Re: [PyMOL] bond connection file
Hi Vishwas, atom connectivity is the same for all states unless you have a discrete object. Try this: PyMOL set connect_mode, 1 PyMOL load file.pdb, discrete=1 Cheers, Thomas Vishwas Vasisht wrote, On 10/05/12 08:59: Hi Thomas, Thanks, it works for single frame. But when I use multiple frame (using MODEL and ENDMDL), the connections which i specified in the first frame is retained for rest of the frames. Am I doing some mistake in the way I wrote my PDB file? Regards Vishwas 2012/10/4 Thomas Holder spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net Hi Vishwas, you can use PDB format with CONECT records. You need to set connect_mode=1 before loading the PDB file into PyMOL. http://pymolwiki.org/index.php/Connect_mode http://www.wwpdb.org/documentation/format33/sect10.html#CONECT Hope that helps. Cheers, Thomas Vishwas Vasisht wrote, On 10/04/12 16:52: Hi, I want to feed in a coordinates of atoms along with bond connection information. Since the bonding is based on some calculation I do, I need to include this information by hand. I tried to output the trajectory from my analysis in .mol format (following some example .mol file), but particles are overlapping on each other. Can somebody suggest me a better way to feed in coordinates and bonding information to pymol. Regards Vishwas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] bond connection file
Does every MODEL ENDMDL have a unique Connection list? Can you show me your PDB file? Jordan On Oct 5, 2012, at 1:59 AM, Vishwas Vasisht vishwas.vasi...@gmail.com wrote: Hi Thomas, Thanks, it works for single frame. But when I use multiple frame (using MODEL and ENDMDL), the connections which i specified in the first frame is retained for rest of the frames. Am I doing some mistake in the way I wrote my PDB file? Regards Vishwas 2012/10/4 Thomas Holder spel...@users.sourceforge.net Hi Vishwas, you can use PDB format with CONECT records. You need to set connect_mode=1 before loading the PDB file into PyMOL. http://pymolwiki.org/index.php/Connect_mode http://www.wwpdb.org/documentation/format33/sect10.html#CONECT Hope that helps. Cheers, Thomas Vishwas Vasisht wrote, On 10/04/12 16:52: Hi, I want to feed in a coordinates of atoms along with bond connection information. Since the bonding is based on some calculation I do, I need to include this information by hand. I tried to output the trajectory from my analysis in .mol format (following some example .mol file), but particles are overlapping on each other. Can somebody suggest me a better way to feed in coordinates and bonding information to pymol. Regards Vishwas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Whoever fights monsters should see to it that in the process he does not become a monster. And when you look into an abyss, the abyss also looks into you. -- Friedrich Nietzsche -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb.
Mike, Many distros have PyMOL already in their package management system. Have you tried that first? I suggest downloading the latest code, v1.5.0.4, from the open-source project page, if you want to build by hand. To build, you need Python 2.7 or later and the process is very simple: sudo python setup.py install sudo python setup2.py install Then, follow the directions for copying pymol to /usr/local/bin or wherever you want. If your machine does have shader issues and they don't automatically disable, please let us know. You do not need a license to run the open-source version. If the splash screen says that, I need to change that. I routinely build on Ubuntu without problems. Just make sure the python you build with is the same that you run with. Cheers, -- Jason On Thu, Oct 4, 2012 at 9:18 PM, Mike Marchywka marchy...