Re: [ccp4bb] while on the subject of stereo
To add my two cents, I am not at all a fun of stereo for routine use, but I appreciate it if I have to look at a long ligand bent 90 deg in the middle to bury in my protein, and all that at 3.0-3.5 A resolution ... So, I must have both types of brain damage that Jan refers to. No surprises here I guess. A. On Mar 23, 2011, at 3:16, Phoebe Rice wrote: My 2 cents worth on the stereo-dependent: 1) They have carpal tunnel syndrome that makes it painful to keep the molecule in motion while rebuilding it (NOTE: enough constant mouse-wiggling and you will get carpal tunnel problems if you don't have them yet!) 2) They work on big, low-resolution structures where you need to see a bigger-picture view. I've had people tell me that can fit 3-3.5A maps just fine without stereo, but having viewed their work, I beg to differ. Phoebe Original message Date: Tue, 1 Mar 2011 22:30:54 + From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Jan Löwe j...@mrc-lmb.cam.ac.uk) Subject: Re: [ccp4bb] while on the subject of stereo To: CCP4BB@JISCMAIL.AC.UK Ah! The question of to stereo or not to stereo! There has to be a scientific reason why this question is more popular than asking for what Linux distro is more fashionable this spring or why an Rmerge of 0.90 in the outermost shell is good for you and your structure. I am offering my two (conflicting) theories (and apologies that both seem to imply some problem): A) people who do use stereo have a problem with their brain because they cannot produce three dimensional vision from depth cues alone. B) people who do not use stereo have a problem with their brain because they cannot see properly in three dimensions and rely on depth cues alone. I personally prefer people with A) when I am their passenger in a car since they do not need to rotate by 90° to see how far the braking lights of the car in front are away :-) jan On 01/03/2011 21:35, Jim Pflugrath wrote: I will offer my view. I hate stereo glasses and hate stereo in general. One should be able to see 3D from the depth-cueing and by keeping the view in motion. For fitting, I like to flip the view by 90 degrees. I know I am going to move in displayX and displayY, but never in displayZ. I then rotate the view around the vertical axis so thatn the old displayZ becomes displayX. Furthermore, I don't waste too much time fitting. I know the software can fit the map better than me, so I let it do its job. I only need to get the coordinates within the radius of convergence of the refinement program. I also know that 9 times out of 10, the displayed electron density is probably suspect, so I believe in stereochemistry more than I believe in the map. The main trick is to realize that as a human being, you really are not that good at fitting the map or that it is unnecessary to waste your time since the software is really so much better than you. Refinement is quick enough that you can try various hypotheses as in: If I move this here, then refinement will do the trick and Well, that didn't work, so I will move that over there and see if refinement will do the trick. As for stereo figures, you should be able to convey what you want to say from a good figure with depth-cueing, shadows, etc. Don't ever use stereo glasses in a public seminar. Maybe my opinion will change with better stereo technology. OK, I know quite a lot of people will disagree with me. :) Jim -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David Roberts Sent: Tuesday, March 01, 2011 10:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] while on the subject of stereo Hi again, I'd like to ask a question about the pedagogy of stereo. That is, using stereo with students in the classroom. Do you all find that, after setting up these elaborate stereo devices, students really use the stereo or do they tend not to? I am a huge fan of stereo - and frankly here we have quite a few options for doing stereo - from the active Nvidia systems that people have recently been discussing to passive zalmans. ... As I mentioned, I like stereo a lot, but really projecting on a nice bright lcd monitor also has it's advantages, and with the ease of moving things using the mouse (or whatever device you use), the overall need for stereo seems to be decreasing. I don't know - I just wonder what peoples views are out there for the actual need for stereo. It's incredibly cool - and I think is a very powerful way to show things - but I'm wondering if we focus too much on it because it's cool and not because it's pedagogically necessary. Just wondering, no worries. Thanks Dave P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept
Re: [ccp4bb] while on the subject of stereo
I never thought I would agree with Tassos :-) But same experience 3D and wiggling with a snaked ligand makes live so much easier. It helps to have a fast graphics card though. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Mar 23, 2011, at 4:21, Anastassis Perrakis a.perra...@nki.nl wrote: To add my two cents, I am not at all a fun of stereo for routine use, but I appreciate it if I have to look at a long ligand bent 90 deg in the middle to bury in my protein, and all that at 3.0-3.5 A resolution ... So, I must have both types of brain damage that Jan refers to. No surprises here I guess. A. On Mar 23, 2011, at 3:16, Phoebe Rice wrote: My 2 cents worth on the stereo-dependent: 1) They have carpal tunnel syndrome that makes it painful to keep the molecule in motion while rebuilding it (NOTE: enough constant mouse-wiggling and you will get carpal tunnel problems if you don't have them yet!) 2) They work on big, low-resolution structures where you need to see a bigger-picture view. I've had people tell me that can fit 3-3.5A maps just fine without stereo, but having viewed their work, I beg to differ. Phoebe Original message Date: Tue, 1 Mar 2011 22:30:54 + From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Jan Löwe j...