[PyMOL] Re:2 questions about Summit drivers w/ Radeon8500 card for stereo...
Hi, Sounds line you didn't have a correct installation of the Xig summit2.2??? I thought the installation was supposed to move all the old mesa/GL stugff to a back up and replace them with the acellerated xig ones? Have you contacted the guys at Xig? If you have paid the 99 dollars or whatever it costs, then their support is usually prompt and effective! Lack of DRI means your graphics hardware is not being used at full speed! On my RH8.0 box, the radeon 8500 64MB with Xig summit 2.2 is working really well for quad buffered stereo. Haven't are upgrade to RH9 yet. I keep hearing about problems! cheers Dan On Wednesday, June 4, 2003, at 01:03 AM, pymol-users-requ...@lists.sourceforge.net wrote: Message: 10 Date: Mon, 02 Jun 2003 14:31:08 -0700 From: Cameron Mura cm...@ucsd.edu Reply-To: cm...@ucsd.edu Organization: UCSD To: pymol-users@lists.sourceforge.net, o-i...@origo.imsb.au.dk CC: Cameron Mura cm...@mccammon.ucsd.edu Subject: [PyMOL] 2 questions about Summit drivers w/ Radeon8500 card for stereo... Dear PyMOL and O list members, I just got stereo working on my machine (PC, Red Hat 9, Radeon8500 (64MB) video card) after installing Xi Graphic's Summit v2.2 DX-Platinum drivers to enable quad-buffered software stereo, but I noticed that 3D stereo rendering in 'PyMOL' and 'O' seems a lot slower than it used to be (same hardware, but w/ Mandrake and v2.1 Summit drivers). So, I have 2 questions (that may or may not be related to the sluggishness): (1) After installing xvsc and summit drivers, is any further configuration required to insure proper usage of the Accelerated-X openGL libraries, include files, etc.? I ask this because I noticed that GL-based programs such as PyMOL are NOT using the Accelerated-X library libXda.so.1... For example, if I type ldd /usr/X11R6/bin/xglinfo I get the following: [r...@cm1 etc]# ldd /usr/X11R6/bin/xglinfo libGLU.so.1 = /usr/lib/libGLU.so.1 (0x4002d000) libGL.so.1 = /usr/X11R6/lib/sav-GL/libGL.so.1 (0x400b2000) libXext.so.6 = /usr/X11R6/lib/libXext.so.6 (0x40125000) libX11.so.6 = /usr/X11R6/lib/libX11.so.6 (0x40134000) libm.so.6 = /lib/tls/libm.so.6 (0x40213000) libc.so.6 = /lib/tls/libc.so.6 (0x4200) libpthread.so.0 = /lib/tls/libpthread.so.0 (0x40235000) libdl.so.2 = /lib/libdl.so.2 (0x40243000) /lib/ld-linux.so.2 = /lib/ld-linux.so.2 (0x4000) I guess I could remove the paths to the old mesa GL libraries and include files (/usr/include/GL/sav-GLinc/ and /usr/X11R6/lib/sav-GL/) from /etc/ld.so.conf, but then other GL-based applications don't seem to work?? So, is there anything special i need to do in order to make the libXda.so.1 module used instead of the standard Mesa openGL ones??? (2) Upon start-up, GL-based applications give the following line: Xlib: extension XFree86-DRI missing on display :0.0. I'm wondering what this problem means (if anything), and how it may be corrected?? Thanks for any advice! Cameron Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] RE: [ccp4bb]: Pymol stereo question
Flip, Thanks for answering that question -- actually, the new PyMOL release (version 0.88, downloadable from http://pymol.sf.net ) makes this a little easier. ray angle=-3 png image1.png ray angle=3 png image2.png This is superior to using the turn command because it also rotates the light source. That way shadows will look right. The problem with having PyMOL generate a stereo pair in a single image is that without knowing the final pixel scaling, PyMOL couldn't guarantee that 66 mm separation. Thus, even with the new version, you have to create two images in PyMOL, and then assemble them outside of PyMOL. We'll make this foolproof in a future version. Cheers, Dr. PyMOL -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: owner-ccp...@dl.ac.uk [mailto:owner-ccp...@dl.ac.uk] On Behalf Of Flip Hoedemaeker Sent: Wednesday, June 04, 2003 3:55 AM To: Claudine Mayer; CCP4 Subject: RE: [ccp4bb]: Pymol stereo question *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Hi Claudine, First of all, there's an excellent bulletin board available for Pymol, where your questions are answered by Mr Pymol himself, Warren Delano see details below. If you want to save stereo pics with ray tracing (side-by-side) you have to generate them separately, e.g. create left pic, ray, png left.png, then rotate around Y by 2-3 degrees and ray, png right.png. If you print them side by side for viewing, remember to scale in such a way that equivalent atoms in both pics are 66 mm apart. Flip ---Pymol list details Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ad...@lists.sourceforge.net ---end Pymol list details -Original Message- From: owner-ccp...@dl.ac.uk [mailto:owner-ccp...@dl.ac.uk]on Behalf Of Claudine Mayer Sent: Wednesday, June 04, 2003 11:12 To: CCP4 Subject: [ccp4bb]: Pymol stereo question *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Dear ccp4 and Pymol users, I am wondering how you manage to generate raytraced stereo pictures. When we display stereo, and as soon as we use the command ray, stereo is disappearing ! Any helps would be really appreciated . Cheers, Claudine -- * Dr Claudine MAYER LMCP Universite Paris 6Boite courrier 115 Tour 16 2eme etagecouloir 16-15, porte 8 4, place Jussieu75252 PARIS Cedex 05 tel : 01 44 27 52 41 fax : 01 44 27 37 85 ou 01 44 27 45 84 e-mail : ma...@lmcp.jussieu.fr *
