[PyMOL] Difficulty with Pymol segfault in CentOS 7 VM
Hello, I have recently installed Pymol 1.7.6 (also tested with 1.7.4 and 1.6.0) using gcc 4.8.3-9 on CentOS 7. The operating system is installed in VMware workstation 10.0.5 with hardware acceleration enabled. I installed the scripts and modules in an independent directory as described here: http://www.pymolwiki.org/index.php/Linux_Install Pymol starts up and appears to run fine, but anytime I quit or load any XYZ file, the program quits unexpedidly and claims there is a segmentation fault. The Representations demo also causes the problem. I am uncertain where to get further details to pinpoint the library causing the fault, but I would like some advice to see if there is anything I can do to correct the problem. I attempted mono and many of the commandline options, but nothing is helping. Interestingly, I ran the pymol benchmark tool from the commandline, which does not cause a segfault. In fact, after opening pymol using the `-b` flag, I can then load any XYZ file without segfault. However, the view keeps blinking during movement. It may also be of interest to note that I have used opencascade without any problems as a 3d rendering and cad visualization software on this same VM. Thank you, Derek Thomas -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ 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] Install pymol on OSX easier than ever
Thanks Camilo! You're absolutely right that it needs python and TK with those options. Sorry that I forgot that. That being said, it should not have installed pymol without those packages. I suggest you run brew updatebefore installing. Also, if you run brew install tk --enable-threads it should automatically install TCL with threads too. Best, Derek Thomas On Wed, Feb 13, 2013 at 2:21 AM, Camilo Andrés Jimenez Cruz camilo.jimen...@gmail.com wrote: Hi all This option to install pymol is great!. However, I tried to install it in my 10.8.2 with xquartz intalled and it was crashing. For it to run well, you need to enable threads, do: brew uninstall tcl brew uninstall tk brew uninstall python brew install tk --enable-threads brew install tcl --enable-threads brew install python --with-brewed-tk -- Camilo Jiménez On Tue, Feb 12, 2013 at 10:22 AM, Derek Ashley Thomas derekatho...@gmail.com wrote: Dear all, We just got pymol into the popular package manager for OSX, homebrew. To install pymol on with brew, just run the following two commands (% stands for the shell prompt and should not be typed in: % brew tap homebrew/science % brew install pymol That's it, you should be on your way to using pymol soon after the installation finishes. Also, this installation switches the stereo/mono graphics paradigm. Recent builds of OSX with intel chips seem to crash with stereo graphics. Therefore, pymol defaults assumes the -M flag has been passed to it. You can switch to stereo graphics (if you know it won't crash your computer) with the -S flag. Alternatively, you can install pymol with original stereo graphics on as default by installing with brew install pymol --default-stereo Hope this helps bring pymol to more people! Best Regards, Derek Thomas -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ 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 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ 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 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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] Getting pymol to open in mono mode by default
Hello all, I am a mac user and have never been able to get pymol to open in stereo mode without crashing my computer, unfortunately. I suspect that apple is either no longer supporting stereo graphics or they're drivers are messed up on recent OS builds. At least this is the case for all iMacs and MacBookPro's I have used in the past couple years. This means that writing programs that rely on pymol need to watch out and explicitly turn off stereo, but this is not a good idea because there may be users out there that want stereo enabled if their hardware supports it. So, I threw a quick patch together that forces pymol to open in mono mode without the -M flag unless the user explicitly uses -S for stereo. You can get the patch here: https://gist.github.com/1b84b2ad3503395f1041 It is designed to be used on the installation directory, but it could also be applied to a pre-existing pymol installation. Hope this comes in handy to anyone out there. Cheers, Derek Thomas -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122912___ 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] Installing pymol from source on OSX 10.8
Hey, I'm a long time user of macports, but recently I have decided to check out homebrew for a number of reasons. Currently there is no standard way to install pymol with this technique, but I thought it should be possible. I set out to install pymol from source without the MacPorts libraries that had helped me before. I had significant trouble installing the current stable tarball. After serious alterations to the setup script and some header files, I finally got it to compile the cmd library, but any time I tried to load it with python I had an error saying that it could not find the symbol `_glutswapbuffers`. Clearly some of this was a known issue because many of these changes were addressed in the most recent trunk/head of the svn repository. I had to make a few minor changes to make sure that it supports non-MacPorts installations (https://gist.github.com/4267806), but it was rather trivial. With this, I could install given I had Xquartz installed and a few other dependencies. I created a homebrew repo that takes advantage of this change here: https://github.com/scicalculator/homebrew-pymol Using the above, you can successfully install pymol using homebrew. The only problem ... the toolbar fails to function. It does not throw any errors if you have Pmw installed, but the toolbar widget never shows itself. I have dome some other testing (https://gist.github.com/4269280) to see if I can get the toolbar to show up, but no luck. Does anyone have any hints as to where to look to get passed this part. Also, if you have any ideas on fixing the `glutswapbuffers` error on the stable branch, I'd love to hear it. Anyway, I hope this helps any users of homebrew out there. Derek Thomas -- 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
[PyMOL] Pymol + Freeglut -- internal error
Hi all, I am developing a crystal-generator and MD simulation debugger running through pymol. It works pretty well on my primary computer, but I hit a bit of a snag when one of my two computers refuses to run pymol. I am using freeglut with pymol. I was easily able to get this to work on a OSX 10.7.3 macbook pro (core i7 cpu). However, after doing the same series of steps to install everything on an iMac with the same OS (core i3 cpu), I get the following error when starting up Pymol: freeglut (pymol): ERROR: Internal error visualInfo could not be retrieved from FBConfig in function fgOpenWindow I haven't been able to find much information on this error and was wondering if anyone had any experience with this. Have I not installed it properly? Is there another alternative to freeglut that might work? I would be very grateful for any help I can get. For further information, I performed both 1) a complete installation from source of freeglut and pymol AND 2) installed from a clean (empty) MacPorts, but both methods resulted in the above error when running Pymol. This error only occurs on the core i3 iMac. The GPU of the macbook is an AMD Radeon HD 6750M (+Intel HD Graphics 3000) while the iMac is an ATI Radeon HD 5670. Of course, the precompiled 1.3 version of pymol that I have does run find, but I am interested in using 1.5 on x11. Thank you in advance for any thoughts or advice. -Derek -- 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
