Re: [ccp4bb] Visualizing Stereo view
You can create stereo images for publications in pymol: http://www.pymolwiki.org/index.php/Stereo_ray Adding labels and getting them to float at the correct depth within the image can be tricky. As for visualizing the stereo images, you can either practice alot and get good at cross eyed stereo viewing, or you can buy a pair of glasses to assist you in seeing the 3d effect. If you google cross eyed stereo glasses, you will get many options to purchase. Old chemistry texts used to come with a pair, but I'm not sure that students actually purchase textbooks anymore. On Sat, Jan 17, 2015 at 23:50 PM, jeorgemarley thomas kirtswab...@gmail.com wrote: Dear all, First of all sorry to put this off topic and silly question on bb. Can anybody suggest me, how to create a stereo image and how it is different from the normal. How can I visualize it, if anybody has answer for this please suggest me its significance in analysis. Thank you very much in advance. Thanks Jeorge -- Sent from MetroMail
Re: [ccp4bb] Visualizing Stereo view
Are most stereo images now for cross-eyed viewing? I thought they were for wall-eyed viewing. Perhaps a warning would be helpful for people starting out at looking at published stereoviews. If you look at a stereoview constructed for wall-eyed viewing but look at it with crossed eyes, you'll change the handedness of the object. And if you're showing surfaces, they get turned inside-out (or something like it). I usually get a headache soon after mixing modes like this and only know that the surfaces are messed up. Also, in answer to one of Jeorge's questions, the two images in stereoviews differ by a small rotation about a vertical axis. The two images are what each of your eyes would see if looking at a single object. Because your eyes are separated by about 2.25 inches (I'm a stubborn non-metrical American...), the left- and right-eye views differ slightly. The amount also depends on how close your eyes are supposed to be from the object. I think long ago things were worked out so the rotation is 6 degrees and that corresponds to the viewer-object distance being about 30 inches. If you place the left eye view on the left, you need to look at the two images in wall-eyed mode. If you place the left eye view on the right, you need to cross your eyes to generate the stereo image. For those of us who can view stereoimages without the assistance of glasses or computers, life is good. I recommend developing the ability to do that. Ron On Sun, 18 Jan 2015, Jim Fairman wrote: You can create stereo images for publications in pymol: http://www.pymolwiki.org/index.php/Stereo_ray Adding labels and getting them to float at the correct depth within the image can be tricky. As for visualizing the stereo images, you can either practice alot and get good at cross eyed stereo viewing, or you can buy a pair of glasses to assist you in seeing the 3d effect. If you google cross eyed stereo glasses, you will get many options to purchase. Old chemistry texts used to come with a pair, but I'm not sure that students actually purchase textbooks anymore. On Sat, Jan 17, 2015 at 23:50 PM, jeorgemarley thomas kirtswab...@gmail.com wrote: Dear all, First of all sorry to put this off topic and silly question on bb. Can anybody suggest me, how to create a stereo image and how it is different from the normal. How can I visualize it, if anybody has answer for this please suggest me its significance in analysis. Thank you very much in advance. Thanks Jeorge -- Sent from MetroMail
Re: [ccp4bb] Visualizing Stereo view
I find that the 'rotation' method of producing the stereo views can be confusing because if you have z-clipping on, different atoms get clipped in the L R images and you see the corresponding atoms which are still visible in the other image in mono, while of course all the rest are in stereo. This gives me a headache, particularly if I have to look cross-eyed at the same time! The solution is to skew, not rotate (this brings to mind from the dim distant past Gerard Bricogne's manual on his 'skew planes' package called 'The Joy of Skewing' - which of course has nothing whatsoever to do with producing stereo images). Assuming the origin is in the centre, the rotation matrix about the vertical y axis (assuming your monitor is mounted in the conventional way) looks like this: [ cos(a) 0 sin(a) ] [ 0 1 0 ] [ -sin(a) 0 cos(a) ] where a = +- 3 deg. for the L R images (I leave it as an exercise for the reader to work out which is which!). This matrix gives for the