[PyMOL] RE: [ccp4bb]: Pymol stereo question
ray angle=-3 png image1.png ray angle=3 png image2.png This method of generating stereo images is correct, but also leads to quite a bit of vertical parallax (the so-called toe-in projection) - this is why many stereoscopic images are hard to view properly (usually, edges of the image are out of focus). What you really want is a non-symmetric camera frustrum (dunno how hard this is to do in pymol) where the two images should look along parallel vectors separated by some distance (something like 1/20 the focal length). Check out Paul Bourke's page for all the details: http://astronomy.swin.edu.au/~pbourke/stereographics/ Hope this helps. Regards, Tim F I believe this would only be true for perspective projections, not orthographic, since there is no real eye position in orthographic projections (which are more common in molecular diagrams). Of course, feel free to correct me if I am wrong :) Jonathan *** Jonathan Parrish ph(780)-492-8249 Alberta Synchrotron Institute University of Alberta Edmonton, Alberta, Canada T6G 2E1 *** Trusting to escape scrutiny by fixing the public gaze upon the exceeding brightness of military glory, that attractive rainbow that rises in showers of blood that serpent's eye, that charms to destroy, he plunged into war. -Abraham Lincoln ***
[PyMOL] RE: [ccp4bb]: Pymol stereo question
You're both right. Perfect ray-traced stereo pictures are impossible in PyMOL because the built-in ray tracer is limited to an orthographic projection. Unfortunately, I optimized all the vector code for this, so we're talking a major rewrite to change that : (. Rotating by a small angle is the best it can currently do unless you send the geometries to an outside rendering package, such as PovRay. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: jparrish [mailto:jparr...@ualberta.ca] Sent: Wednesday, June 04, 2003 10:34 AM To: Warren L. DeLano; Tim F Cc: pymol-users@lists.sourceforge.net; Claudine Mayer; Flip Hoedemaeker Subject: RE: [ccp4bb]: Pymol stereo question ray angle=-3 png image1.png ray angle=3 png image2.png This method of generating stereo images is correct, but also leads to quite a bit of vertical parallax (the so-called toe-in projection) - this is why many stereoscopic images are hard to view properly (usually, edges of the image are out of focus). What you really want is a non-symmetric camera frustrum (dunno how hard this is to do in pymol) where the two images should look along parallel vectors separated by some distance (something like 1/20 the focal length). Check out Paul Bourke's page for all the details: http://astronomy.swin.edu.au/~pbourke/stereographics/ Hope this helps. Regards, Tim F I believe this would only be true for perspective projections, not orthographic, since there is no real eye position in orthographic projections (which are more common in molecular diagrams). Of course, feel free to correct me if I am wrong :) Jonathan *** Jonathan Parrish ph(780)-492-8249 Alberta Synchrotron Institute University of Alberta Edmonton, Alberta, Canada T6G 2E1 *** Trusting to escape scrutiny by fixing the public gaze upon the exceeding brightness of military glory, that attractive rainbow that rises in showers of blood - that serpent's eye, that charms to destroy, he plunged into war. -Abraham Lincoln ***
[PyMOL] RE: [ccp4bb]: Pymol stereo question (fwd)
Very true. It would be great to have a feature where we have access to a camera object, with control of the: 1. camera root (where the camera) 2. camera target (where it's looking) 3. focal length control 4. and all associated 6D transforms. :) JP -- Forwarded message -- Date: Wed, 4 Jun 2003 13:51:16 -0400 (EDT) From: Tim F f...@brandeis.edu To: Warren L. DeLano war...@delanoscientific.com Cc: 'Flip Hoedemaeker' f...@keydp.com, 'Claudine Mayer' claudine.ma...@lmcp.jussieu.fr, 'CCP4' ccp...@dl.ac.uk, pymol-users@lists.sourceforge.net Subject: RE: [ccp4bb]: Pymol stereo question *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** On Wed, 4 Jun 2003, Warren L. DeLano wrote: ray angle=-3 png image1.png ray angle=3 png image2.png This method of generating stereo images is correct, but also leads to quite a bit of vertical parallax (the so-called toe-in projection) - this is why many stereoscopic images are hard to view properly (usually, edges of the image are out of focus). What you really want is a non-symmetric camera frustrum (dunno how hard this is to do in pymol) where the two images should look along parallel vectors separated by some distance (something like 1/20 the focal length). Check out Paul Bourke's page for all the details: http://astronomy.swin.edu.au/~pbourke/stereographics/ Hope this helps. Regards, Tim F -- - Tim Fenn f...@brandeis.edu Rosenstiel Basic Medical Sciences Research Center Brandeis University, Mail Stop 029 415 South Street Waltham, MA 02454 Phone: (781) 736-4942 FAX: (781) 736-2405 -
