Re: [PyMOL] svn version number is ... ?
Hi, On Fri, Oct 20, 2017 at 11:37:56AM -0700, mathog wrote: > Pymol 2.0 was recently announced That announcement was misleading, while the subject indeed said that, what was actually announced was the proprietary Pymol *incentive* 2.0 release. The open source 2.0 release is apparently pushed back to early next year, this was also mentioned in the announcement. Michael -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ 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] Race condition when running scripts in stdin mode
Hi, on Debian, we got a bug report which looks like the bug reported here as well: http://sourceforge.net/p/pymol/bugs/130/ Unfortunately, there has been no discussion of this bug so far. There seems to be some race condition for scripts, does anybody a work-around, and/or fix for this? Or is this a platform-dependent (or even Debian/Ubuntu dependent) issue? Thanks, Michael -- Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical virtual servers, alerts via email sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o ___ 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] PyMOL 1.7.2 on Ubuntu 15.04
Hi, On Sat, Jun 13, 2015 at 09:38:40PM +1000, Brenton Horne wrote: set ray_opaque_background, 1 png Trimethoprim_img0003.png, dpi=500, ray=1, width = 4000, height = 2325 to render a structure of Trimethoprim I had loaded. While the rendering was somewhat better than that generated on 1.7.6, as it wasn't blank, it was far from perfect as the output image Trimethoprim_img0003.png was 1146px by 668px in size, not the 4000px by 2325px I specified in this script. Anyone know of any difference in 1.7.2 that would explain this besides a bug in the Deb package available for Ubuntu? I think it's a bug in Debian, we switched on prior=1 for batch files (see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=560412) which appears to have been ill-advised. If I add prior=0 to your script, it duly crashes with an out-of-memory error while trying to render 4000x2325 here - if I half your output image, I get a png, but it seems to be empty... Michael -- ___ 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] PyMOL v1.7 Released
Hi, On Tue, Jan 14, 2014 at 05:11:51PM -0600, Jason Vertrees wrote: We are happy to announce the release of PyMOL v1.7.0.0! Congrats! One thing though: the open-source splash image has not been updated for 1.7 and still says 1.6.x. Michael -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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] mutagenesis wizard data file loading
Hi, I noticed that the mutagenesis wizard uses PYMOL_PATH/data to locate the chempy sidechains, however, PYMOL_DATA would be more appropriate if the data is not installed alongside the pymol modules. The attached patch fixes this. Michael --- ./modules/pymol/wizard/mutagenesis.py.orig 2014-01-20 17:13:54.041469301 +0100 +++ ./modules/pymol/wizard/mutagenesis.py 2014-01-20 17:21:25.203791774 +0100 @@ -52,8 +52,8 @@ self.dep = default_dep -self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+ - /data/chempy/sidechains/sc_bb_ind.pkl) +self.ind_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+ + /chempy/sidechains/sc_bb_ind.pkl) self.load_library() self.status = 0 # 0 no selection, 1 mutagenizing self.bump_check = 1 @@ -217,8 +217,8 @@ def load_library(self): if self.dep == 'dep': if not hasattr(self,'dep_library'): -self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+ - /data/chempy/sidechains/sc_bb_dep.pkl) +self.dep_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+ + /chempy/sidechains/sc_bb_dep.pkl) def set_mode(self,mode): cmd=self.cmd -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ 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] PyMOL 1.6 pre-release announcement
Hi, On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote: The pre-release version of PyMOL 1.6 has been pushed to the open source repository on SourceForge. Besides several minor fixes and improvements, this version should complete the transition to shader-based rendering for all on-screen drawing. For non-integrated chipsets this typically means higher quality and quicker rendering. [...] As always, we welcome bug reports and positive feedback. Works fine for me so far, I noticed one thing though: In Wizard - Demo - Sculpting, the protein backbone mostly disappears if I rotate a bond, I just see the angle and the spheres, while the backbone is almost invisible. This does not seem to happen if I rotate around a bond at the outside of the protein. In 1.5.0.1, the appearance does not change between dragging atoms and rotating bonds which made it easier to rotate around bonds. This is with a Lenovo T400 and internal Intel Graphics. Michael -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ 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] PyMOL 1.6 pre-release announcement