@mrc-lmb.cam.ac.uk) Subject: Re: [ccp4bb] while on the subject of stereo To: CCP4BB@JISCMAIL.AC.UK Ah! The question of to stereo or not to stereo! There has to be a scientific reason why this question is more popular than asking for what Linux distro is more fashionable this spring or why an Rmerge of 0.90 in the outermost shell is good for you and your structure. I am offering my two (conflicting) theories (and apologies that both seem to imply some problem): A) people who do use stereo have a problem with their brain because they cannot produce three dimensional vision from depth cues alone. B) people who do not use stereo have a problem with their brain because they cannot see properly in three dimensions and rely on depth cues alone. I personally prefer people with A) when I am their passenger in a car since they do not need to rotate by 90° to see how far the braking lights of the car in front are away :-) jan On 01/03/2011 21:35, Jim Pflugrath wrote: I will offer my view. I hate stereo glasses and hate stereo in general. One should be able to see 3D from the depth-cueing and by keeping the view in motion. For fitting, I like to flip the view by 90 degrees. I know I am going to move in displayX and displayY, but never in displayZ. I then rotate the view around the vertical axis so thatn the old displayZ becomes displayX. Furthermore, I don't waste too much time fitting. I know the software can fit the map better than me, so I let it do its job. I only need to get the coordinates within the radius of convergence of the refinement program. I also know that 9 times out of 10, the displayed electron density is probably suspect, so I believe in stereochemistry more than I believe in the map. The main trick is to realize that as a human being, you really are not that good at fitting the map or that it is unnecessary to waste your time since the software is really so much better than you. Refinement is quick enough that you can try various hypotheses as in: If I move this here, then refinement will do the trick and Well, that didn't work, so I will move that over there and see if refinement will do the trick. As for stereo figures, you should be able to convey what you want to say from a good figure with depth-cueing, shadows, etc. Don't ever use stereo glasses in a public seminar. Maybe my opinion will change with better stereo technology. OK, I know quite a lot of people will disagree with me. :) Jim -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David Roberts Sent: Tuesday, March 01, 2011 10:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] while on the subject of stereo Hi again, I'd like to ask a question about the pedagogy of stereo. That is, using stereo with students in the classroom. Do you all find that, after setting up these elaborate stereo devices, students really use the stereo or do they tend not to? I am a huge fan of stereo - and frankly here we have quite a few options for doing stereo - from the active Nvidia systems that people have recently been discussing to passive zalmans. ... As I mentioned, I like stereo a lot, but really projecting on a nice bright lcd monitor also has it's advantages, and with the ease of moving things using
Re: [ccp4bb] while on the subject of stereo
Hi Dave, We recently equipped a pool of 25 computers with Nvidia 3D shutter glasses, they're used in structural biology courses for undergraduate students of biochemistry . We teach mainly PyMOL, but (in an advanced course) also model building in COOT. Of course, we let the students decide whether they want to use hardware stereo or not. They all try. After several courses now I realized no more than 30% of the students keep using them in visualization and model building, while the majority of students put the glasses aside... Some of the 30% said, it helps, but could also do without. Haven't assessed this properly yet... ;-) Christoph David Roberts wrote: Thanks for the comments, I do appreciate them. I guess we went off in a direction I wasn't thinking of - related to your personal like or dislike of stereo. What I am really looking for is an answer to a simple question in that is stereo a nice thing from a pedagogy standpoint for showing students complex biomolecules. I am in a chemistry department - undergraduate only. We focus on 3-dimensional shape and the importance of shape of chemical function/reactivity/etc... With small molecules (PF5, etc...), it's easy to see how shape works by simply rotating the molecule. The molecules are small enough, the concept of 3D can be visualized easily in these systems. Furthermore, they can make a simple model using your standard organic or inorganic model kit, no worries. Now, bring in a huge protein, or a protein-protein complex. The issue of 3Dness becomes fuzzier. It's not so easy to see which hydrogen will get plucked off during a chemical reaction, even with careful zooming and mouse manipulation. So my question still is, how many of you feel stereo is important from a pedagogy standpoint (not looking at maps, just structures that are huge and complex). Is it something that we need to try to bring to the classroom, or is it just a cool toy like the 3D TV that hopefully is going nowhere and will soon fade out like the viewmaster of old. I know a large percentage of people cannot see stereo (at least the way we present it), and so it isn't for everybody. But, does it help, and if so, does it help when done in a huge classroom or when put on an individual screen. Has anybody tried to assess this (there's a horrible word for you). That's what I was wondering about. Presenting the stereo is a different issue (how is that done), but I think there are lots of avenues for that depending on your particular situation. Thanks again Dave
Re: [ccp4bb] while on the subject of stereo