[PyMOL] Roving Density Tips
Warren, Can you tell me how to get the roving density to active? Just downloaded v88 and this looks like a nice new feature. At a minimum, load a map and a model. Then set roving_detail, 1 set roving_map1_name, map-name to change level: set roving_map1_level, map-level to change amount of density shown: set roving_isomesh, distance-cutof to remove sticks: set roving_sticks,0 and for improved clarity: set line_width, 3 You can have up to three maps loaded at three different levels. Use map2 and map3 in place of map1 above. By default map1 is level 1.0, map2 is level 2.0, and map3 is level 3.0. One of the tricky things about roving is you really need to learn how to move the clipping planes forward and back using SHIFT-Right-Click-And-Drag. That way you can Move in Z as well as X and Y. See the manual page for details: http://pymol.sourceforge.net/newman/user/S0200start.html#5_4_3 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: Thomas Earnest [mailto:tnearn...@lbl.gov] Sent: Wednesday, June 04, 2003 11:14 AM To: Warren L. DeLano Subject: Re: Thomas -- Thomas Earnest Center Head / Senior Scientist Berkeley Center for Structural Biology Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley CA 94720 tnearn...@lbl.gov 510 486 4603 510 486 5664 [FAX] 510 495 2450 [Stacey Goff, Administrator]
[PyMOL] Re: [ccp4bb]: Pymol stereo question
I experimented with this method a decade ago when I was working on a stereo 16mm film for the late Kent Wilson. The parallel line-of-sight method was described in a popular book on stereo methods .. sorry I don't remember the reference and it would take a lot of digging to find it. To be honest, I have never liked this parallel method. I feel that it simply fails to give as good a stereo effect as the traditional toe-in method (in my subjective opinion). As the apparent object comes closer to the face, it seems to me that the approximation of parallel lines of sight separated by a small constant simply breaks down. Why not try both and judge for yourself. The fact that points on the object that are very close to the viewer or very far away appear double (and out of focus) is also exactly what happens with real vision. Here's an experiment to try: Put the index finger of one hand a few inches from your nose and place the index finger of your other hand about a foot away. Now keep your vision focused on the far finger. The near finger, which should remain out of focus, will in fact appear double. Why then is it a problem? In real vision we can change our focal point (the place where the image is in focus and the lines of sight of our two eyes converge) at will. In a fixed stereo image (not dynamic as in VR), we are stuck with the point the artist chooses. When we are distracted to look at another part of the object, it looks wrong. This effect is minor when objects are far away. There is also another phenomenon at work here too, which I learned about when I worked in virtual reality. If you project a stereo image on a wall (say 5 feet away from the viewer) but depict an object that is very close to the viewer (or visa versa), it will appear out of focus when viewed with both eyes and in focus when viewed with one eye. The brain takes its cue for focus from the degree of convergence of the eyes. Sorry, I offer no fixes here. There is a very cool stereo supply company worth looking at however: http://www.stereoscopy.com/reel3d/ Also be sure to check out Richard Gillilan MacCHESS, Cornell This method of generating stereo images is correct, but also leads to quite a bit of vertical parallax (the so-called toe-in projection) - this is why many stereoscopic images are hard to view properly (usually, edges of the image are out of focus). What you really want is a non-symmetric camera frustrum (dunno how hard this is to do in pymol) where the two images should look along parallel vectors separated by some distance (something like 1/20 the focal length). Check out Paul Bourke's page for all the details: http://astronomy.swin.edu.au/~pbourke/stereographics/ Hope this helps. Regards, Tim F
RE: [PyMOL] CGOs and TRIANGLE primitive