Hi Stephen, On Mon, Mar 25, 2013 at 01:33:16PM -0400, Stephen P. Molnar wrote: On Sun, 24 Mar 2013 11:02:08 +0100 Thomas Holder thomas.hol...@schrodinger.com wrote: The pre-release version of PyMOL 1.6 has been pushed to the open source repository on SourceForge. Besides several minor fixes and improvements, this version should complete the transition to shader-based rendering for all on-screen drawing. For non-integrated chipsets this typically means higher quality and quicker rendering. Please also note that the URL of the SVN repository changed due to an upgrade of the SourceForge website: svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol As always, we welcome bug reports and positive feedback. Cheers, - The PyMOL Team at Schrödinger I managed to download the source code. There were a lot of warnings during the compilation and I got the following error message: usr/include/python2.7 -c layer1/TypeFace.c -o build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math -funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error: ft2build.h: No such file or directory compilation terminated. I don't have the faintest idea as to what supplies ft2build.h and would appreciate a point in the correct direction. It's shipped by the libfreetype development package. Michael -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ 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] PyMOL 1.6 pre-release announcement
Hi, On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote: The pre-release version of PyMOL 1.6 has been pushed to the open source repository on SourceForge. Besides several minor fixes and improvements, this version should complete the transition to shader-based rendering for all on-screen drawing. For non-integrated chipsets this typically means higher quality and quicker rendering. Please also note that the URL of the SVN repository changed due to an upgrade of the SourceForge website: svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol As always, we welcome bug reports and positive feedback. Great! Is there some pre-release version number assigned to that commit, like 1.6.0pre1 or 1.6.0rc1, assuming a final 1.6.0 will follow at some point? Best regards, Michael -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ 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] Improved Plugin Manager
On Mon, Apr 30, 2012 at 01:14:39PM -0400, Jason Vertrees wrote: This is just a quick note to let you know that as of revision 3997 PyMOL has an improved plugin/script manager. This system was written by Thomas Holder as part of his PyMOL Open Source Fellowship. Some new features include: * install script/plugin from the PyMOLWiki directly * install from a URL * install from a custom path on your file system * setup and install into multiple repositories * scripts/plugins requiring a citation will bring up a dialog telling you so (authors, please see the docs for information on how to require a citation) * ...and more. One thing which bugged me about scripts and the pymol wiki is that it has never been very clear about what license those scripts/plugin were under (PyMOL license, other open source license, all rights reserved...). Maybe this has changed in the meantime (I haven't looked for a while), but it might be nice if the plugin manager could help a bit by at least offering plugins/scripts to declare their license as part of some (presumably existing) meta-information. Michael -- 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] Improved Plugin Manager
Hi, On Wed, May 02, 2012 at 09:39:59AM -0400, Jason Vertrees wrote: Thanks for this feedback. Since the inception the Script Library on the PyMOLWiki the policy is that all deposited scripts are open-source: http://pymolwiki.org/index.php/Category_talk:Script_Library#Policy. This link is Policy from the PyMOLWiki Scripts page. Awesome! (also about the meta-information in the plugin manager) Michael -- 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] Intel Video - Please Respond
Hi, On Mon, Apr 09, 2012 at 11:01:35AM -0400, Jason Vertrees wrote: The latest commit (3995) should fix this for the Intel card. Try pulling the latest (3996) from the open source branch. That worked splendidly, I am uploading pymol-1.5.0.1 with some subversion changesets to Debian now. Are you going to roll/upload a 1.5.0.4 version with those changes? That would be great. Or does the addition of the plugin manager mean subversion is now en route to 1.6 or 1.5.1? Many thanks, Michael -- 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] Intel Video - Please Respond
Hi, On Thu, Apr 05, 2012 at 08:01:11AM -0400, Jason Vertrees wrote: Due to the number of problems that arise when rendering on Intel video cards, we're going to automatically disable new rendering features if an Intel video card is detected. You will be able to use PyMOL, but with the older, slower, uglier rendering. Also, you can override this autodetection by manually setting use_shaders to 1 and sphere_mode to 9. The Intel Express and Intel HD chipsets are the worst offenders, but a review also indicated others are problematic as well. If someone has an Intel card that works perfectly and renders nicely with shaders, please let me know what card it is. To do this, just start PyMOL and copy these lines into an email for me: This Executable Build integrates and extends Open-Source PyMOL 1.5.0.3. Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: XXX GL_RENDERER: XXX GL_VERSION: XXX where XXX will vary based on your card. We will attempt to more finely detect which Intel cards are good and which are bad so that we can still deliver good performance to those whose video cards can handle it. On my Thinkpad T42 with a Radeon R300 (RV350 4E50), pymol-1.5.0.1 segfaults when I run the Representations Demo: Detected OpenGL version prior to 2.0. Shaders and volumes unavailable. OpenGL graphics engine: GL_VENDOR: DRI R300 Project GL_RENDERER: Mesa DRI R300 (RV350 4E50) 20090101 x86/MMX/SSE2 TCL DRI2 GL_VERSION: 1.5 Mesa 7.7.1 Segmentation fault On my Tinkpad T400 with Mobile Intel GM45 Express, I see only lines, mesh and dots in the Representations Demo, and a couple of unsupported IR in fragement shader 13 messages: Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: Tungsten Graphics, Inc GL_RENDERER: Mesa DRI Mobile Intel® GM45 Express Chipset GEM 20091221 2009Q4 GL_VERSION: 2.1 Mesa 7.7.1 Detected 2 CPU cores. Enabled multithreaded rendering. unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 unsupported IR in fragment shader 13 This is both on Debian stable. So I have held off uploading pymol-1.5 to unstable for now and just put it into experimental. Michael -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ 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] Autodock plugin
Hi, On Tue, Feb 16, 2010 at 08:26:00PM +0100, Daniel Seeliger wrote: take a look into ~/.ADplugin/pymol_autodock_plugin.conf and set the path to the autodocktools scripts correctly. Then the plugin should find them. Speaking of which, I was just taking a look about including your autodock plugin (it looks really nice) into the official Debian/Ubuntu packages, however, it depends on the non-free autodocktools scripts as far as I can tell. While autodocktools is shipped in Debian non-free, we will not be able to fully integrate this easily in order to keep pymol in Debian proper. Is there any work-around to get a fully free autodock plugin solution and/or is it planned to reimplement the missing parts from autodocktools in the autodock pymol plugin or maybe pymol itself? Thanks, Michael -- ___ 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] pymol and freemol
On Thu, Apr 15, 2010 at 11:53:06AM -0600, Maia Cherney wrote: I downloaded apbs and pdb2pqr, but I don't know how to install them on my ubuntu 9.04. Is it possible to make an easy to install release? For now, could you please send me the instruction. apbs is available in Ubuntu (via Debian) since at least hardy. We tried to get pdb2pqr into Debian (and thus, Ubuntu), but it was rejected due to unclear licensing/copyright status and other issues. We will hopefully try again, but it will obviously be too late for lucid. Michael -- 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
[PyMOL] subversion revision for 1.2?
Hi, maybe I missed it in the announcement, but what is the subversion revision for 1.2? I can't find a tag in the repo, nor any obvious commit message. Thanks, Michael -- ___ 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] GIT'r Done
On Mon, May 04, 2009 at 11:09:06PM +0200, Justin Lecher wrote: Waren points me to the fact, that it might be good to explain how to work with the github. I wrote a little howto, but there are alot more in the web, which can be easily be found via google. I think nonetheless it is a good starting point to contribute to our script repo. Not sure whether it has been done yet, but it would also be good to encourage script/plugin authors to properly copyright and license their code, preferably with the same license that pymol has. That way, the scripts/plugins could also potentionally shipped by distributions as pymol-addons. Michael -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] image on pymol.org
On Thu, Mar 19, 2009 at 05:24:41PM +0100, Justin Lecher wrote: some time ago I asked for the script you used for the image on pymol.org and I lost it somewhere. Could you post it again, please? If you mean the main image at the top, you can probably get the effect using the QuteMol Like section at the bottom of http://www.pymolwiki.org/index.php/Gallery Michael
Re: [PyMOL] python/pymol malfunction on new Ubuntu installation
On Tue, Jul 22, 2008 at 03:38:53PM +0100, Daniel Rigden wrote:
First let me confess that my problem does not just involved pymol.
However, it is hampering my use of pymol amongst other things and there
must be many python experts who read this list.
My problem, on a completely fresh Ubuntu 8.04 install, is that python
can find modules when asked to import them. So
Are you saying python cannot find any modules? In that case, the
problem does not sound pymol specific at all.
export PYMOL_PATH=/var/lib/python-support/python2.5/pymol/
export PYTHONHOME=/usr/lib/python2.5
python2.5 ${PYMOL_PATH}/__init__.py
gives me
'import site' failed; use -v for traceback
Traceback (most recent call last):
File /var/lib/python-support/python2.5/pymol//__init__.py, line 109,
in module
import threading
ImportError: No module named threading
Are you running the Ubuntu pymol package, or a self-compiled one? If
the former, does simply running pymol work or not?
