Re: [PyMOL] installing pymol in redhat linux 8.0
I have been trying to install pymol in red hat linux 8.0 using the redhat rpm package for this version. I am getting an error saying error: Failed dependencies: tkinter = 2.0.0 is needed by pymol-0.97-1.rh80.py22 How do I get tkinter 2.0.0? http://rpmfind.net is available for all your rpm needs. Your RH8 specific package is at ftp://rpmfind.net/linux/redhat/8.0/en/os/i386/RedHat/RPMS/tkinter-2.2.1-17.i386.rpm
[PyMOL] setting a ray resolution then outputting a png doesn't always work
Hi, I set smooth lines from the menu, then I did: set orthoscopic=1 set antialias=1 ray 1200,1200 png file.png and file.png was the same size as the display window (less than 1200x1200), and I could still see jagged lines, as if it outputted exactly the quality seen in the display window. I got this to work once with a different pse file, tried restarting pymol but I can't get it to work anymore. I'm using 0_98beta27 on linux. Thanks, Sabuj Pattanayek
Re: [PyMOL] setting a ray resolution then outputting a png doesn't always work
Hi, bug 1) I think the problem is with what is saved in the pse. The pse which is giving me these problems does not display the message I can't display an oversized image. So I decided to recreate the scene from my .pml command file. bug 2) Now this leads to another possible bug. I setup my scene with the .pml file, and do ray 1200,1200 I get the I can't display an oversized image message. Then I do png file.png while the message is still on the display window and I get the ray-traced image. But when you open file.png some of the carbon bonds/atoms in stick mode that should be gray (as seen in the display window) are green in the file.png (I tried looking at the image using eog, gimp, konqueror and all show the same problem). bug 3) using movie - render frames no longer shows a rendered frame in the display window. Is this the normal behavior, because it used to work? Tried restarted several times and used only the .pml command file and not the buggy pse, but no luck. bug 4) When movie - render frames used to work, I believe it displayed all the colors properly, but the same thing happens as with bug 2 when you output the png (some carbon atoms that are gray in the display window become green in the png file). Here are the contents of the pml file causing all the bugs: load file.pdb hide all bg_color white create 901, (resi 901 and chain a) show sticks, (901) color gray, (elem c) color red, (elem o) color yellow, (elem p,pa,pb,pg) color cyan, (elem s) create near901A, (byres (901 around 3 and chain a)) show sticks, (near901A) color green, (near901A and elem c) create near901B, (byres (901 around 3 and chain b)) show sticks, (near901B) color cyan, (near901B and elem c) set orthoscopic=1 set antialias=1.0 Now here is a very similar .pml file which does not cause all these bugs, the only difference is that in the buggy pml I use the byres and around commands while in this one I explicitly identify which residues I want displayed. load file.pdb hide all bg_color white create 903, (resi 903 and chain a) show sticks, (903) color gray, (elem c) color red, (elem o) color yellow, (elem p,pa,pb,pg) color cyan, (elem s) create near903A, (resi 218,241,89 and chain a) show sticks, (near903A) color green, (near903A and elem c) create near903B, (resi 230,232 and chain b) show sticks, (near903B) color cyan, (near903B and elem c) set orthoscopic=1 set antialias=1.0 The only explanation I can give for the green carbons being outputted rather than gray is that the byres around commands are also coloring the 901 carbon atoms green (since it is itself within 3 angstroms), but in the display window I see it as gray ..strange. Sorry if this is really confusing, but I hope it's some error in the pml and not in pymol. Thanks, Sabuj Pattanayek Matt Franklin wrote: Sabuj Pattanayek wrote: Hi, I set smooth lines from the menu, then I did: set orthoscopic=1 set antialias=1 ray 1200,1200 png file.png and file.png was the same size as the display window (less than 1200x1200), and I could still see jagged lines, as if it outputted exactly the quality seen in the display window. I got this to work once with a different pse file, tried restarting pymol but I can't get it to work anymore. I'm using 0_98beta27 on linux. Thanks, Sabuj Pattanayek This could be a genuine bug, but did you do anything between the ray command and the png command? If you click in the graphics window, the raytraced image goes away and you get the OpenGL image again. Was the message I can't display an oversized image still in the window when you did the png command? - Matt
Re: [PyMOL] M. Lerner's APBS tools - errors
Please see: http://chips.csb.ki.se/pymol/msg02737.html ..even after using the server at http://nbcr.sdsc.edu/pdb2pqr/index.html and generating a pqr file, apbs still may not work. e.g. I have this problem with PDBID: 1TF7. Too bad there is no grasp for linux (its really fast for a general electrostatics overview), and well i can't get the delphi source to recompile for larger sets of atoms on linux using g77. I hope this helps and that the apbs server works for you. ..Sabuj Pattanayek fredb wrote: Hi Everyone, When I try to use PyMol and APBS (according to the instructions on Michael Lerner's web page, http://www-personal.umich.edu/~mlerner/PyMOL/) to display an electrostatic potential surface, I get a few errors (see output that follows). Does anyone know why this is happening and how to fix it? I'm using RedHat 9.0, PyMol v. 0.97 Thanks, Fred coarsedim is [131.55450687408447, 133.26979846954345, 121.22360420227051] finedim is [97.385004043579102, 98.393999099731445, 91.308002471923828] center is [57.759501457214355, 49.317999839782715, 78.048002243041992] finegridpoints is [225, 225, 193] radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr WARNING: 124 atoms did not have formal charges assigned WARNING: 305 atoms did not have properties assigned -- APBS -- Adaptive Poisson-Boltzmann Solver Version 0.3.2 Nathan A. Baker (ba...