rotated x z co-ordinates: x' = x cos(a) + z sin(a) z' = -x sin(a) + z cos(a) so z' is different for the L R images, particularly for atoms with large |x| near the L R sides of the screen (because the sine changes sign) which get clipped differently in the two images. If I recall correctly the skew matrix looks like this: [ cos(a) 0 sin(a) ] [ 0 1 0 ] [ 0 0 1 ] so: x' = x cos(a) + z sin(a) (i.e. same as above) z' = z So now whereas x' is still different for the L R images (and gives you the stereo effect), z' is the same so both eyes see exactly the same view even if z clipping is on. You may of course argue that skewing will distort the image whereas rotation won't. This is true; however the amount of distortion is tiny and not noticeable (and certainly well worth the price of making the stereo image much less confusing). Cheers -- Ian On 18 January 2015 at 19:34, Ronald E Stenkamp stenk...@u.washington.edu wrote: Are most stereo images now for cross-eyed viewing? I thought they were for wall-eyed viewing. Perhaps a warning would be helpful for people starting out at looking at published stereoviews. If you look at a stereoview constructed for wall-eyed viewing but look at it with crossed eyes, you'll change the handedness of the object. And if you're showing surfaces, they get turned inside-out (or something like it). I usually get a headache soon after mixing modes like this and only know that the surfaces are messed up. Also, in answer to one of Jeorge's questions, the two images in stereoviews differ by a small rotation about a vertical axis. The two images are what each of your eyes would see if looking at a single object. Because your eyes are separated by about 2.25 inches (I'm a stubborn non-metrical American...), the left- and right-eye views differ slightly. The amount also depends on how close your eyes are supposed to be from the object. I think long ago things were worked out so the rotation is 6 degrees and that corresponds to the viewer-object distance being about 30 inches. If you place the left eye view on the left, you need to look at the two images in wall-eyed mode. If you place the left eye view on the right, you need to cross your eyes to generate the stereo image. For those of us who can view stereoimages without the assistance of glasses or computers, life is good. I recommend developing the ability to do that. Ron On Sun, 18 Jan 2015, Jim Fairman wrote: You can create stereo images for publications in pymol: http://www.pymolwiki.org/index.php/Stereo_ray Adding labels and getting them to float at the correct depth within the image can be tricky. As for visualizing the stereo images, you can either practice alot and get good at cross eyed stereo viewing, or you can buy a pair of glasses to assist you in seeing the 3d effect. If you google cross eyed stereo glasses, you will get many options to purchase. Old chemistry texts used to come with a pair, but I'm not sure that students actually purchase textbooks anymore. On Sat, Jan 17, 2015 at 23:50 PM, jeorgemarley thomas kirtswab...@gmail.com wrote: Dear all, First of all sorry to put this off topic and silly question on bb. Can anybody suggest me, how to create a stereo image and how it is different from the normal. How can I visualize it, if anybody has answer for this please suggest me its significance in analysis. Thank you very much in advance. Thanks Jeorge -- Sent from MetroMail
Re: [ccp4bb] Visualizing Stereo view
Hi Jeorge, The easiest was of making a stereo image is with CCP4mg. You just need to tick a box when you make an image. Looking at stereo images takes practice, but it is a useful skill. It also helps with those spot-the-differences puzzles :) Cheers, Robbie -Oorspronkelijk bericht- Van: jeorgemarley thomas kirtswab...@gmail.com Verzonden: 18-1-2015 08:51 Aan: CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Visualizing Stereo view Dear all, First of all sorry to put this off topic and silly question on bb. Can anybody suggest me, how to create a stereo image and how it is different from the normal. How can I visualize it, if anybody has answer for this please suggest me its significance in analysis. Thank you very much in advance. Thanks Jeorge
[ccp4bb] Visualizing Stereo view
Dear all, First of all sorry to put this off topic and silly question on bb. Can anybody suggest me, how to create a stereo image and how it is different from the normal. How can I visualize it, if anybody has answer for this please suggest me its significance in analysis. Thank you very much in advance. Thanks Jeorge