Michael
Re: [PyMOL] chempy documentation
On Mon, Nov 20, 2006 at 10:27:48AM -0800, DeLano Scientific wrote: My preference would be for a fast, clean, back-end cheminformatics library with a simple C API that could be exposed to and interporate with Python, Java, C, C++, SQL, and .NET. Several proprietary examples of this design exist, and they are all quite successful. We need an open-source equivalent! Well, openbabel tries to do that but could need more help from the community maybe. (It is C++ rather than C, though, but has binding for python and other languages). Michael
Re: [PyMOL] debian: error in opening pymol
On Fri, Jun 09, 2006 at 12:30:01PM +0530, Arvind Marathe wrote: Error: unable to initialize plugin 'apbs_tools'. I don't think this is the default, did you install over a local version or something? Michael
Re: [PyMOL] Warning: Nvidia 6111 drivers for linux
On Wed, Oct 13, 2004 at 06:12:11PM +0200, peter.du...@cellbio.unige.ch wrote: According to a thread on PyKDE, The tls (thread local storage) stuff only works if you are running a tls-enabled glibc on a 2.6 kernel, and when installing nvidia-glx, you are normally asked by debconf on what to use. This suggests anyone running the new nvidia drivers on a 2.4.x kernel may encounter this problem. Admittedly, I haven't tested them on a 2.6.x kernel, so I can't be sure the problem doesn't occur there either. AFAIK, Debian's glibc uses tls/nptl only on Linux-2.6, not on Linux-2.4. So using a 2.6 kernel should be fine. However, I do not have Nvidia hardware to test this. cheers, Michael
Re: [PyMOL] PyMOL tutorial (moved and slightly updated)
On Fri, Aug 20, 2004 at 09:37:00AM -0700, chuit...@interchange.ubc.ca wrote: In any case, you ask a useful question: I too would like to know what license, if any, is granted by the tutorial's authors. If released under an appropriate license, it could be modified for Linux/Unix/MacOSX users, and used in course material, distributed with PyMOL, etc. I haven't really thought about licenses for releasing the tutorial under, I'm not familiar with the different types of licenses. I would like to see the tutorial treated as the program Having it under the same copyright license as pymol seems like a good idea to me. where you can't sell it or claim you created it. Why do you think pymol cannot be sold? The copyright license does not seem to imply this[1], and such a restriction would render pymol not Open Source. Warren, can you tell us what you think on this? Michael [1] Permission to use, copy, modify, distribute, and distribute modified versions of this software and its documentation for any purpose and without fee is hereby granted [...]
Re: [PyMOL] PyMOL tutorial (moved and slightly updated)
On Fri, Aug 13, 2004 at 08:34:17AM -0500, D. Joe Anderson wrote: I have a small tutorial for getting started with PyMOL and I have no idea if people actually use it... Anyway, our server has changed and the webpage has been moved to: http://www.microbiology.ubc.ca/eltis/pymol/ Can you tell me what license this tutorial is under? I guess I would include it in the Debian package if it is compatible with the Debian Free Software Guidelines. Michael
Re: [PyMOL] PyMOL-Debian-linux x86 package
On Thu, Jul 29, 2004 at 04:44:32PM +0200, Vladimir Daric wrote: Hello I made a Debian package for Pymol (only for x86 arch). Here are instructions for how to get it and how to use it. There are two ways to install pymol from a Debian package : The automatic way: add this line in your /etc/apt/sources.list file or ask your sys admin to do so. deb http://debian.acidspace.net custom/ The advantage of this method is that you will always have an up to date version of PyMOL What are the advantages over running the official Debian pymol package? Michael
Re: [PyMOL] GLX error
On Tue, May 11, 2004 at 05:18:37PM -0500, rbax...@uchicago.edu wrote: I am running Pymol 0.95 on Mandrake Linux 10.0, or at least I was until today. Yesterday I performed a standard update on the system, and today pymol crashes with the following error: GLUT: Fatal Error in pymol.exe: OpenGL GLX extension not supported by display: :0.0 PyMOL: abrupt program termination. That looks like a problem with your XServer not supporting OpenGL/GLX/3D stuff in general, not something specific to pymol. Try running 'glxgears' or any other OpenGL application, does that work? Michael