@biochem.wustl.edu) Dept. Biochemistry and Molecular Biophysics Center for Computational Biology Washington University in St. Louis Additional contributing authors listed in the code documentation. Copyright (c) 2002-2004. Washington University in St. Louis. All Rights Reserved. Portions Copyright (c) 1999-2002. The Regents of the University of California. Portions Copyright (c) 1995. Michael Holst. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -- APBS uses PMG and FEtk to solve the Poisson-Boltzmann equation numerically. FEtk and PMG are developed and maintained by the Holst Research Group at UC San Diego. PMG is designed to solve the nonlinear Poisson-Boltzmann equation and similar problems with linear space and time complexity through the use of box methods, inexact Newton methods, and algebraic multilevel methods. FEtk is designed to solve general coupled systems of nonlinear partial differential equations accurately and efficiently using adaptive multilevel finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about PMG and FEtk may be found at http://www.FEtk.ORG. -- This executable compiled on Nov 10 2004 at 10:51:17 Vio_ctor2: Gethostbyname fail INET sock dueto VIO_UNKNOWN_ERROR(0) Parsing input file pymol-generated.in... parsePBE: Warning -- parsed deprecated bcfl 1 statement parsePBE: Please use bcfl sdh instead. NOsh: Warning -- parsed deprecated statment chgm 1. NOsh: Please use chgm spl2 instead! parsePBE: Warning -- parsed deprecated srfm 1 statement. parsePBE: Please use srfm smol instead. parsePBE: Warning -- parsed deprecated calcenergy 0 statement. parsePBE: Please use calcenergy no instead. parsePBE: Warning -- parsed deprecated calcforce 0 statement. parsePBE: Please use calcforce no instead. Parsed input file. Got PQR paths for 1 molecules Reading PQR-format atom data from pymol-generated.pqr. Vio_ctor2: Gethostbyname fail INET sock dueto VIO_UNKNOWN_ERROR(0) Valist_readPDB: Unable to parse resSeq token (A) as int! Valist_readPDB: Error while parsing residue name! Valist_readPQR: Error parsing ATOM field! Error while reading molecule from pymol-generated.pqr Error reading molecules! ObjectMapLoadDXFile-Error: Unable to open file! --- SF email is sponsored by - The IT Product Guide Read honest candid reviews on hundreds of IT Products from real users. Discover which products
vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver
Yeah I have the same problem in the beta pymol, haven't tried the stable version: OpenGL-based graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro4 750 XGL/AGP/SSE/3DNOW! GL_VERSION: 1.5.3 NVIDIA 71.67 Hardware stereo capability detected. Adapting to Quadro hardware... Detected 2 CPUs. Enabled multithreaded rendering. /usr/bin/pymol: line 14: 8852 Segmentation fault $PYMOL_PATH/pymol.exe $* and 7167 won't compile on 2.6.10-11? kernels either, need 2.6.12-rc1, haven't tested others. I get similar crashes in VMD 1.8.2+ using 7167 also. For instance, if you load a pdb and try to make a licorice representation, vmd just closes/crashes. I also think this maybe a Quadro problem and not a a problem with GeForce cards. I have a GeForce 5500 FX on another machine and it doesn't have these programs, and realtime GLSL rendering works very nicely in vmd 1.8.3. Sorry for posting this on both mailing lists, just trying to avoid reposting. ..Sabuj Pattanayek HuiZhe Li wrote: just upgraded nvidia driver from 6629 to 7167 (Linux, RHEL 4) and pymol crashes when a molecule is load. is there a fix? (pymol worked fine with 6629 driver). OpenGL-based graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro FX 1400/PCI/SSE2 GL_VERSION: 1.5.3 NVIDIA 71.67 Adapting to Quadro hardware... /usr/local/bin/pymol: line 14: 4575 Segmentation fault (core dumped) $PYMOL_PATH/pymol.exe $* __ Do you Yahoo!? Yahoo! Small Business - Try our new resources site! http://smallbusiness.yahoo.com/resources/ --- SF email is sponsored by - The IT Product Guide Read honest candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595alloc_id=14396op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: vmd-l: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver
Hi, Unfortunately I can't get pymol-0.97 0.98beta29/27 to open a pdb without crashing instantly. I also tested Chimera (1.2105), O v9.0.7, and rasmol and these seem to work ok but I guess they aren't using quads/quad strips. Thanks for your insight, I'll email nvidia with the contents of your email. ..Sabuj Pattanayek John Stone wrote: Sabuj, That's really interesting. It sounds to me like NVidia's new driver has some sort of problem with drawing quads or quad strips in immediate mode. If that's what's going on, then a lot of other programs are going to crash too, not just VMD and Pymol, so I suspect they'll have to fix this very soon :-) All of the VMD reps you listed as having problems draw quadrilateral strips at some point, so that's my personal guess as to what is happening with their new driver. The Isosurface rep is one exception, it is drawing triangle strips, so I'm not sure why you'd have trouble with it, given that several of the others you listed do as well. Please email these results to linux-b...