I think the weight of the shutter glasses puts them off. Compared to the 30g or less of the Zalmans the shutter glasses feel like bricks. I would estimate them to at least 270g. After one hour wearing them you feel them on your nose. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Mar 23, 2011, at 9:40, Christoph Parthier cparth...@googlemail.com wrote: Hi Dave, We recently equipped a pool of 25 computers with Nvidia 3D shutter glasses, they're used in structural biology courses for undergraduate students of biochemistry . We teach mainly PyMOL, but (in an advanced course) also model building in COOT. Of course, we let the students decide whether they want to use hardware stereo or not. They all try. After several courses now I realized no more than 30% of the students keep using them in visualization and model building, while the majority of students put the glasses aside... Some of the 30% said, it helps, but could also do without. Haven't assessed this properly yet... ;-) Christoph David Roberts wrote: Thanks for the comments, I do appreciate them. I guess we went off in a direction I wasn't thinking of - related to your personal like or dislike of stereo. What I am really looking for is an answer to a simple question in that is stereo a nice thing from a pedagogy standpoint for showing students complex biomolecules. I am in a chemistry department - undergraduate only. We focus on 3-dimensional shape and the importance of shape of chemical function/reactivity/etc... With small molecules (PF5, etc...), it's easy to see how shape works by simply rotating the molecule. The molecules are small enough, the concept of 3D can be visualized easily in these systems. Furthermore, they can make a simple model using your standard organic or inorganic model kit, no worries. Now, bring in a huge protein, or a protein-protein complex. The issue of 3Dness becomes fuzzier. It's not so easy to see which hydrogen will get plucked off during a chemical reaction, even with careful zooming and mouse manipulation. So my question still is, how many of you feel stereo is important from a pedagogy standpoint (not looking at maps, just structures that are huge and complex). Is it something that we need to try to bring to the classroom, or is it just a cool toy like the 3D TV that hopefully is going nowhere and will soon fade out like the viewmaster of old. I know a large percentage of people cannot see stereo (at least the way we present it), and so it isn't for everybody. But, does it help, and if so, does it help when done in a huge classroom or when put on an individual screen. Has anybody tried to assess this (there's a horrible word for you). That's what I was wondering about. Presenting the stereo is a different issue (how is that done), but I think there are lots of avenues for that depending on your particular situation. Thanks again Dave
Re: [ccp4bb] while on the subject of stereo
Those must be older ones... The current Nvidia shutter glasses we use are about 50g. http://www.nvidia.co.uk/object/product_GeForce_3D_VisionKit_uk.html Christoph Jürgen Bosch wrote: I think the weight of the shutter glasses puts them off. Compared to the 30g or less of the Zalmans the shutter glasses feel like bricks. I would estimate them to at least 270g. After one hour wearing them you feel them on your nose. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Mar 23, 2011, at 9:40, Christoph Parthiercparth...@googlemail.com wrote: Hi Dave, We recently equipped a pool of 25 computers with Nvidia 3D shutter glasses, they're used in structural biology courses for undergraduate students of biochemistry . We teach mainly PyMOL, but (in an advanced course) also model building in COOT. Of course, we let the students decide whether they want to use hardware stereo or not. They all try. After several courses now I realized no more than 30% of the students keep using them in visualization and model building, while the majority of students put the glasses aside... Some of the 30% said, it helps, but could also do without. Haven't assessed this properly yet... ;-) Christoph David Roberts wrote: Thanks for the comments, I do appreciate them. I guess we went off in a direction I wasn't thinking of - related to your personal like or dislike of stereo. What I am really looking for is an answer to a simple question in that is stereo a nice thing from a pedagogy standpoint for showing students complex biomolecules. I am in a chemistry department - undergraduate only. We focus on 3-dimensional shape and the importance of shape of chemical function/reactivity/etc... With small molecules (PF5, etc...), it's easy to see how shape works by simply rotating the molecule. The molecules are small enough, the concept of 3D can be visualized easily in these systems. Furthermore, they can make a simple model using your standard organic or inorganic model kit, no worries. Now, bring in a huge protein, or a protein-protein complex. The issue of 3Dness becomes fuzzier. It's not so easy to see which hydrogen will get plucked off during a chemical reaction, even with careful zooming and mouse manipulation. So my question still is, how many of you feel stereo is important from a pedagogy standpoint (not looking at maps, just structures that are huge and complex). Is it something that we need to try to bring to the classroom, or is it just a cool toy like the 3D TV that hopefully is going nowhere and will soon fade out like the viewmaster of old. I know a large percentage of people cannot see stereo (at least the way we present it), and so it isn't for everybody. But, does it help, and if so, does it help when done in a huge classroom or when put on an individual screen. Has anybody tried to assess this (there's a horrible word for you). That's what I was wondering about. Presenting the stereo is a different issue (how is that done), but I think there are lots of avenues for that depending on your particular situation. Thanks again Dave
Re: [ccp4bb] while on the subject of stereo