Re: [PyMOL] installation problem
On Thu, Apr 15, 2004 at 10:27:32AM -0400, Shu-Hsien Sheu wrote: [mfitz...@man local]$ sudo rpm -V pymol-0.95-1 package pymol-0.95-1 is not installed Just a shot in the dark, but are you sure the package is called pymol-0.95-1 and not just pymol? Michael
Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
On Thu, Feb 19, 2004 at 12:24:53PM +0100, Michael Banck wrote: On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote: For me PyMol on SuSE 8.2 crashed always when raytracing a line element. That seems to be identical to Debian Bug #229080 (http://bugs.debian.org/229080) The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I got the same crash with gcc 3.3.1, but not with gcc 2.95. I have not tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only) solved the problem for me. See PyMol bugreport 806361. Thanks for the information, I will see whether that helps on Debian, too. For the record, the current gcc-3.3 in Debian testing/unstable seems to work fine again for rendering sticks and lines, so I uploaded 0.95-1 using the standard gcc on all architectures again. Michael
Re: [PyMOL] 64-bit
On Mon, Mar 08, 2004 at 10:55:15AM -0800, Warren DeLano wrote: It has been a while since anyone's tried to build/run PyMOL on a 64-bit system...it may not currently be 64-bit clean. For the record, 64 bit Debian packages are built on alpha and ia64 (I believe the other architectures are currently 32bit) and the test suite passes at least. I've had a few bug reports from an alpha user (Helge Kreutzmann), though, but they are quite minor (see http://bugs.debian.org/pymol). cheers, Michael
Re: [PyMOL] Ray Tracing Crash
On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote: Regarding my problems raytracing on my debian/testing machine. What is the exact version of the pymol .deb you're using? 0.93-2? What architecture are you running on? i386 or something else? Do you use pymol's internal raytracer, or povray? Does the raytracing-demo from the demo-menu work? thanks, Michael
Re: [PyMOL] Ray Tracing Crash
On Tue, Jan 20, 2004 at 10:52:17PM -0800, Morri Feldman wrote: My debian/testing system at home also has trouble ray tracing, especially with sticks. When it fails I get a segmentation fault. What architecture are you running on? i386 or something else? Do you use pymol's internal raytracer, or povray? Is my problem at home also due to an unpatched glibc? glibc in debian/testing should be fairly recent. Perhaps it suffers from a different bug, but the one described earlier should be fixed by now, if it ever pertained to Debian. The error message is: /usr/bin/pymol: line 7: 32460 Segmentation fault python /usr/lib/python2.3/site-packages/pymol/__init__.py $* As Warren said, a detailed description of the scene you were trying to raytrace would be welcomed. Michael
Re: [PyMOL] pyopengl broken?
Did somebody (Warren?) look into this? Could anybody reproduce it (i.e. running examples/devel/gl01.py)? Or is this just a problem on Debian GNU/Linux? thanks, Michael This was the text of the bug report: --8-- On Fri, Oct 03, 2003 at 11:53:53AM +0200, Gabor E. Tusnady wrote: I would like to use pymol with python-opengl script. On my laptop I use pymol-0.86 width redhat 8.0. This package contains a lot of python example script, for example example/devel/gl01.py script. Running this script I have got a simple coordinate system displayed on the screen (the script is attached), while pymol reports: OpenGL based graphics front end: GL_VENDOR: Mesa project: www.mesa3d.org GL_RENDERER: Mesa GLX Indirect GL_VERSION: 1.3 Mesa 4.0.4 Executive: object gl01 created. Using the debianized version of pymol-0.90 with debian-sid on my workstation, I have got the following error message: OpenGL based graphics front end: GL_VENDOR: NVIDIA Corporation GL_RENDERER: GeForce2 MX/AGP/SSE GL_VERSION: 1.4.0 NVIDIA 44.96 Adapting to GeForce hardware... Detected 2 CPUs. Enabled multithreaded rendering. Traceback (most recent call last): File /usr/lib/python2.3/site-packages/pymol/parser.py, line 