@nvidia.com so they are aware of the problem. If you can do similar tests with Pymol, that will help convince them it's a new problem with the driver and not just one bad software package, which is likely their default assumption. John On Tue, Mar 29, 2005 at 11:11:54AM -0600, Sabuj Pattanayek wrote: Hi John, This is what I was able to test on vmd 1.8.3, I think 1.8.2 will do the same (note this only affects the quadro cards and not geforce): Representation Result -- -- Lines (Default) ok Bonds crash DynamicBondscrash HBonds ok Points ok VDW ok CPK crash Licoricecrash Trace crash Tubecrash Ribbons ok NewRibbons ok Cartoon crash NewCartoon ok!!! MSMSok Surfok Dotted ok Solvent ok Isosurface(points) ok Isosurface(solid) crash Isosurface(wireframe) ok VolumeSlice ok? ..not sure what datatype this wants (never used this before), i was using a brix map but couldn't see anything Thanks, Sabuj Pattanayek David A. Horita wrote: Hi, I Haven't tried VMD yet, but Windows XP-pro pymol crashes upon file open under the 71.84 drivers, but not the 70.78 drivers. (Quadro 1300, XP-Pro servicepack 2) David Horita -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of John Stone Sent: Monday, March 28, 2005 10:10 AM To: Sabuj Pattanayek Cc: pymol-users@lists.sourceforge.net; vm...@ks.uiuc.edu Subject: Re: vmd-l: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver Hi, Have you reported the crashes to NVidia? I'd suggest sending an email to their linux-b...@nvidia.com mail address. The fact that multiple packages crash with the new driver indicates that they may have a new bug in their drivers. You mentioned that making a licorice rep crashes your VMD on that driver, what about VDW or bonds? Do they have a similar effect? John Stone v...@ks.uiuc.edu On Sat, Mar 26, 2005 at 04:42:42PM -0600, Sabuj Pattanayek wrote: Yeah I have the same problem in the beta pymol, haven't tried the stable version: OpenGL-based graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro4 750 XGL/AGP/SSE/3DNOW! GL_VERSION: 1.5.3 NVIDIA 71.67 Hardware stereo capability detected. Adapting to Quadro hardware... Detected 2 CPUs. Enabled multithreaded rendering. /usr/bin/pymol: line 14: 8852 Segmentation fault $PYMOL_PATH/pymol.exe $* and 7167 won't compile on 2.6.10-11? kernels either, need 2.6.12-rc1, haven't tested others. I get similar crashes in VMD 1.8.2+ using 7167 also. For instance, if you load a pdb and try to make a licorice representation, vmd just closes/crashes. I also think this maybe a Quadro problem and not a a problem with GeForce cards. I have a GeForce 5500 FX on another machine and it doesn't have these programs, and realtime GLSL rendering works very nicely in vmd 1.8.3. Sorry for posting this on both mailing lists, just trying to avoid reposting. ..Sabuj Pattanayek HuiZhe Li wrote: just upgraded nvidia driver from 6629 to 7167 (Linux, RHEL 4) and pymol crashes when a molecule is load. is there a fix? (pymol worked fine with 6629 driver). OpenGL-based graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro FX 1400/PCI/SSE2 GL_VERSION: 1.5.3 NVIDIA 71.67 Adapting to Quadro hardware... /usr/local/bin/pymol: line 14: 4575 Segmentation fault (core dumped) $PYMOL_PATH/pymol.exe $*
Re: [PyMOL] NVidia [7174] Drivers Nuccyl
Hi all, I'm still having the same problems with 7174 drivers on quadro (IA32, don't have any x86_64 machines to test), everything is ok on geforce. Can't get pymol-0.98beta31 to open with default rendering, but I'm getting a new error now with the double free or corruption at hex address when I start it: OpenGL-based graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro4 750 XGL/AGP/SSE/3DNOW! GL_VERSION: 1.5.3 NVIDIA 71.74 Hardware stereo capability detected. Adapting to Quadro hardware... Detected 2 CPUs. Enabled multithreaded rendering. ObjectMolecule: Read crystal symmetry information. Symmetry: Found 16 symmetry operators. CmdLoad: 1JGO.pdb loaded as 1JGO. *** glibc detected *** double free or corruption (!prev): 0x088d9858 *** /usr/bin/pymol: line 14: 26572 Aborted $PYMOL_PATH/pymol.exe $* VMD still crashes with certain representation that I outlined in a previous email to vmd-l. Thanks, Sabuj Pattanayek tree wrote: NVidia: I just got the 7174 driver (for 64-bit Linux). PyMol works fine, no crashes. What do other folks see with 7174? My openGL apps run nominally faster on 7174 than they do on 6629. Nuccyl: As there was little response from the PyMol audience, I will go ahead an add Nuccyl to the PyMol wiki myself. Please make changes as you see fit, since I'm not nucleic acids/Nuccyl savvy. Regards, -- Jason
Re: [PyMOL] hardware stereo
Hi, For SGI run 'xsetmon', if you see any resolution modes with an 's' after the refresh (e.g. 1024x768_96s) then click that mode and click 'load'. You can also check if your video card supports stereo by running 'glxinfo'. If you see a 'y' underneath anything in the 'stnewlinero' column then stereo in a window may work. Depending on your video card Pymol may automatically change your desktop resolution to the highest stereo supporting resolution. For example I'm running 1280x1024_30f and when I switch on Quad Buffered Stereo in pymol-0_98beta27-bin-irix65-r10k the screen resolution automatically changes to 1024x768_96s from 1280x1024_30f (I wish it would switch back when i turn off hardware stereo, but it does not). Hope that helps, Sabuj Pattanayek Ambert Nicolas wrote: Hello PYMOLers, I've recently installed Pymol v0.97 on an SGI but the hardware stereo mode was not detected. Is there somebody successfully using PyMol with this mode on an SGI ? If yes, could you please help me to fix this problem? My SGI: - Irix 64 Release 6.5 - Model Indigo 2 Impact 1 - Main Mem: 128 MB - CPU: 175 MHz Thanks a lot, Nicolas Ambert.
Re: [PyMOL] the conserved residues can be overlapped?