My 2 cents worth on the stereo-dependent: 1) They have carpal tunnel syndrome that makes it painful to keep the molecule in motion while rebuilding it (NOTE: enough constant mouse-wiggling and you will get carpal tunnel problems if you don't have them yet!) 2) They work on big, low-resolution structures where you need to see a bigger-picture view. I've had people tell me that can fit 3-3.5A maps just fine without stereo, but having viewed their work, I beg to differ. Phoebe Original message Date: Tue, 1 Mar 2011 22:30:54 + From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Jan Löwe j...@mrc-lmb.cam.ac.uk) Subject: Re: [ccp4bb] while on the subject of stereo To: CCP4BB@JISCMAIL.AC.UK Ah! The question of to stereo or not to stereo! There has to be a scientific reason why this question is more popular than asking for what Linux distro is more fashionable this spring or why an Rmerge of 0.90 in the outermost shell is good for you and your structure. I am offering my two (conflicting) theories (and apologies that both seem to imply some problem): A) people who do use stereo have a problem with their brain because they cannot produce three dimensional vision from depth cues alone. B) people who do not use stereo have a problem with their brain because they cannot see properly in three dimensions and rely on depth cues alone. I personally prefer people with A) when I am their passenger in a car since they do not need to rotate by 90° to see how far the braking lights of the car in front are away :-) jan On 01/03/2011 21:35, Jim Pflugrath wrote: I will offer my view. I hate stereo glasses and hate stereo in general. One should be able to see 3D from the depth-cueing and by keeping the view in motion. For fitting, I like to flip the view by 90 degrees. I know I am going to move in displayX and displayY, but never in displayZ. I then rotate the view around the vertical axis so thatn the old displayZ becomes displayX. Furthermore, I don't waste too much time fitting. I know the software can fit the map better than me, so I let it do its job. I only need to get the coordinates within the radius of convergence of the refinement program. I also know that 9 times out of 10, the displayed electron density is probably suspect, so I believe in stereochemistry more than I believe in the map. The main trick is to realize that as a human being, you really are not that good at fitting the map or that it is unnecessary to waste your time since the software is really so much better than you. Refinement is quick enough that you can try various hypotheses as in: If I move this here, then refinement will do the trick and Well, that didn't work, so I will move that over there and see if refinement will do the trick. As for stereo figures, you should be able to convey what you want to say from a good figure with depth-cueing, shadows, etc. Don't ever use stereo glasses in a public seminar. Maybe my opinion will change with better stereo technology. OK, I know quite a lot of people will disagree with me. :) Jim -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David Roberts Sent: Tuesday, March 01, 2011 10:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] while on the subject of stereo Hi again, I'd like to ask a question about the pedagogy of stereo. That is, using stereo with students in the classroom. Do you all find that, after setting up these elaborate stereo devices, students really use the stereo or do they tend not to? I am a huge fan of stereo - and frankly here we have quite a few options for doing stereo - from the active Nvidia systems that people have recently been discussing to passive zalmans. ... As I mentioned, I like stereo a lot, but really projecting on a nice bright lcd monitor also has it's advantages, and with the ease of moving things using the mouse (or whatever device you use), the overall need for stereo seems to be decreasing. I don't know - I just wonder what peoples views are out there for the actual need for stereo. It's incredibly cool - and I think is a very powerful way to show things - but I'm wondering if we focus too much on it because it's cool and not because it's pedagogically necessary. Just wondering, no worries. Thanks Dave
Re: [ccp4bb] while on the subject of stereo
what about the fashion statement made by cool glasses? From: Phoebe Rice [pr...@uchicago.edu] Sent: Tuesday, March 22, 2011 10:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] while on the subject of stereo My 2 cents worth on the stereo-dependent: 1) They have carpal tunnel syndrome that makes it painful to keep the molecule in motion while rebuilding it (NOTE: enough constant mouse-wiggling and you will get carpal tunnel problems if you don't have them yet!) 2) They work on big, low-resolution structures where you need to see a bigger-picture view. I've had people tell me that can fit 3-3.5A maps just fine without stereo, but having viewed their work, I beg to differ. Phoebe Original message Date: Tue, 1 Mar 2011 22:30:54 + From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Jan Löwe j...@mrc-lmb.cam.ac.uk) Subject: Re: [ccp4bb] while on the subject of stereo To: CCP4BB@JISCMAIL.AC.UK Ah! The question of to stereo or not to stereo! There has to be a scientific reason why this question is more popular than asking for what Linux distro is more fashionable this spring or why an Rmerge of 0.90 in the outermost shell is good for you and your structure. I am offering my two (conflicting) theories (and apologies that both seem to imply some problem): A) people who do use stereo have a problem with their brain because they cannot produce three dimensional vision from depth cues alone. B) people who do not use stereo have a problem with their brain because they cannot see properly in three dimensions and rely on depth cues alone. I personally prefer people with A) when I am their passenger in a car since they do not need to rotate by 90° to see how far the braking lights of the car in front are away :-) jan On 01/03/2011 21:35, Jim Pflugrath wrote: I will offer my view. I hate stereo glasses and hate stereo in general. One should be able to see 3D from the depth-cueing and by keeping the view in motion. For fitting, I like to flip the view by 90 degrees. I know I am going to move in displayX and displayY, but never in displayZ. I then rotate the view around the vertical axis so thatn the old displayZ becomes displayX. Furthermore, I don't waste too much time fitting. I know the software can fit the map better than me, so I let it do its job. I only need to get the coordinates within the radius of convergence of the refinement program. I also know that 9 times out of 10, the displayed electron density is probably suspect, so I believe in stereochemistry more than I believe in the map. The main trick is to realize that as a human being, you really are not that good at fitting the map or that it is unnecessary to waste your time since the software is really so much better than you. Refinement is quick enough that you can try various hypotheses