccp4bb] Popularity of Stereo graphics in crystallography
Hello, Personally I don't really care if I have a stereo setup or not. I have not really used stereo to build in probably 3-4 years. The majority of the users of my facility on the other hand really want stereo. Usually in the initial and final stages of building and analysis. It is becoming harder to maintain stereo systems overall. You are tied in to a very limited number of graphics cards and as seen on the BB setup of the drivers/libraries can sometimes lead to the urge to pitch the systems out of highest window possible. It would be nice to have some sort of 'standard' 3D system for crystallography, but with the rapid change in computers and graphics hardware it probably is not a really viable possibility. We are currently looking to upgrade our systems and the biggest problems I have encountered in building a system is the on the graphics end. Just my 1/2 a cent worth. Len On Jun 20, 2007, at 9:45 AM, P Hubbard wrote: Hi, Thanks for the e-mail. The current results of the survey would certainly put you in the minority! Stereo graphics are not dead after all. I have used systems with and without stereo graphics. I personally prefer them, and think they are great for helping newbies refine, and for non-structural biologists and students to look at molecular architecture. It seems a lot of other people, for whatever reason, like them too. Paul From: Kevin Cowtan [EMAIL PROTECTED] Reply-To: Kevin Cowtan [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 17:27:04 +0100 More likely the issue is that some of us do not find stereo to be necessary of beneficial for crystallographic model building. In which case, given the power of modern PCs and graphics cards, a basic off-the-shelf PC costing $1000/£500 is completely adaquate for typical structure solution and model building problems. I use coot a lot and I haven't even bothered installing the graphics drivers for my graphics card. All the 3D stuff gets gone in software, and most of the graphics hardware sits around doing nothing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those listed on www.stereo3d.com). However, the price of peripherals like a 3D LCD monitor are prohibitively expensive (and the quality of the images is supposed to be poor). Do you know of a relatively inexpensive way of displaying 3D images on PCs? Any other comments would be greatly appreciated. Paul _ Get a preview of Live Earth, the hottest event this summer - only on MSN http://liveearth.msn.com?source=msntaglineliveearthhm Leonard M. Thomas Ph.D. Director, Macromolecular Crystallography Laboratory Howard Hughes Medical Institute California Institute of Technology Division of Biology 1200 E. California Blvd. MC 114-96 Pasadena, CA 91125 626-395-2453 [EMAIL PROTECTED] http://www.br.caltech.edu/cmclab
Re: [ccp4bb] Popularity of Stereo graphics in crystallography
I agree with Kevin. We have stereo on about half of our workstations, and no one has used them in about three years. We typically use O. Also, we have three large servers which are relatively fast. So the main purpose of a workstation is building, not computing here. That way you can easily work on multiple structures on a workstation at the same time, while you're refining and building them. We have a few people that use PC's and Coot as well. Bernie On Wed, June 20, 2007 11:45 am, P Hubbard wrote: Hi, Thanks for the e-mail. The current results of the survey would certainly put you in the minority! Stereo graphics are not dead after all. I have used systems with and without stereo graphics. I personally prefer them, and think they are great for helping newbies refine, and for non-structural biologists and students to look at molecular architecture. It seems a lot of other people, for whatever reason, like them too. Paul From: Kevin Cowtan [EMAIL PROTECTED] Reply-To: Kevin Cowtan [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 17:27:04 +0100 More likely the issue is that some of us do not find stereo to be necessary of beneficial for crystallographic model building. In which case, given the power of modern PCs and graphics cards, a basic off-the-shelf PC costing $1000/£500 is completely adaquate for typical structure solution and model building problems. I use coot a lot and I haven't even bothered installing the graphics drivers for my graphics card. All the 3D stuff gets gone in software, and most of the graphics hardware sits around doing nothing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those listed on www.stereo3d.com). However, the price of peripherals like a 3D LCD monitor are prohibitively expensive (and the quality of the images is supposed to be poor). Do you know of a relatively inexpensive way of displaying 3D images on PCs? Any other comments would be greatly appreciated. Paul _ Get a preview of Live Earth, the hottest event this summer - only on MSN http://liveearth.msn.com?source=msntaglineliveearthhm
Re: [ccp4bb] Popularity of Stereo graphics in crystallography
I've found that many of my undergraduates like the stereo capability, although I personally rarely use it. So I guess it's worth the pain of getting the stereo hardware to play nice with the OS and specialized applications. We put the cheapest stereo-ready cards available at the time(Quadro 980XGL) in our Linux workstations, along with NuVision 60GX glasses, and none of the workstations cost more than $2000 to build. If you don't need stereo, clearly almost any reasonable PC will do. Even the lowliest of Nvidia or ATI graphics cards are more than ample for running O, Coot, Pymol, etc. Cheers, ___ Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Santarsiero, Bernard D. Sent: Wednesday, June 20, 2007 1:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Popularity of Stereo graphics in crystallography I agree with Kevin. We have stereo on about half of our workstations, and no one has used them in about three years. We typically use O. Also, we have three large servers which are relatively fast. So the main purpose of a workstation is building, not computing here. That way you can easily work on multiple structures on a workstation at the same time, while you're refining and building them. We have a few people that use PC's and Coot as well. Bernie On Wed, June 20, 2007 11:45 am, P Hubbard wrote: Hi, Thanks for the e-mail. The current results of the survey would certainly put you in the minority! Stereo graphics are not dead after all. I have used systems with and without stereo graphics. I personally prefer them, and think they are great for helping newbies refine, and for non-structural biologists and students to look at molecular architecture. It seems a lot of other people, for whatever reason, like them too. Paul From: Kevin Cowtan [EMAIL PROTECTED] Reply-To: Kevin Cowtan [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 17:27:04 +0100 More likely the issue is that some of us do not find stereo to be necessary of beneficial for crystallographic model building. In which case, given the power of modern PCs and graphics cards, a basic off-the-shelf PC costing $1000/£500 is completely adaquate for typical structure solution and model building problems. I use coot a lot and I haven't even bothered installing the graphics drivers for my graphics card. All the 3D stuff gets gone in software, and most of the graphics hardware sits around doing nothing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if you price things together to make something that performs well I doubt you'll get much change out of $2000. I am aware of other 3D systems (such as those listed on www.stereo3d.com). However, the price of peripherals like a 3D LCD monitor are prohibitively expensive (and the quality of the images is supposed to be poor). Do you know of a relatively inexpensive way of displaying 3D images on PCs? Any other comments would be greatly appreciated. Paul _ Get a preview of Live Earth, the hottest event this summer - only on MSN http://liveearth.msn.com?source=msntaglineliveearthhm