Hi, I was trying to find information online/and in the archives of the mailing list to do what you are asking. You can try help fit which will give you some more commands to try. You can also try help pair_fit. Unfortunately I know I'm doing something wrong so I can't get these commands to work properly without always returning an ExecutiveRMS-error. So for structure matching I exclusively use Chimera. Open your two structures, Tools-Homology-Matchmaker . The rest is self-explanatory. It will return an RMSD, has several algorithms and matching matrices to choose from, and will even show you the sequence alignment if you want. You can even interesting residues in the sequence alignment window and it will select them in realtime in the structure viewing window. Hope that helps, Sabuj Pattanayek yunbo.song wrote: Ok, thanks. But, its not what I meant. I want to let 2 proteins automatically overlap according to the amino acid sequence alignment,i.e. the conserved residues can be overlapped. Can I do it use pymol or any other program? thanks May 5 hi, I had a similar question, and here is the answer. Jennifer, Yes.?Switch the mouse into 3 button editing mode, and then shift-left-click-and-drag to rotate and shift-middle-click-and-drag to translate. Cheers, Warren I found that this approach works best if you are in stick or line mode. I hope this helps. -Jennifer Pfingsten (UCHSC) -Original Message- From: pymol-users-ad...@lists.sourceforge.net on behalf of yunbo.song Sent: Thu 5/5/2005 11:56 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] can superimpose two protein structures ? Hi, all, Can I use pymol to superimpose two protein structures ? How should I do? If it cannot, anybody can tell me what program can do superposition very easily? thanks! May 5
Re: [PyMOL] APBS binary location
Hi, I just checked the apbs download page and I couldn't find apbs binaries available for windows. The only way I've seen (through previous mailing lists posts) is to compile it using cygwin, but the performance is less than optimal. So if you or someone else has compiled apbs for windows, the binary location is the path to the apbs executable. For example apbs on your windows system may be in c:\cygwin\usr\local\apbs\bin\i686\apbs . Furthermore the psize.py should be located at: c:\cygwin\usr\local\apbs\tools\manip\psize.py ..maybe something like that. Yes the plugin is asking for the .dx electrostatic map. By default the electrostatic map is placed into %TEMP% (maybe c:\documents and settings\you\temp or c:\windows\temp). You can check what %TEMP% or %TMP% is set to by going to control panels - system - advanced tab - environment variables. Otherwise you can directly specify where the pymol-generated.dx file should go by changing it in the Temporary File Locations tab of the APBS tools (e.g. Temporary DX file: c:\mydir\pymol-generated.dx). Also may I suggest that for a fast overall electrostatics calculation, without having to compile anything, to look into GRASP2 for windows. It is at http://trantor.bioc.columbia.edu/grasp2/ . You can import the .phi maps from grasp into many applications including pymol and visualize them also. Hope that helps, Sabuj Pattanayek migalepa wrote: I've been trying to generate an electrostatic potential map of the surface of a protein using Pymol but haven't been successful. I'm working with the latest version of pymol (0.98, windows version), which brings the APBS plugin (I have as well installed the APBS plugin apbs_tools.py) that is supposed to do the necessary calculation in a straightforward way, according to the guidelines provided in http://www-personal.umich.edu/~mlerner/Pymol/. I've follewed them but the plugin asks for an APBS binary location. I do not know what a binary location is or where to find it. I'm using PDB files converted to PQR files, as indicated in http://www.csb.yale.edu/userguides/graphics/pymol/electro.html., and run the APBS tool selecting a ramdonly chosen APBS binary location. The program seems to do calculations on the surface of the protein although does not generate any figure representing the results. By clicking on visualization the plugin warms that at least a molecule and a map must be loaded. Is the plugin asking for the calculated electrostatic surface map? Is so, how do I find it? Does it have to be with the APBS binary location issue? Well, lots of questions... Thank you beforehand... --- This SF.Net email is sponsored by: NEC IT Guy Games. How far can you shotput a projector? How fast can you ride your desk chair down the office luge track? If you want to score the big prize, get to know the little guy. Play to win an NEC 61 plasma display: http://www.necitguy.com/?r=20 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Pymol on MacMini: performances
Hi, I can run pymol smoothly on my celeron-m 1.3ghz laptop with intel i855gmch embedded graphics chip. This has no dedicated memory and uses a portion of the 512MB system ram for graphics processing. The specs say that mac mini's come standard with ati r9200 with 32mb *dedicated* ram for graphics so you should have no problems. In general a dedicated ati or nvidia chip has more opengl capabilities than embedded intel or sis graphics chips. A $50 upgrade to 512MB would help tremendously however. Hope that helps, Sabuj Pattanayek Luca Fenu wrote: Hi everyone, I'm thinking of buying a Mac mini to use as minimal computer for home, and will need it to run pymol smoothly. is this the case, or the little machine doesn't have enough juice to handle, let's say, visualisation of a protein active site and ligand docked into it, with different level of transparence and such? I need pymol essentially to look at my structure and generate pretty pictures for my phD thesis... many thanks to anyone can give insights... luca
pymol in powerpoint/openoffice was Re: [PyMOL] pngs and structures simultaneously?
Hi Has anyone thought about a way to embed pymol (or other molecular modelling apps) directly into openoffice or powerpoint similar to what accelrys weblab activex viewer does in powerpoint? Can this already be done? This would simultaneously solve a problem like that described below, would be good for conferences, and would be geeky cool also. thanks in advance, Sabuj Pattanayek Andreas Henschel wrote: Hi there, Is it possible to display both a png file (using load_png) AND some molecule at the same time? It sure sounds geeky, but the rationale is that I would like to do a short presentation completely in pymol. I want to load some powerpoint slides (converted to png) in the background and have the full power of pymol scripting and molecule viewing. At least I can do it seperately... Just a thought. Also, any idea, how I can call a function with just pressing a single key? Cheers, Andreas
Re: [PyMOL] Shadows
It looks like a CGO (compiled graphics object) behind the molecule, then rendered using pov-ray, probably a script floating around to do this somewhere on the internets. Corinne Zeitler wrote: Hi, I was wondering if anyone knows how to produce the type of image in Pymol that is on the Pymol Galleray page (http://pymol.sourceforge.net/pmimag.html). I would like to know specifically how to make the shadow of the molecule appear in the background. Thank you! Corinne Zeitler Graduate Student Baylor College of Medicine
Re: [PyMOL] What is the best 3 button mouse for PyMOL on a Mac OSX?