@hotmail.com wrote: CC: pymol-users@lists.sourceforge.net From: li...@cowsandmilk.net Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. Date: Thu, 4 Oct 2012 22:03:59 -0400 To: marchy...@hotmail.com You don't need a license for the open source version. If you provided details on what OS/distribution you are building on, people may try to replicate and understand why the python version hung. In my experience, using setup.py generally worked out of the box. Well, I thought there may be a dev list or something for the most of this stuff but in any case I'm on Ubuntu but that probably was not a big factor for some of the issues I ran into I just wanted to display 2 molecules side by side and could not get jmol or gdis to work right away and someone suggested this. ( fwiw, I have my own molecule viewer that IIRC I wrote to learn glut on cygwin but I imagine that would be an even bigger chore to port LOL). If I can reconstruct, I apparently started with pymol-v1.5.0.1.tar and I think at some point I ran autoreconf -l thinking I could go the configure route but then did python setup.py build and install in separeate steps., This seemed to work but attempts to display the test pdb files never displayed anything, I could not get any more menu's and one core was running at 100 percent until I killed it. Going the confugre route, I think the first problem was with a bunch of undefined CGO things. but you can see the changes below. The EXT thing was spurious probably as there was a missing -lGLEW and I had to relink. This is obviously a raw dump of things that I tried along with stuff that ultimately worked but fwiw. marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name *.h ./layer0/os_gl.h ./contrib/uiuc/plugins/include/molfile_plugin.h ./generated/include/ShaderText.h ./config.h marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name *.c ./layer0/ShaderText.c ./layer0/ShaderMgr.c ./layer3/Executive.c ./generated/src/ShaderText.c ./layer2/ObjectVolume.c ./layer1/CGO.c ./layer1/Scene.c marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm `find -mtime -2 -name *.c ` ./layer0/ShaderMgr.c:97: FeedbackAdd(G, mjm forcing glew ok Shaders available.\n); ./layer0/ShaderMgr.c:98:// this should work but turn off for now mjm ./layer0/ShaderMgr.c-99-//if (GLEW_VERSION_2_0) ./layer0/ShaderMgr.c-100-if (1) -- ./layer3/Executive.c:76:// mjm ./layer3/Executive.c-77-#includemodules/cealign/src/ce_types.h ./layer3/Executive.c-78-/* Externals for CEAlign */ -- ./layer1/Scene.c:2910://mjm ./layer1/Scene.c-2911- 1.0F, 1.0F, 0.1F, 1.f ./layer1/Scene.c-2912- }; -- ./layer1/Scene.c:1: //mjm ./layer1/Scene.c-10001-//glBlitFramebufferEXT (0, 0, I-offscreen_width / 2, I-offscreen_height, ./layer1/Scene.c-10002- glBlitFramebuffer (0, 0, I-offscreen_width / 2, I-offscreen_height, -- ./layer1/Scene.c:10007://mjm ./layer1/Scene.c-10008- glBlitFramebuffer (I-offscreen_width / 2, 0, I-offscreen_width, I-offscreen_height, ./layer1/Scene.c-10009- //glBlitFramebufferEXT (I-offscreen_width / 2, 0, I-offscreen_width, I-offscreen_height, -- ./layer1/Scene.c:10016: //mjm ./layer1/Scene.c-10017- //glBlitFramebufferEXT (0, 0, I-offscreen_width, I-offscreen_height, ./layer1/Scene.c-10018- glBlitFramebuffer (0, 0, I-offscreen_width, I-offscreen_height, -- ./layer1/Scene.c:10024: //mjm ./layer1/Scene.c-10025-// glBlitFramebufferEXT (0, 0, I-offscreen_width, I-offscreen_height, ./layer1/Scene.c-10026- glBlitFramebuffer (0, 0, I-offscreen_width, I-offscreen_height, marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm `find -mtime -2 -name *.h ` ./layer0/os_gl.h:6:// mjm ./layer0/os_gl.h-7-//#if defined(_PYMOL_IOS) || defined(ANDROID) ./layer0/os_gl.h-8-#if 1 ./layer0/os_gl.h:9:// mjm ./layer0/os_gl.h-10-//
Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb.