as in: If I move this here, then refinement will do the trick and Well, that didn't work, so I will move that over there and see if refinement will do the trick. As for stereo figures, you should be able to convey what you want to say from a good figure with depth-cueing, shadows, etc. Don't ever use stereo glasses in a public seminar. Maybe my opinion will change with better stereo technology. OK, I know quite a lot of people will disagree with me. :) Jim -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David Roberts Sent: Tuesday, March 01, 2011 10:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] while on the subject of stereo Hi again, I'd like to ask a question about the pedagogy of stereo. That is, using stereo with students in the classroom. Do you all find that, after setting up these elaborate stereo devices, students really use the stereo or do they tend not to? I am a huge fan of stereo - and frankly here we have quite a few options for doing stereo - from the active Nvidia systems that people have recently been discussing to passive zalmans. ... As I mentioned, I like stereo a lot, but really projecting on a nice bright lcd monitor also has it's advantages, and with the ease of moving things using the mouse (or whatever device you use), the overall need for stereo seems to be decreasing. I don't know - I just wonder what peoples views are out there for the actual need for stereo. It's incredibly cool - and I think is a very powerful way to show things - but I'm wondering if we focus too much on it because it's cool and not because it's pedagogically necessary. Just wondering, no worries. Thanks Dave
Re: [ccp4bb] while on the subject of stereo
There are actually a bunch of depth cues that humans use to perceive 3-dimensionality. Existing computer displays only reproduce a few. Because of redundancy, people can function with only a subset, but it can be a serious handicap. Individuals who are stereoblind can learn to judge distances (such as how far away a stop sign is) from the sizes of familiar objects and other cues ... but it doesn't work that well. Conflicting depth cues are one thing that causes motion sickness. Rocking or rotating an image is a type of depth cue. Perspective is a depth cue. Lighting effects, such as fading the brightness of an object with distance or placing an object in fog are also depth cues. Focus is a depth due, and so is convergence of the eyes ... neither of those are reproduced by current computer graphics displays (except perhaps experimental ones). There is more to that list. A fair number of people have poor stereo vision ... some don't even realize it. It does not help that stereo systems are sometimes poorly adjusted and sometimes not even done mathematically correctly. Proper stereo transformations require that you know where the person's eyes are located with respect to the screen. A number of years ago, when I ran Cornell's virtual reality CAVE, one visitor told me he was stereo blind and so would not get much out of the experience. But something very unusual happened: when he put on the glasses and motion tracking system, he was apparently able to see stereo for the first time. Perhaps it was something to do with some misalignment in our system that compensated for his vision problem. Anyhow, it was a remarkable experience for him. I've fit density with and without stereo, and personally, I find that stereo adds a great deal. It's not everything, but why throw out a perfectly good depth cue and work stereoblind? It will be interesting to see if the current trend in stereo movies and 3D TV continues or fizzles (as it did in the 50's). Richard Gillilan MacCHESS On Mar 22, 2011, at 11:01 PM, Mayer, Mark (NIH/NICHD) [E] wrote: what about the fashion statement made by cool glasses? From: Phoebe Rice [pr...@uchicago.edu] Sent: Tuesday, March 22, 2011 10:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] while on the subject of stereo My 2 cents worth on the stereo-dependent: 1) They have carpal tunnel syndrome that makes it painful to keep the molecule in motion while rebuilding it (NOTE: enough constant mouse-wiggling and you will get carpal tunnel problems if you don't have them yet!) 2) They work on big, low-resolution structures where you need to see a bigger-picture view. I've had people tell me that can fit 3-3.5A maps just fine without stereo, but having viewed their work, I beg to differ. Phoebe Original message Date: Tue, 1 Mar 2011 22:30:54 + From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Jan Löwe j...@mrc-lmb.cam.ac.uk) Subject: Re: [ccp4bb] while on the subject of stereo To: CCP4BB@JISCMAIL.AC.UK Ah! The question of to stereo or not to stereo! There has to be a scientific reason why this question is more popular than asking for what Linux distro is more fashionable this spring or why an Rmerge of 0.90 in the outermost shell is good for you and your structure. I am offering my two (conflicting) theories (and apologies that both seem to imply some problem): A) people who do use stereo have a problem with their brain because they cannot produce three dimensional vision from depth cues alone. B) people who do not use stereo have a problem with their brain because they cannot see properly in three dimensions and rely on depth cues alone. I personally prefer people with A) when I am their passenger in a car since they do not need to rotate by 90° to see how far the braking lights of the car in front are away :-) jan On 01/03/2011 21:35, Jim Pflugrath wrote: I will offer my view. I hate stereo glasses and hate stereo in general. One should be able to see 3D from the depth-cueing and by keeping the view in motion. For fitting, I like to flip the view by 90 degrees. I know I am going to move in displayX and displayY, but never in displayZ. I then rotate the view around the vertical axis so thatn the old displayZ becomes displayX. Furthermore, I don't waste too much time fitting. I know the software can fit the map better than me, so I let it do its job. I only need to get the coordinates within the radius of convergence of the refinement program. I also know that 9 times out of 10, the displayed electron density is probably suspect, so I believe in stereochemistry more than I believe in the map. The main trick is to realize that as a human being, you really are not that good at fitting the map or that it is unnecessary to waste your time since the software is really so much better than you