I use a cheap microsoft optical (or basic optical) usb mouse on linux, so it should work on your macosx. If you want something more configurable under macosx and don't want to destroy the Appleness of your computer with an MS mouse then this might work for you http://www.apple.com/mightymouse/ . I hear there will be a wireless version soon. Sarina Bromberg wrote: I have a logitech MX700 Cordless Optical Mouse that claims to be a 3- button mouse, but I can never get it to produce the results provided for 3-button viewing or editing by PyMOL. Perhaps I do not have it configured correctly (I cannot find a clue in the instructions or in simple experiments), or perhaps this is not the kind of 3-button mouse I need. Does anyone have a good solution? Tx, Sarina Bromberg --- SF.Net email is Sponsored by the Better Software Conference EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile Plan-Driven Development * Managing Projects Teams * Testing QA Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] question on cctbx and pymol
Hi, This worked. Thanks, ..Sabuj Robert Campbell wrote: prefixing a directory path. If you were like me and had: /usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $* in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to: python $PYMOL_PATH/modules/launch_pymol.py $*
Re: [PyMOL] Shelx maps in Pymol?
Doesn't shelx output map files in O (brix/dsn6) format? from shelxpro: [M] Map file for O from .fcf If that doesn't work directly for pymol try using mapman to convert O to whatever format you want. Johanna Hakanpää wrote: Hi, Is there a way to read Shelx density maps to Pymol, directly or by converting them to different format? Regards, Johanna Johanna Hakanpää MSc Department of Chemistry, University of Joensuu PO Box 111 FIN-80101 Joensuu tel. +358 013 2512043
Re: [PyMOL] PyMOL featured on Apple Store site?
Do you have the URL? D. Joe Anderson wrote: So, that sure looks like PyMOL to me (actually, four instances of it) running on the display of a PowerMac G5 on the newly-updated Apple Store website today. My question is, which structure is that?
Re: [PyMOL] PyMOL featured on Apple Store site?
nm, I found the url: http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore.woa/72303/wo/iG1ZdpmENibK2kKdLwyNuAAR9NW/0.SLID?nclm=PowerMacmco=586014F6 D. Joe Anderson wrote: So, that sure looks like PyMOL to me (actually, four instances of it) running on the display of a PowerMac G5 on the newly-updated Apple Store website today. My question is, which structure is that?
Re: [PyMOL] question about ray after alter and rebuild
Or you can dump to povray and render at whatever resolution you want, but the image will not resemble exactly what is seen in the pymol viewer window. Peter Adrian Meyer wrote: multiple structura alignment. I pointed out three structures for further processing within all 12 structures. However, when I try to ray the structural resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000, 2000', I always received a low resolution (as screen resolution only) result. How could I do? Thanks a lot! Pymol can't display a ray-traced image to higher resolution than your screen can show, but it can write it to a png file at that resolution (I'm assuming you're talking about pixel resolution, not diffraction resolution here). ray 2000,2000 ; png HighRes.png Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Mac OS X 10.4.3
I don't know if it will make a difference (I don't even have a Mac) but try opening it from a console using: pymol -M Serge Cohen wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Got exactly the same problem on a 800MHz TiBook I was planning to try on a Dual G5, but had not the time today... Serge. Le 3 nov. 05 à 23:05, Brian J Goodfellow a écrit : Hi Mac users, has anyone noticed an annoying flickering appearing when rotating a molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present under 10.4.2? The problem appears on both my iBookG4 and iMacG5. If the window is moved then the flickering disappears. However, if a ray trace is then drawn the problem starts again until the window is moved again - very annoying! Brian Goodfellow *** Dr. Serge COHEN GPG Key ID: 9CBB58FB N.K.I. Department of Molecular Carcinogenesis Plesmanlaan 121 1066 CX Amsterdam; NL E-Mail: s.co...@nki.nl Tel : +31 20 512 2053 *** -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.1 (Darwin) iD8DBQFDapuW5EPeG5y7WPsRAlA1AJ93hPA3eALJX10AQ/HVo7J6dA914gCeMz1E AJkFJDwrG820njkblBCpqeE= =F8UC -END PGP SIGNATURE- --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] EMizing an xray structure
You can create an mrc map from a PDB using the pdb2mrc program in the EMan package (http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/ and http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/doc/progs/pdb2mrc.html). Pdb2mrc allows you to specify parameters that would affect what a theoretical cryo EM 3D reconstruction would look like. If you are looking for a theoretical negative stain EM image, EMan can create flattened projections of the mrc from multiple angles as well. I don't know if pymol can read MRC though (I know Chimera can). Andreas Förster wrote: Hey all, I'm trying to make a figure from a pdb that's supposed to look like an EM structure. According to an older post from Warren I should increase solvent_radius and alter vdw. For most combinations of the two, artefacts appear all over the place, like missing surface and surface floating about. I succeeded in making a figure without artifacts (high vdw increase, minimal solvent_radius increase), but it looks more like a lychee than a protein. Has anyone found numbers that work well? Or a different approach to creating an EM reconstruction-like figure. Merci bien. Andreas
Re: [PyMOL] fofc map
try changing the name of the map to fofc.ccp4 load fofc.ccp4, fofc isomesh fo1,fofc,3.0,(chain D),buffer=2.0,carve=2.8 S. Shanmuga Sundara Raj wrote: Hi, I tried to show the fofc map by using the following lines: load fofc.map, fofc isomesh fo1, fofc,3.0, (chain D), buffer=2.0 but it gives the error as, Isomesh: map or brick object fofc not found. i would like to show at different contour levels. Thanks in advance Raj What are the most popular cars? Find out at Yahoo! Autos http://us.rd.yahoo.com/evt=38382/_ylc=X3oDMTEzNWFva2Y2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDMmF1dG9z/*http://autos.yahoo.com/newcars/popular/thisweek.html
Re: [PyMOL] sporadic pymol/X-server freezes?