Hi Mike, I suggest downloading the latest code, v1.5.0.4, from the open-source project page, if you want to build by hand. see comments in my last post, I think that is what I did. Although autoreconf may not have helped anything. I see the confusion now. We'll update SourceForge on our next release so that it says the latest is v1.5.0.5, not v1.5.0.1. To get the latest code, please do this: svn co https://pymol.svn.sourceforge.net/svnroot/pymol/root/pymol/trunk/pymol pymol To build, you need Python 2.7 or later and the process is very simple: sudo python setup.py install sudo python setup2.py install that was what created the first version I ran, it seemed fine until I tried to display a test pdb then it hung in 100 cpu on one core. What kind of computer is this? What video card do you have? I don't really recall what the first version said, I think it was hypothetical as in may need license etc. The version from ./configure had a whole bunch of problems- simple syntax errors like missing comma to no link to the ccealignmodule but once I kluged around the CGO problems I think I was on my own :) The make; make install setup was deprecated a long time ago which is why this didn't work. We use Python distutils to build, as you've found out. Anyway it seems fine now, although attempting to use fit on my 2 molecules gave a non-intuitive result I think the one was so mangled that it had problems aligning them. Glad it's working. Fit is a mathematically optimal superposition of vector sets. Are your atom pairings correct? If you want to specify them manually, check out Wizard Pair Fitting. If you send me the molecules I'm happy to take a look for you, too. Cheers, -- Jason On Thu, Oct 4, 2012 at 9:18 PM, Mike Marchywka marchy...@hotmail.com wrote: CC: pymol-users@lists.sourceforge.net From: li...@cowsandmilk.net Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. Date: Thu, 4 Oct 2012 22:03:59 -0400 To: marchy...@hotmail.com You don't need a license for the open source version. If you provided details on what OS/distribution you are building on, people may try to replicate and understand why the python version hung. In my experience, using setup.py generally worked out of the box. Well, I thought there may be a dev list or something for the most of this stuff but in any case I'm on Ubuntu but that probably was not a big factor for some of the issues I ran into I just wanted to display 2 molecules side by side and could not get jmol or gdis to work right away and someone suggested this. ( fwiw, I have my own molecule viewer that IIRC I wrote to learn glut on cygwin but I imagine that would be an even bigger chore to port LOL). If I can reconstruct, I apparently started with pymol-v1.5.0.1.tar and I think at some point I ran autoreconf -l thinking I could go the configure route but then did python setup.py build and install in separeate steps., This seemed to work but attempts to display the test pdb files never displayed anything, I could not get any more menu's and one core was running at 100 percent until I killed it. Going the confugre route, I think the first problem was with a bunch of undefined CGO things. but you can see the changes below. The EXT thing was spurious probably as there was a missing -lGLEW and I had to relink. This is obviously a raw dump of things that I tried along with stuff that ultimately worked but fwiw. marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name *.h ./layer0/os_gl.h ./contrib/uiuc/plugins/include/molfile_plugin.h ./generated/include/ShaderText.h ./config.h marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name *.c ./layer0/ShaderText.c ./layer0/ShaderMgr.c ./layer3/Executive.c ./generated/src/ShaderText.c ./layer2/ObjectVolume.c ./layer1/CGO.c ./layer1/Scene.c marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm `find -mtime -2 -name *.c ` ./layer0/ShaderMgr.c:97: FeedbackAdd(G, mjm forcing glew ok Shaders available.\n); ./layer0/ShaderMgr.c:98:// this should work but turn off for now mjm ./layer0/ShaderMgr.c-99-// if (GLEW_VERSION_2_0) ./layer0/ShaderMgr.c-100- if (1) -- ./layer3/Executive.c:76:// mjm ./layer3/Executive.c-77-#includemodules/cealign/src/ce_types.h ./layer3/Executive.c-78-/* Externals for CEAlign */ -- ./layer1/Scene.c:2910://mjm ./layer1/Scene.c-2911- 1.0F, 1.0F, 0.1F, 1.f ./layer1/Scene.c-2912- }; -- ./layer1/Scene.c:1: //mjm ./layer1/Scene.c-10001-//glBlitFramebufferEXT (0, 0, I-offscreen_width / 2, I-offscreen_height, ./layer1/Scene.c-10002- glBlitFramebuffer (0, 0, I-offscreen_width / 2, I-offscreen_height, --
Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb.