Re: [ccp4bb] while on the subject of stereo
Dear Dave, Here come my five pence... I personally found stereo graphics useful in two cases. 1. When you first introduce students to biomolecular structure and/or biocrystallography. Showing stereo certainly helps 'building up' the initial fascination, which is very important of course. But since we do not have a classroom stereo setup, I am just speaking of seating a new/prospective (graduate) student in front of a stereo workstation. 2. When one performs more difficult tasks while doing research (although it was not your question). This includes building difficult regions in poor/low resolution maps as already mentioned, but maybe even more importantly when trying to make sense of a difficult MR case and finally when dealing with protein docking. However: 1. In my experience, what at least the better students do is to look at a structure using a simple program like Swiss PDB Viewer or Rasmol and their 300 euro laptop. No arguments can persuade them to use the 3000 euro lab stereo setup -- because they can manage to see what they want to see by just rotating the molecule... 2. For both teaching purposes and publications, I remain an adept of printed stereo pairs. Get each of your students a 5 euro stereo viewer and give them a handout full of stereo pairs rather than mono images. The very important this is that, on paper, one can make notes and drawings. An active digestion of the teaching material (rather than passive starring at your screen) has been known to help efficient learning since long ago... I can summarize my view as follows: for /most/ purposes, you should be fine by using one of the two: simple mono graphics to achieve the 3D effect by rotation -- or printed stereo pairs. HTH Sergei Thanks for the comments, I do appreciate them. I guess we went off in a direction I wasn't thinking of - related to your personal like or dislike of stereo. What I am really looking for is an answer to a simple question in that is stereo a nice thing from a pedagogy standpoint for showing students complex biomolecules. I am in a chemistry department - undergraduate only. We focus on 3-dimensional shape and the importance of shape of chemical function/reactivity/etc... With small molecules (PF5, etc...), it's easy to see how shape works by simply rotating the molecule. The molecules are small enough, the concept of 3D can be visualized easily in these systems. Furthermore, they can make a simple model using your standard organic or inorganic model kit, no worries. Now, bring in a huge protein, or a protein-protein complex. The issue of 3Dness becomes fuzzier. It's not so easy to see which hydrogen will get plucked off during a chemical reaction, even with careful zooming and mouse manipulation. So my question still is, how many of you feel stereo is important from a pedagogy standpoint (not looking at maps, just structures that are huge and complex). Is it something that we need to try to bring to the classroom, or is it just a cool toy like the 3D TV that hopefully is going nowhere and will soon fade out like the viewmaster of old. I know a large percentage of people cannot see stereo (at least the way we present it), and so it isn't for everybody. But, does it help, and if so, does it help when done in a huge classroom or when put on an individual screen. Has anybody tried to assess this (there's a horrible word for you). That's what I was wondering about. Presenting the stereo is a different issue (how is that done), but I think there are lots of avenues for that depending on your particular situation. Thanks again Dave
Re: [ccp4bb] while on the subject of stereo
On Wed, 2011-03-02 at 19:23 -0500, David Roberts wrote: What I am really looking for is an answer to a simple question in that is stereo a nice thing from a pedagogy standpoint for showing students complex biomolecules. Of course it is. Exactly how much excitement it generates among the millennials with their iThings is hard to gauge, but it definitely has greater potential as a teaching tool than the formula for phased translation function. Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] while on the subject of stereo
My take on things is that the helpfulness of stereo depends inversely on the resolution (and/or quality) of the data. If I'm dealing with a 4-5 Angstrom map, stereo is more or less required. For high quality 2-3 Angstrom data, not so much. For teaching purposes, it's probably a good idea to use relatively good maps. So stereo might not be necessary; other than to introduce people to it. One thing I've noticed in training post-docs and grad students (in lab, not in a classroom) is that people who've played video games have an easier time adapting to graphics software than those who haven't. So for new students it might be more helpful to tell them to go play a FPS, or (driving|flight) simulator for a few hours than keep reminding them to use the stereo glasses. Pete David Roberts wrote: Hi again, I'd like to ask a question about the pedagogy of stereo. That is, using stereo with students in the classroom. Do you all find that, after setting up these elaborate stereo devices, students really use the stereo or do they tend not to? I am a huge fan of stereo - and frankly here we have quite a few options for doing stereo - from the active Nvidia systems that people have recently been discussing to passive zalmans. I went from SGI systems and crystaleyes to linux systems using nuvision glasses, and finally have settled for Zalman stereo - as I think it is the best thing out there. Zalman is passive - go to the movies and get a free pair of glasses (realD glasses work fine), and you don't have to have any video card requirements (I haven't tried using it with onboard stereo - I do have graphics cards, but I have a feeling onboard stereo wouldn't be bad). When in a classroom - we project using glasses that work on an emitter based system (so it's active stereo - we are thinking of going passive in the classroom as well). When we use stereo in a classroom, we find you take just as much time telling students they need to look forward as we do talking about active sites. In some cases, the stereo may be distracting. Many can't get it to work - and when they do I don't know how effective it is. I teach a crystallography class, and for that I have a linux lab setup with 6 computers equipped with Zalman stereo (recent, it was active nuvision before). Students have to fit a map and build a MIR structure (from scratch totally) using coot. It's a great experience, but I find that I have to constantly get them to put on stereo glasses to get the best fit of their model in the map. They tend to not do it, and so I'm trying to see if it's the type of stereo used (as I said, I had a few options, and this class actually has their range of devices) or if it's just that they can do it good enough without stereo. They do prefer the LCD monitor over a CRT display (and that is a brightness thing I think - they are just crisper and newer). When on the CRT's, they will use stereo (active), but when on the LCD displays stereo is not necessarily used (they don't seem to need it as much). As I mentioned, I like stereo a lot, but really projecting on a nice bright lcd monitor also has it's advantages, and with the ease of moving things using the mouse (or whatever device you use), the overall need for stereo seems to be decreasing. I don't know - I just wonder what peoples views are out there for the actual need for stereo. It's incredibly cool - and I think is a very powerful way to show things - but I'm wondering if we focus too much on it because it's cool and not because it's pedagogically necessary. Just wondering, no worries. Thanks Dave
Re: [ccp4bb] while on the subject of stereo
Thanks for the comments, I do appreciate them. I guess we went off in a direction I wasn't thinking of - related to your personal like or dislike of stereo. What I am really looking for is an answer to a simple question in that is stereo a nice thing from a pedagogy standpoint for showing students complex biomolecules. I am in a chemistry department - undergraduate only. We focus on 3-dimensional shape and the importance of shape of chemical function/reactivity/etc... With small molecules (PF5, etc...), it's easy to see how shape works by simply rotating the molecule. The molecules are small enough, the concept of 3D can be visualized easily in these systems. Furthermore, they can make a simple model using your standard organic or inorganic model kit, no worries. Now, bring in a huge protein, or a protein-protein complex. The issue of 3Dness becomes fuzzier. It's not so easy to see which hydrogen will get plucked off during a chemical reaction, even with careful zooming and mouse manipulation. So my question still is, how many of you feel stereo is important from a pedagogy standpoint (not looking at maps, just structures that are huge and complex). Is it something that we need to try to bring to the classroom, or is it just a cool toy like the 3D TV that hopefully is going nowhere and will soon fade out like the viewmaster of old. I know a large percentage of people cannot see stereo (at least the way we present it), and so it isn't for everybody. But, does it help, and if so, does it help when done in a huge classroom or when put on an individual screen. Has anybody tried to assess this (there's a horrible word for you). That's what I was wondering about. Presenting the stereo is a different issue (how is that done), but I think there are lots of avenues for that depending on your particular situation. Thanks again Dave
Re: [ccp4bb] while on the subject of stereo
I will offer my view. I hate stereo glasses and hate stereo in general. One should be able to see 3D from the depth-cueing and by keeping the view in motion. For fitting, I like to flip the view by 90 degrees. I know I am going to move in displayX and displayY, but never in displayZ. I then rotate the view around the vertical axis so thatn the old displayZ becomes displayX. Furthermore, I don't waste too much time fitting. I know the software can fit the map better than me, so I let it do its job. I only need to get the coordinates within the radius of convergence of the refinement program. I also know that 9 times out of 10, the displayed electron density is probably suspect, so I believe in stereochemistry more than I believe in the map. The main trick is to realize that as a human being, you really are not that good at fitting the map or that it is unnecessary to waste your time since the software is really so much better than you. Refinement is quick enough that you can try various hypotheses as in: If I move this here, then refinement will do the trick and Well, that didn't work, so I will move that over there and see if refinement will do the trick. As for stereo figures, you should be able to convey what you want to say from a good figure with depth-cueing, shadows, etc. Don't ever use stereo glasses in a public seminar. Maybe my opinion will change with better stereo technology. OK, I know quite a lot of people will disagree with me. :) Jim -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David Roberts Sent: Tuesday, March 01, 2011 10:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] while on the subject of stereo Hi again, I'd like to ask a question about the pedagogy of stereo. That is, using stereo with students in the classroom. Do you all find that, after setting up these elaborate stereo devices, students really use the stereo or do they tend not to? I am a huge fan of stereo - and frankly here we have quite a few options for doing stereo - from the active Nvidia systems that people have recently been discussing to passive zalmans. ... As I mentioned, I like stereo a lot, but really projecting on a nice bright lcd monitor also has it's advantages, and with the ease of moving things using the mouse (or whatever device you use), the overall need for stereo seems to be decreasing. I don't know - I just wonder what peoples views are out there for the actual need for stereo. It's incredibly cool - and I think is a very powerful way to show things - but I'm wondering if we focus too much on it because it's cool and not because it's pedagogically necessary. Just wondering, no worries. Thanks Dave