Hi, Has anyone else run into cases where pymol will freeze the X-server (pymol doesn't repond to mouse or keyboard input; keyboard non-responsive to caps-lock on/off)? no. I've only seen this while looking at several maps/masks (but that's most of what I use pymol for, so I'm not sure if that's the cause). same here, how big are your map files in MB, how much ram and swap space do you have? I've seen this error on both suse 10.0 and kubuntu (3.10? whatever the lastest apt-get dist upgrade got me; two different machines) using source builds of pymol-0.98, and 0.99rc6 with ext-0.98,ext-0.99rc6, and ext-0.95. Any suggestions on how to fix this (or get debugging information out of pymol to narrow down the problem)? I haven't the slightest clue. Does this happen immediately after loading the map or while rotating or what? But I can tell you that I'm running gentoo, w/vanilla sources 2.6.15 running in x86_64 mode (straight from kernel.org), 1.0.8178 nvidia drivers on a quadro4 980xgl video card. You might try as was suggested to upgrade your kernel. You can get 2.6.16 from kernel.org, copy your current .config into the root of the source directory, run make oldconfig, hit enter a bunch of times, then compile the kernel with make make modules_install. You will have to recompile the nvidia drivers for the new kernel too. Hope that helps, Sabuj Pattanayek
Re: [PyMOL] sporadic pymol/X-server freezes?
No consistent pattern. Both machines are x86, non-nvidia graphics cards (which probably isn't helping). But, score at least one working setup (yours) as a fully functional combination. Yes always go with nvidia on linux x86/x86_64 if you can. Do you have an ati/sis/3dlabs/intel product?
Re: [PyMOL] pymol on amd64?
I use gentoo linux's portage to do all the compile work (emerge pymol). From the ebuild it looks like you need these prerequisites: python, pmw (python library), numeric (python library), tk, libpng, zlib, and glut . Praedor Atrebates wrote: Is anyone running pymol on an AMD64 system? If so, did you find a prebuilt binary or did you build it yourself? If you built it yourself...HOW DID YOU DO IT? I'd greatly appreciate help in this regard. Thank you, praedor
Re: [PyMOL] APBS - libreadline
This is using the binary distributions of APBS? Becker, Joseph W wrote: I'm trying to install APBS on a LINUX (IBM T43P) box running SuSE 9.3 Professional. I've successfully installed maloc, but the apbs install gives: error: Failed dependencies libreadline.so.4 is needed by apbs-0.4.0-1 What to do? Thanks, Joe Becker Merck Research Labs
Re: [PyMOL] FW: APBS - libreadline
I just installed the binary -i686 (not -i386), x86_64, and ia64 versions of apbs and apbs tools for some redhat machines and tested them all yesterday. None of the machines return anything when I do rpm -qa | grep maloc . Do you actually need maloc if you're not compiling from source? Becker, Joseph W wrote: Yes, apbs-0.4.0-1.i386.rpm Joe
Re: [PyMOL] FW: APBS - libreadline
I have these versions installed on i686 RH boxes: readline-4.3-13 readline-devel-4.3-13 At http://rpmfind.net/linux/rpm2html/search.php?query=readlinesubmit=Search+... it shows that SuSE 9.3 uses readline-5.0-7.2.i586.rpm . I don't know if that is going to be a problem. You may have to re-compile. venkataraman kabaleeswaran wrote: Hi I had the same problem while installing the apbs, I contacted the apbs-users mailing list , they adviced me to install readline, I did but still didnot work , after installation I got the same error. check and see if your system as readline library if not install that and try againg, good luck. Try post your problem at apbs-us...@lists.sourceforge.net. cheers vk
[PyMOL] RealD (Stereographics) E2SGI emitter on Quadro 3450?
Hi all, Anyone know if it's possible to use a RealD (Stereographics) E2SGI emitter on Quadro hardware? Thanks, Sabuj Pattanayek
[PyMOL] minimum recommended version of python for pymol 1.0r0
Hi, What's the minimum recommend version of python against which pymol 1.0r0 should be run? I've seen that it doesn't work at all with 2.3 but does with 2.4. Latest is 2.5.1. Thanks, Sabuj
Re: [PyMOL] 3D Glasses. Where to buy them ?
EPF (Esben Peter Friis) wrote: Hi David Try http://www.edimensional.com/. They have a UK sales office. Do these only work for programs under Linux that specifically implement page flipping stereo? The software that they describe which must be installed seems to be only for Windows (which also gives you page flipping stereo on LCDs). Thanks, Sabuj
Re: [PyMOL] 3D Glasses. Where to buy them ?