From: jason.vertr...@schrodinger.com Date: Fri, 5 Oct 2012 09:36:29 -0500 Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. To: marchy...@hotmail.com CC: li...@cowsandmilk.net; pymol-users@lists.sourceforge.net Hi Mike, I suggest downloading the latest code, v1.5.0.4, from the open-source project page, if you want to build by hand. see comments in my last post, I think that is what I did. Although autoreconf may not have helped anything. I see the confusion now. We'll update SourceForge on our next release so that it says the latest is v1.5.0.5, not v1.5.0.1. To get the latest code, please do this: svn co https://pymol.svn.sourceforge.net/svnroot/pymol/root/pymol/trunk/pymol pymol To build, you need Python 2.7 or later and the process is very simple: sudo python setup.py install sudo python setup2.py install that was what created the first version I ran, it seemed fine until I tried to display a test pdb then it hung in 100 cpu on one core. What kind of computer is this? What video card do you have? Dell Laitittude, but this is probably due to other issues. I don't really recall what the first version said, I think it was hypothetical as in may need license etc. The version from ./configure had a whole bunch of problems- simple syntax errors like missing comma to no link to the ccealignmodule but once I kluged around the CGO problems I think I was on my own :) The make; make install setup was deprecated a long time ago which is why this didn't work. We use Python distutils to build, as you've found out. I never use python and I probably never would have gotten .1 to work if I had to deal with that :) I'm not sure of the rationale here but while you were phasing out a number of things I thought that make was just lagging, intended for developers. Anyway it seems fine now, although attempting to use fit on my 2 molecules gave a non-intuitive result I think the one was so mangled that it had problems aligning them. Glad it's working. Fit is a mathematically optimal superposition of vector sets. Are your atom pairings correct? If you want to specify them manually, check out Wizard Pair Fitting. If you send me the molecules I'm happy to take a look for you, too. Thanks, I have no idea. Naive overlap was a bit confusing but I'm dealing with simple things right now. I have 2 beta-carotene xtz files created from scripts, one from the mmcif files on pdb.org and another derived from jdftx after 300 position iterations using very simple C and H models. In any case, I think part of the problem is just using .53 for atomic/angstrom conversions but it looks like fit results were bizarre: the 2 ends of the molecule were in about the same place but the chains extended in opposite directions from there ( it wasn't immediately obvious if I created some wierd linking errors based on this behaviour LOL). Cheers, -- Jason On Thu, Oct 4, 2012 at 9:18 PM, Mike Marchywka marchy...@hotmail.com wrote: CC: pymol-users@lists.sourceforge.net From: li...@cowsandmilk.net Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. Date: Thu, 4 Oct 2012 22:03:59 -0400 To: marchy...@hotmail.com You don't need a license for the open source version. If you provided details on what OS/distribution you are building on, people may try to replicate and understand why the python version hung. In my experience, using setup.py generally worked out of the box. Well, I thought there may be a dev list or something for the most of this stuff but in any case I'm on Ubuntu but that probably was not a big factor for some of the issues I ran into I just wanted to display 2 molecules side by side and could not get jmol or gdis to work right away and someone suggested this. ( fwiw, I have my own molecule viewer that IIRC I wrote to learn glut on cygwin but I imagine that would be an even bigger chore to port LOL). If I can reconstruct, I apparently started with pymol-v1.5.0.1.tar and I think at some point I ran autoreconf -l thinking I could go the configure route but then did python setup.py build and install in separeate steps., This seemed to work but attempts to display the test pdb files never displayed anything, I could not get any more menu's and one core was running at 100 percent until I killed it. Going the confugre route, I think the first problem was with a bunch of undefined CGO things. but you can see the changes below. The EXT thing was spurious probably as there was a missing -lGLEW and I had to relink. This is obviously a raw dump of things that I tried along with stuff that ultimately worked but fwiw.
Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)
Hi Ben, If your machine does have shader issues and they don't automatically disable, please let us know. What would be the symptoms/output if this is happening? I get occasional reports from our users with errors like this: CShaderPrg_New-Error: vertex shader compilation failed name='default'; log follows. infoLog=cI PyMOLShader_NewFromFile-Warning: default shader files not found, loading from memory. CShaderPrg_Link-Error: Shader program failed to link name='default'; GL_MAX_VARYING_FLOATS=124 log follows. $^? CShaderPrg_New-Error: vertex shader compilation failed name='volume'; log follows. They seem to be informational, since PyMOL seeems to run reasonably well even after outputting those messages, but I can't say for sure. The graphics start up message on the machine looks pretty normal to me: Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro 4000/PCIe/SSE2 GL_VERSION: 2.1.2 NVIDIA 304.37 Adapting to Quadro hardware. Detected 24 CPU cores. Enabled multithreaded rendering. The key seems to be, PyMOLShader_NewFromFile-Warning: default shader files not found, loading from memory. We load shaders from disk, but when they're not found we just read in some basic default shaders from code, which is what this is doing. Did you move or change $PYMOL_DATA? Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)
Hi Jason, If your machine does have shader issues and they don't automatically disable, please let us know. What would be the symptoms/output if this is happening? I get occasional reports from our users with errors like this: CShaderPrg_New-Error: vertex shader compilation failed name='default'; log follows. infoLog=cI PyMOLShader_NewFromFile-Warning: default shader files not found, loading from memory. CShaderPrg_Link-Error: Shader program failed to link name='default'; GL_MAX_VARYING_FLOATS=124 log follows. $^? CShaderPrg_New-Error: vertex shader compilation failed name='volume'; log follows. They seem to be informational, since PyMOL seeems to run reasonably well even after outputting those messages, but I can't say for sure. The graphics start up message on the machine looks pretty normal to me: Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro 4000/PCIe/SSE2 GL_VERSION: 2.1.2 NVIDIA 304.37 Adapting to Quadro hardware. Detected 24 CPU cores. Enabled multithreaded rendering. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] 3D projector for low cost 3D Protein Cave
Hello stereophiles, many thanks to Jason Vertrees, Roger Rowlett and Sabuj Pattanayek for sending me information about their 3D stereo beamer setup. I recently purchased the following equipment and was not even sure it would work: - Optoma GT750, 1280 x 720 pixel resolution, 3000 ansi lumen, short throw ( 2 meter distance = fantastic 120 wide picture), 3D ready, HD ready - Lenovo w530, nvidia k1000m (with 192 cuda units), produces up to an amazing 1920 × 1080 pixel @ 120 HZ (!), VGA, mini display port - ASUS VG278H (not the HE model!) including one pair of nvidia glasses, HDMI (blue-ray stereo content), VGA, DVI (720p @ 120Hz), build-in IR emitter Concerning the mobile workstation (running windows 7 professional) and the ASUS display: - if the monitor is connected by a simple mini display to HDMI adaptor, the resolution is 1920 × 1080 pixel @ 24 Hz, HD 3D is running at 1920 × 1080 pixel @ 96 Hz (I assume because 2 x 24 Hz x 2 eyes = 96 Hz which is below the 120 Hz the monitor can handle). PYMOL and COOT can be viewed in stereo making use of the build-in IR emitter and the nvidia glasses that came with the screen. The picture looks stable and better than what I remember from the good old CTR Monitors. - The small k1000m has an amazing graphics power (equal to the old Quadro 2000) but I had to buy a really expensive adaptor ( Club3D /Mini DisplayPort to Active DVI/ Dual Link, /CAC/-/1151/) for displaying 1920 × 1080 pixel @ 120 HZ on the 27 inch stereo screen. In this mode, the build-in IR emitter does not work. I needed to buy the nvidia glasses with IR emitter, which is connected to the USB port of the workstation. 120 Hz picture is stable as a rock! In summary for this part, I should have maybe better purchased a mobile workstation with a true DVI-D outlet (not even sure those exsist!?) and safe me spending 150 US$ for the adaptor (the cheaper ones will not work!). Although, those mobiels are probably much more expensive as I merely spend 1950 US$ for the quad core with 16 GB memory and 256 GB solid state drive. Concerning the mobile workstation (running windows 7 professional) and the GT750 beamer: - the beamer is a truely pleasant surprize for the money paid (800 US$). One can choose DLP link stereo (short white flash in between pictures) or IR emitter using the build-in vesa 3-pin connector that works with all the old IR emitters we have in the lab. - at less than 2 meters distance the beamer displays a fantastic 120 wide stereo picture (the bigger the picture the better the 3D effect) - using the DLP linked glasses from optoma there is no ghosting at all in the stereo pictures displayed and this setup works great for group meetings and small class room setting as the glasses are not that expensive compared to the IR models. So, finally the low cost 3D Protein Cave (and the monitor) is up and running under windows 7 professional. - Jeroen - p.s. this particualr setup works for me and I did not try it under linux. The k1000m graphics card has no 3-pin vesa stereo connector which is required for displaying 3D content under linux (see nvidia website). But I have some hope that the beamer could work using the DLP link option... Am 13.06.12 19:48, schrieb mesters: Hi, I am planing to purchase/build a LOW-COST 3D Protein Cave consisting of a 3D capable projector (720p @ 120Hz or DLP 3D Ready?) and a windows 7 computer with a quadro 2000 card. However, I am a bit sceptic about the sync problem causing ghosting. Main Questions: 1) Is anyone out there succesfully operating a 3D projektor (with true stereoscopic 3D at 720p @ 120Hz) that has ist own 3-pin vesa out (!) to drive the nvidia emitter (like modern 3D-TVs do)? This would be the best solution to avoid ghosting (i.e. the output device drives the glasses, not the video card)! 