[PyMOL] Pymol crashing when executed on Windows 7_64Bit
Hi, We have some computers with Windows 7, 64 Bit installed. When invoking Pymol (incentive) Version 1.4 or 1.4.1 it crashes immediately giving the following error output: Faulting application name: pymol.exe, version: 0.0.0.0, time stamp: 0x4d85901b Faulting module name: pymol.exe, version: 0.0.0.0, time stamp: 0x4d85901b Exception code: 0xc005 Fault offset: 0x0001ed86 Faulting process id: 0x25a8 Faulting application start time: 0x01cc2506140daba7 Faulting application path: Q:\apps\pymol\1.4\pymol.exe Faulting module path: Q:\apps\pymol\1.4\pymol.exe Report Id: 54d45971-90f9-11e0-9553-001d60e011a1 This is independent of using the 64- or 32-bit version of pymol. We had to revert to Version 1.2, which is working. Does anyone have an advice? Regards, Joachim Greipel -- Dr. rer. nat. Joachim Greipel Med. Hochschule Hannover Biophys. Chem. OE 4350 Carl-Neuberg-Str. 1 30625 Hannover Germany Fon: +49-511-532-3718 Fax: +49-511-532-8924 smime.p7s Description: S/MIME cryptographic signature -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-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] surface display in new pymol
On versions 1.3, 1.4, I cannot display a surface of anything that is not in the standard dictionary. For example trying to draw a surface of tRNA shows gaps in the modified bases. Drawing a surface of a ligand such as an antibiotic similarly is just a blank. This was not true in the older versions, e.g. 0.98 or 0.99. I'm using Mac OS X 10.6.7 Does anyone else have this problem and is there a way around it? Thanks, Venki -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-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] surface display in new pymol
Hi Venki, You need to first issue the following command: set surface_mode, 1 Best, Luca On Jun 8, 2011, at 17:05 , V. Ramakrishnan wrote: On versions 1.3, 1.4, I cannot display a surface of anything that is not in the standard dictionary. For example trying to draw a surface of tRNA shows gaps in the modified bases. Drawing a surface of a ligand such as an antibiotic similarly is just a blank. This was not true in the older versions, e.g. 0.98 or 0.99. I'm using Mac OS X 10.6.7 Does anyone else have this problem and is there a way around it? Thanks, Venki -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-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 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-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] Problem with distutils build 3951 on Ubuntu Lucid 10.04 : X Error of failed request: BadRequest
Hi I just build the svn build of pymol 3951 on 64 bit Ubuntu Lucid . I first had to installing libglew and libglew-dev after which the build progressed fine , but when I run the built pymol I get the following errors ( below) and pymol does not launch. I tried with a clean repo checked out from svn and get the same error. I also tried the makefile route but get a cetypes.h include error. I know the distutils way is the recommended approach.. Any help to resurrect my pymol will be greatly appreciated. Thanks Hari hari@hari:~/pymol-read-only/trunk/pymol$ ./pymol PyMOL(TM) Molecular Graphics System, Version 1.4.1. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at http://www.pymol.org;. Enter help for a list of commands. Enter help command-name for information on a specific command. Hit ESC anytime to toggle between text and graphics. Detected OpenGL version 2.0 or greater. Shaders available. X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (GLX) Minor opcode of failed request: 169 () Serial number of failed request: 46 Current serial number in output stream: 46 PyMOL: abrupt program termination. Thanks hari -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-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] Problem with distutils build 3951 on Ubuntu Lucid 10.04 : X Error of failed request: BadRequest
Hari, Hit ESC anytime to toggle between text and graphics. Detected OpenGL version 2.0 or greater. Shaders available. X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (GLX) Minor opcode of failed request: 169 () Serial number of failed request: 46 Current serial number in output stream: 46 This sounds like a driver problem. Can you run the 'glxgears' program? Does it give the same error? Do you have the latest driver installed? Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-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