Hi, EPF (Esben Peter Friis) wrote: Hi Sabuj Do these only work for programs under Linux that specifically implement page flipping stereo? They deliver some drivers, which is for Windows only. On Linux, You must use a stereo-enabled graphics card (ie. most Nvidia Quadro series, no cheap GForce cards). That's what I thought, but then I saw this: http://imsb.au.dk/pipermail/o-info/2003-April/006644.html The edimensional glasses also comes with a break-out box to mount between the graphics card and the monitor. This cannot be used with Linux, but the IR-emitter fits directly in the stereo port on the graphics card. Still it's cheaper than stereo card + nuvision or stereographics. Do you know if these work on SGI's? How long is the cable on the IR transmitter? Thanks, Sabuj
Re: [PyMOL] [ccp4bb] While on the subject of stereo
Hi, Warren DeLano wrote: 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. I'm not sure what the technical term for this effect is, but is there some way to increase the perspective-ness of the molecule being displayed (more so than the default perspective mode), i.e. atoms in the back are smaller than they should be and atoms near the front are larger than they should be in vs an orthographic projection? This might increase the stereo effect when moving from side to side. Anyone found optimal settings in the molviz control panel so as to reduce jitter? Thanks, Sabuj
[PyMOL] Linux 195.22 Nvidia binary driver + 120Hz LCD Samsung 2233RZ + Quadro FX 3700 + Nvidia 3D vision = working quad buffered stereo
Hi all, Just wanted to mention that I've updated some of the info on the wiki here: http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options#LCD_Displays_.28120_Hz.29 to note that quad buffered stereo (QBS) on the 120Hz Samsung 2233RZ LCD monitor works on Linux. It's nowhere as cheap as the Zalman solution but will work with any other visualization apps out there that have QBS support which don't support the Zalman. HTH, Sabuj Pattanayek -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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] Laptops for stereo 3D
On Wed, Feb 24, 2010 at 4:50 AM, Stefano Marzi ma...@igbmc.fr wrote: Hi everybody, Do you have any suggestion about new laptops that can support Active or Passive Stereo 3D visualization with Pymol? AS5738DG-6165 http://us.acer.com/acer/productv.do?LanguageISOCtxParam=enkcond61e.c2att101=56746sp=page16ectx2.c2att1=25link=ln438eCountryISOCtxParam=USctx1g.c2att92=447ctx1.att21k=1CRC=1856145400 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] Viewsonic VX2268wm confirmed to work in stereo under Linux
Graphics Card is a nVidiaGEFORCE QUADRO FX 1800. See the Active Stereo 3D (High-Refresh) Displays section on this pymol wiki page: http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options#Active_Stereo_3D PyMOL official recommendations was the Zalman ZMM220W, but this is not I don't think MOE, Sybyl, or most other proprietary viz applications support Zalman stereo. -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] Laptops for stereo 3D
On Thu, Feb 25, 2010 at 7:12 AM, Christine Lee biobr...@gmail.com wrote: Dear, Based on my personal experience, I do not recommend Acer, It is really poor hardware. Or give it a try and after some time you will realize how poor it is. Yeah, I agree. But anyone know of any other 3D laptops? There are these Asus laptops that can use the Nvidia 3D vision kit: http://www.google.com/products?hl=enq=asus+3d+vision+laptopum=1ie=UTF-8ei=wXmGS-qsL5DsM8mvxL4Msa=Xoi=product_result_groupct=titleresnum=3ved=0CBoQrQQwAg but it has a builtin GEForce card which will only do stereo on Windows for full screen DirectX apps/games. -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] Viewsonic VX2268wm confirmed to work in stereo under Linux
I just tried exactly the same thing with OpenSuSE 11.2 and couldn't get it to work at all. The reason, at least how I got it after a long, long discussion with custhelp.nvidia appears to be that some distributions mount USB devices under /proc/bus/usb/devices (works...) and some under /dev/bus/usb (doesn't work). In OpenSuSE, which belongs to the latter class, the driver appears to look under the non existing /proc/bus/usb/devices, doesn't find the entry for the 3D-Vision emitter and refuses to switch on stereo. The nvidia guys tested it with RHEL 5, which belongs to the former class of distributions. Unfortunately the USB Emitter must be recognized for reasons I do not know by the driver although the sync signal runs via the 3-Pin Mini-Din. Did you try in /etc/fstab: none/proc/bus/usb usbdevfsdefaults 0 0 or were you able to get it work in suse using some other method? Another question of concern is wether the chipset on the FX1800 is supported by the 195.x driver at all. You should look this up with nvidia. You need at least a quadro 3700. -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] PC based docking program!
Try hex: http://www.loria.fr/~ritchied/hex/ On Fri, May 7, 2010 at 6:48 AM, Sona Vasudevan sona.vasude...@gmail.com wrote: Hello All, I would greatly appreciate if anyone can suggest a PC based docking program for teaching purposes? I am trying ArgusLab, but that seems too unstable. Thanks much! Sona -- ___ 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-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] Stereoscopic visualization
Hi, On Sun, May 9, 2010 at 11:16 AM, Emiliano Ippoliti e.ippol...@grs-sim.de wrote: Dear Users, in my University I have an hardware system formed by: 1 - PC with Nvidia Quadro FX 4800 graphics card. 2 - 64-bit Operating system Windows 7 Professional 3 - Projector ACER H5360 DLP 720P (3D ready) connected to the PC by HDMI 4 - Nvidia GeForce 3D Vision Emitter connected to the PC by USB 5 - Nvidia GeForce 3D Vision glasses I have successfully tested the stereoscopic visualization with some DEMOs from Nvidia. Now, I would like to use it with PyMOL. You're not supposed to need the 3 pin mini din connected for 3d vision in windows but go ahead and plug that in anyways since you've got that connector on your card. Also make sure you're not hotplugging the emitter, i.e. make sure you rebooted with all connectors (including the 3 pin min din) plugged in and the proper 3d drivers installed. However when I try to open PyMOL and select in the stereo mode menu the Quad buffered stereo visualization, the projector visualizes the two images for the left and right eye (I see the image is double) but the emitter does not start and so I can not see the stereoscopic effect by the glasses. I tried to enter the Nvidia driver in order to change the default setting for PyMOL program and force explicitly to use the 3D DLP display settings though I have had no results. Looking at the Tips Tricks manual of Nvidia GeForce 3D Vision package, I read that it currently supports only the full screen applications and cannot run in windowed mode. Is this the problem with my hardware? Or do you think that the problem is elsewhere? I've tested windowed stereo with 3d vision and a low end quadro 370 for pymol and chimera on win xp, but with a 120 Hz LCD. Do you have a 120Hz LCD monitor you can test with? See this page for more info: http://pymolwiki.org/index.php/Stereo_3D_Display_Options Let us know if you get this to work. Thanks, Sabuj -- ___ 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 successful cases