Thanks for taking the time to answer. I understand the concepts of blending normals and the importance of vertex ordering in terms of normal generation. Is vertex ordering important to PyMol CGOs (after normals have already been generated).? My ray traced images look good, however, they can only be displayed during ray tracing. If you have time, can you give me an example of a triangle primitive (not begin, triangles, end) that can be displayed without having to ray trace it The point is, I would like to be able to see the surface while I am rotating it. Thanks again. - Mike -Original Message- From: Warren L. DeLano [mailto:war...@delanoscientific.com] Sent: Tuesday, June 03, 2003 6:15 PM To: 'Mike Brown'; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] CGOs and TRIANGLE primitive Mike, Triangle rendering isn't as simple as you might think -- you need to make sure your triangles have the correct handedness (vertex ordering), and if you are trying to create a surface, then you need to blend the normals at each vertex. I left transparent CGOs out of this release...perhaps in the next version -- I'll need to in order to make cartoons transparent, which is a planned enhancement. For now, you're probably out of luck, unless you call OpenGL Directly via PyOpenGL. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ow...@lists.sourceforge.net [mailto:pymol-users-ow...@lists.sourceforge.net] On Behalf Of Mike Brown Sent: Sunday, June 01, 2003 11:26 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] CGOs and TRIANGLE primitive I am developing software for lead optimization that analyzes the differences between multiple enzymes implicated in drug targets. I wanted to implement some method for visualization of these differences and PyMol seemed like an ideal tool for rendering since it is already capable of displaying molecular structures and accepts outside graphics objects. I am having trouble rendering triangulated surfaces using CGO's however (Please know that I am no expert in computer graphics). When the CGO contains the triangles/normals in the BEGIN, TRIANGLES, ... , END format, the surface is displayed, but is very angular and ray tracing does not smooth the edges. When the CGO uses TRIANGLE primitives instead, the surface is ray traced very nicely, but cannot be seen until it is ray traced. When I rotate the surface, it disappears again. Also, it would be nice if there was a method by which I could make the surfaces loaded as a CGO transparent. Any help would be GREATLY appreciated. Thanks for your time. - Mike --- This SF.net email is sponsored by: eBay Get office equipment for less on eBay! http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] C-alpha trace
Hi All, What is the simplist way to draw a C-alpha trace using pymol? Martin Martin Kienetz 429 MSB Department of Biochemistry University of Alberta Edmonton AB T6G 2H7 (780) 492-2422
[PyMOL] Re: [ccp4bb]: Pymol stereo question
On Wed, 4 Jun 2003, Richard Gillilan wrote: The fact that points on the object that are very close to the viewer or very far away appear double (and out of focus) is also exactly what happens with real vision. Here's an experiment to try: True, but you're describing horizontal (distance between left and right eye projections relative to the focal plane) parallax - vertical parallax (difference in vertical height of two points between the two stereoscopic images) is the subject at hand with scene rotations. If you want to make the eyeball analogy, toe-in is similar to viewing things in double (i.e. cross-eyed) vision. Sorry, I offer no fixes here. Agreed, toe-in tends to work just fine (and its used extensively), but the problem increases as the size of the field of view increases, to the point where its too difficult to view. On Wed, 4 Jun 2003, jparrish wrote: I believe this would only be true for perspective projections, not orthographic, since there is no real eye position in orthographic projections (which are more common in molecular diagrams). Of course, feel free to correct me if I am wrong :) Yes, although the depth of the object can't be large relative to the focal distance (I forget how much...). Regards, Tim F -- - Tim Fenn f...@brandeis.edu Rosenstiel Basic Medical Sciences Research Center Brandeis University, Mail Stop 029 415 South Street Waltham, MA 02454 Phone: (781) 736-4942 FAX: (781) 736-2405 -
RE: [PyMOL] C-alpha trace
Martin, hide show ribbon set ribbon_sampling,1 And if your model only contains CA atoms, you'll also need to issue: set ribbon_trace,1 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ow...@lists.sourceforge.net [mailto:pymol-users- ow...@lists.sourceforge.net] On Behalf Of mkienetz Sent: Wednesday, June 04, 2003 1:33 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] C-alpha trace Hi All, What is the simplist way to draw a C-alpha trace using pymol? Martin Martin Kienetz 429 MSB Department of Biochemistry University of Alberta Edmonton AB T6G 2H7 (780) 492-2422 --- This SF.net email is sponsored by: Etnus, makers of TotalView, The best thread debugger on the planet. Designed with thread debugging features you've never dreamed of, try TotalView 6 free at www.etnus.com. ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