Re: [ccp4bb] while on the subject of stereo
Ah! The question of to stereo or not to stereo! There has to be a scientific reason why this question is more popular than asking for what Linux distro is more fashionable this spring or why an Rmerge of 0.90 in the outermost shell is good for you and your structure. I am offering my two (conflicting) theories (and apologies that both seem to imply some problem): A) people who do use stereo have a problem with their brain because they cannot produce three dimensional vision from depth cues alone. B) people who do not use stereo have a problem with their brain because they cannot see properly in three dimensions and rely on depth cues alone. I personally prefer people with A) when I am their passenger in a car since they do not need to rotate by 90° to see how far the braking lights of the car in front are away :-) jan On 01/03/2011 21:35, Jim Pflugrath wrote: I will offer my view. I hate stereo glasses and hate stereo in general. One should be able to see 3D from the depth-cueing and by keeping the view in motion. For fitting, I like to flip the view by 90 degrees. I know I am going to move in displayX and displayY, but never in displayZ. I then rotate the view around the vertical axis so thatn the old displayZ becomes displayX. Furthermore, I don't waste too much time fitting. I know the software can fit the map better than me, so I let it do its job. I only need to get the coordinates within the radius of convergence of the refinement program. I also know that 9 times out of 10, the displayed electron density is probably suspect, so I believe in stereochemistry more than I believe in the map. The main trick is to realize that as a human being, you really are not that good at fitting the map or that it is unnecessary to waste your time since the software is really so much better than you. Refinement is quick enough that you can try various hypotheses as in: If I move this here, then refinement will do the trick and Well, that didn't work, so I will move that over there and see if refinement will do the trick. As for stereo figures, you should be able to convey what you want to say from a good figure with depth-cueing, shadows, etc. Don't ever use stereo glasses in a public seminar. Maybe my opinion will change with better stereo technology. OK, I know quite a lot of people will disagree with me. :) Jim -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David Roberts Sent: Tuesday, March 01, 2011 10:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] while on the subject of stereo Hi again, I'd like to ask a question about the pedagogy of stereo. That is, using stereo with students in the classroom. Do you all find that, after setting up these elaborate stereo devices, students really use the stereo or do they tend not to? I am a huge fan of stereo - and frankly here we have quite a few options for doing stereo - from the active Nvidia systems that people have recently been discussing to passive zalmans. ... As I mentioned, I like stereo a lot, but really projecting on a nice bright lcd monitor also has it's advantages, and with the ease of moving things using the mouse (or whatever device you use), the overall need for stereo seems to be decreasing. I don't know - I just wonder what peoples views are out there for the actual need for stereo. It's incredibly cool - and I think is a very powerful way to show things - but I'm wondering if we focus too much on it because it's cool and not because it's pedagogically necessary. Just wondering, no worries. Thanks Dave
Re: [ccp4bb] while on the subject of stereo
Jim Pflugrath wrote: One should be able to see 3D from the depth-cueing and by keeping the view in motion. Don't ever use stereo glasses in a public seminar. putting the molecule in motion is a good way to let the audience see 3D. I like to make a small animated gif (rocking gif) which rotates back and forth through 3 or 5 pictures covering 5-10 degrees of rotaton about Y. It seems recent versions of powerpoint have dropped support for animated gif, so if I ever have to upgrade PP beyond office97 or 2000, I will have to use movies, which I suspect will be significantly larger. I heard somewhere that the reason chickens (which have eyes on the opposite sides of their heads, giving binocular vision a different meaning) bob their heads up and down is to get a 3D perspective. Definitely Jan Löwe's type B beings. eab
Re: [ccp4bb] while on the subject of stereo
I heard somewhere that the reason chickens (which have eyes on the opposite sides of their heads, giving binocular vision a different meaning) bob their heads up and down is to get a 3D perspective. Check out egrets when they are fishing--definitely triangulating, maybe refraction-artifact-cancelling. JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] While on the subject of stereo
Hi David, This has already been done with PyMOL. There's a video at: http://molviz.cs.toronto.edu/molviz/ and the code is downloadable. The stereo effect isn't so great with both eyes open, but I do think there is potential for use of head or object tracking as a means of controlling rotation. Cheers, Warren From: CCP4 bulletin board on behalf of David Roberts Sent: Wed 5/14/2008 12:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] While on the subject of stereo OK, so we weren't on this subject, and all of you are tired of me asking. However, the following link came to me and I wanted to see some programmers opinions on this one. The thing I'm wondering is, what needs to be done on the programming end to make this something that we could use in a classroom to show molecules in stereo. It seems like it would be fun, and I actually think it would work well, though I don't know if it would work with more than one person looking at the screen at a time (now that I really think about it, probably not - nevermind). If it only works with one person, can we use this for modeling? Just curious www.ted.com/index.php/talks/view/id/245 Dave