We've had great success with the ViewSonic PJD6531w (http://www.viewsonic.com/products/pjd6531w.htm). It's bright, clear So are you guys using the DLP link (3d sync) technology of the projector with DLP link capable glasses? -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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] NVIDIA Quadro 600
Yes, you can do nvidia 3d vision with this card under win 7 (not linux!) with a 120Hz LCD monitor or a 120Hz DLP projector. On Wed, Feb 8, 2012 at 2:03 AM, smit...@atlas.cz wrote: Hi all, I would like to ask whether it is nvidia quadro 600 compatible with pymol 3d stereo on windows 7? Do you have any experiemce with this card? Thank you for help Smith -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ 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 -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ 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
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? Yes, we have theInfocus IN3116 which does active DLP 3D @ 720p (120Hz), but you can now get the IN3118HD which supposedly does 1080p @ 120Hz for about the same price ~$1.4k. We also purchased about 30 of these active goggles to go with it : http://www.ultimate3dheaven.com/uldlpliwi3dg.html Our setup looks like this : 1st Projector connection - 10ft hdmi rapidrun flying lead - 50ft rapidrun red digital cable - 10ft hdmi rapidrun flying lead - $1 hdmi to dvi converter - nvidia quadro 600 in a dell precision T3500 workstation (dual boots linux and windows7 ) 2nd Projector connection - 10ft HD15 + audio rapidrun flying lead - 50ft rapidrun yellow runner - 10ft HD15 + audio rapidrun flying lead - available for guests/laptop connections -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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
Re: [PyMOL] Viewing PyMol in 3D
You don't need a quadro with a 3 pin port to do stereo in linux anymore, but you do need a new model quadro, e.g. a quadro 600. The tradeoff is that you'll pay more for the 120hz monitors with the built-in 3d vision v2 emitters, see here : http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-November/008177.html I haven't' tested a standalone 3d vision v2 emitter with linux, it may behave the same way as the lcd's with the built-in v2 emitter. NVIDIA quadro card and Nvidia 3D kit. The only caveat is that under Linux you need to have a card which supports the external 3 pin stereo connector, you don’t need that under any of the windows flavors. Check the Nivida -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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] Viewing PyMol in 3D
It takes a bit of understanding. Am I correct that if the monitor does not have a built in emitter, the glasses need to be triggered from either a remote transmitter plugged into the 3 pin mini din port of a suitable quadro card for quad buffered, or to a USB port in the case of consumer GTX (not quad buffered and not supported by molecular modeling software, for software enabled games etc.). In Windows I don't know if the GTX cards allow qbs in a window. I haven't tested such a configuration at all. But with a quadro and external emitter in Windows you only need the USB connection to the emitter. In linux you need both the 3 pin and usb connections for external emitters. If the monitor does have a built in emitter, the glasses are triggered from the monitor directly with no link to the video board except the video signal, so any quad-buffered board will work. Are the glasses triggered effectively directly by the sync-signals within the monitor? If so why won't Linux work? Let's be specific. The glasses are triggered from a sync signal that comes out of the emitter housed at the top of the monitor. The signal is sent over the dual link DVI-D cable from the quadro, there's no usb or 3 pin mini din cable involved anywhere. The catch is the linux windows nvidia drivers have built in code specifically to detect monitors that have the built-in 3d vision v2 emitters such as the Asus VG278H. Again, this works fine in Linux and Windows with recent quadro's, but I don't know if GTX cards can do the qbs in a window in Windows (definitely not in Linux). Asus VG236HE, Acer GD235Hzbid, or BenQ XL2420T are difficult to find here and very expensive compared to normal list price. I don't know what price range you're looking for but the ones with the built-in emitters like the VG278H are more expensive. It's currently ~$500 USD, so your total with a quadro 600 would be ~$650, or you could get a refurbished quadro 3700 or quadro 370 for much less than the $130 I'm seeing for the 600. There's a list of 3d vision capable monitors below. I assume the Acer GR235HAbmii won't work with PyMol, Chimera, VMD etc as it is a passive system. Am I correct? I don't think that's passive since it says it supports one of the 3d methods that bluray devices use (HDMI 1.4) use, but it's not 3d vision or qbs, see Q12 here : http://www.mitsubishi-tv.com/feature/3DTV/3D_FAQ i.e. frame packing != frame sequential != qbs Can you advise whether the smaller 23 S23A750D might work with a suitable Quadro e.g. 300, 410, 600. This model includes 3D glasses but I can't work out whether it has a compatible 3d vision v2 built-in emitter or not. Looking more at these samsung monitors, I don't think any of these are 3d vision, incl the one I posted on the chimera mailing list. I found this list here of the 3d vision v2 compatible monitors with the lightboost tech : http://hardforum.com/showthread.php?t=1680564 and this is a list from nvidia which includes monitors with built-in emitters and without : http://www.nvidia.com/object/3d-vision-system-requirements.html I also think I found the code that your previous stackoverflow link was referencing : http://stackoverflow.com/questions/6827737/how-do-i-output-3d-images-to-my-3d-tv/6828590#6828590 ..and they're basically saying the same thing regarding quadro's and quad buffers, except this bit is interesting : With any luck, Direct3D 12 will require QBS, and thus NVIDIA (and AMD) will expose it in OpenGL (for consumer cards). -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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] Invitation to visit at ACS New Orleans
Specifically, we'll have a demo version of PyMOL v1.6, PyMOL on the iPad, and even a sneak peek of Leap Motion (https://www.leapmotion.com/) controller integration with PyMOL. Do you have it working under linux? -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ 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