2) Is anyone out there succesfully running a 3D projektor using the DLP Link option (white flash in between images to sync the glasses). Is this technique being used at all (for true stereoscopic 3D software such as Pymol, Coot, Yasara, etc.) by anyone? Optional: 3) What about the new 3D Monitors with a build-in IR emitter. Do those work well for 3D steroscopic viewing with software like Pymol? Any input is welcome, I do not want to spend a lot of money to find out it does not work after all Jeroen. -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives:
Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)
Hi Jason, The key seems to be, PyMOLShader_NewFromFile-Warning: default shader files not found, loading from memory. We load shaders from disk, but when they're not found we just read in some basic default shaders from code, which is what this is doing. Did you move or change $PYMOL_DATA? Ah, I bet this is because they are running it via X-forwarding over an ssh tunnel. I'm pretty certain that one of the reports came from a user running PyMOL this way, and I can duplicate the error messages running over a tunnel. Is this actually going to break anything? Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)
Ben, Ah, I bet this is because they are running it via X-forwarding over an ssh tunnel. I'm pretty certain that one of the reports came from a user running PyMOL this way, and I can duplicate the error messages running over a tunnel. Is this actually going to break anything? Yes -- volumes won't render correctly and the high-performance and -quality graphics won't be enabled. However, you should still have basic rendering and functionality. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] ray_trace_mode 1
Hi all, I would like to use ray_trace_mode 1 to render some structures. However, I am also using isomeshes within the same picture and do not want them to have a black outline. Is there any way to have the black outline only for specified objects or to make them transparent in isomeshes? Cheers, Arne -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)
Hi Jason, Ah, I bet this is because they are running it via X-forwarding over an ssh tunnel. I'm pretty certain that one of the reports came from a user running PyMOL this way, and I can duplicate the error messages running over a tunnel. Is this actually going to break anything? Yes -- volumes won't render correctly and the high-performance and -quality graphics won't be enabled. However, you should still have basic rendering and functionality. Is there a suggested workaround? I wonder how the shaders are actually loaded. In my local test case, the PyMOL directory is hosted on NFS and automounted to/from the same location, so in theory no matter which side is trying the fopen (or whatever), it should be able to find the file on disk at the same path. Thanks for your help. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] ray_trace_mode 1
Hi Arne, Unfortunately, ray_trace_mode is a global setting. You get the gain on all objects. I agree is looks poor on isomeshes. We should consider making ray_trace_gain object/atom level. Cheers, -- Jason On Fri, Oct 5, 2012 at 2:26 PM, Arne Dieckmann adiec...@googlemail.com wrote: Hi all, I would like to use ray_trace_mode 1 to render some structures. However, I am also using isomeshes within the same picture and do not want them to have a black outline. Is there any way to have the black outline only for specified objects or to make them transparent in isomeshes? Cheers, Arne -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] 3D projector for low cost 3D Protein Cave
On Fri, Oct 5, 2012 at 3:48 PM, Bradford R. Battey, Jr. bbat...@umich.edu wrote: On Oct 5, 2012, at 4:33 PM, Sabuj Pattanayek sab...@gmail.com wrote: We've tried the Asus VG278H with the built-in emitter and the nvidia 3d vision v2 goggles (one pair included with the monitor) in Linux and it works without the need for an expensive quadro with the 3 pin mini Hi Sabuj, How is this configured? We're in the process of trying to get three workstations put together and obtaining the older 3D monitors is being problematic. From the driver readme, I don't see where 3D Stereo over HDMI is supported. Many thanks! The monitor comes with HDMI, VGA, and DVI inputs. We've only connected to it using dual link DVI (using the cable it comes with which supports 120Hz @ 1080p) from the video cards we've tested, currently a quadro 370 and a quadro 3700 . Plan on testing a GTX 680 with it soon but probably won't be testing the mini hdmi to hdmi link. xorg.conf needs to be set to option stereo 10 as usual. -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