203, in parse execfile(args[nest][0],pymol_names,pymol_names) File gl01.py, line 1, in ? from pymol.opengl.gl import * File /usr/lib/python2.3/site-packages/pymol/opengl/gl/__init__.py, line 32, in ? import _opengl ImportError: /usr/lib/python2.3/site-packages/pymol/opengl/gl/_opengl.so: undefined symbol: glTexGeniv I don't know whether I have not installed something, or it is a bug in the debianized pymol-0.90, or this error come from the NVIDIA opengl driver. I'm really happy, if you can help me resolving this discrepancy. Gabor --8-- On Sat, Oct 04, 2003 at 11:11:05PM +0200, Michael Banck wrote: Hi, I've got a bug on pyopengl (http://bugs.debian.org/214026). Seems the immeadiate fix is --- pymol-0.90.orig/setup.py +++ pymol-0.90/setup.py @@ -32,7 +32,7 @@ else: inc_dirs=[layer0,layer1,layer2,layer3,layer4,layer5] libs=[GL,GLU,glut,png] - pyogl_libs = [] + pyogl_libs = [GL,GLU,glut,png] lib_dirs=[/usr/X11R6/lib] def_macros=[(_PYMOL_MODULE,None), # (_PYMOL_NUMPY,None), Is there a reason why these libraries are not defined in pyogl_libs? With that fix, examples/devel/gl01.py works fine. gl02.py gl03.py still fail though, with this error message: Executive: object gl02 created. Traceback (most recent call last): File gl02.py, line 39, in __call__ glVertexPointer(3,0,self.vert) NameError: global name 'glVertexPointer' is not defined Digging a bit into contrib/pyopengl[1], I found that glVertexPointer will only get exported when NUMERIC is defined. As you can see from the patch above, _PYMOL_NUMPY is not defined and thus neither will be NUMERIC. If I uncomment that line above, I get this error while trying to build pymol: building 'pymol.opengl.glu._glu_num' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -D_PYMOL_MODULE -D_PYMOL_NUMPY -D_HAVE_LIBPNG -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/python2.3 -c contrib/pyopengl/_glu_nummodule.c -o build/temp.linux-i686-2.3/contrib/pyopengl/_glu_nummodule.o In file included from contrib/pyopengl/_glu_nummodule.c:8: contrib/pyopengl/_glumodule.c:660:25: arrayobject.h: No such file or directory In file included from contrib/pyopengl/_glu_nummodule.c:8: contrib/pyopengl/_glumodule.c: In function `py_glu_Build2DMipmaps': contrib/pyopengl/_glumodule.c:737: error: `PyArrayObject' undeclared (first use in this function) contrib/pyopengl/_glumodule.c:737: error: (Each undeclared identifier is reported only once contrib/pyopengl/_glumodule.c:737: error: for each function it appears in.) contrib/pyopengl/_glumodule.c:737: error: `ap' undeclared (first use in this function) contrib/pyopengl/_glumodule.c:754: warning: implicit declaration of function `PyArray_Check' contrib/pyopengl/_glumodule.c:755: error: syntax error before ')' token contrib/pyopengl/_glumodule.c:758: error: syntax error before ')' token contrib/pyopengl/_glumodule.c: At top level: contrib/pyopengl/_glumodule.c:132: warning: `GLUquadricType' defined but not used error: command 'gcc' failed with exit status 1 make: *** [install] Error 1 Finally, when I add HAVE_NUMERIC_ARRAYOBJECT_H to the defines in setup.py, pymol compiles fine[2] but gl02.py still fails: Executive: object gl02 created. Traceback (most recent call last): File gl02.py, line 39, in __call__ glVertexPointer(3,0,self.vert) _opengl_num.error: Can't convert this type of array! That's where I stopped debugging stuff, can anybody help me? thanks, Michael [1] btw, is this the standard pyopengl module? Why is it shipped
Re: [PyMOL] searchable archive?
On Mon, Jan 05, 2004 at 11:11:15AM -0800, Mark Wilke wrote: Is there a searchable archive of this newsgroup? There's a browsable archive at http://sourceforge.net/mailarchive/forum.php?forum_id=60 Dunno whether one can search it, too. Michael
Re: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (almost working)
On Wed, Dec 17, 2003 at 06:00:44PM -0500, Michael George Lerner wrote: I've gotten the code much closer to working. Also, I think it's factored well enough that most of it should be non-GPL-contaminated. After I actually get it working completely, I'll email the APBS folks to see if they care about licensing issues. What's the problem? Both PyMOL and APBS are licensed under the GPL so I see no problems there. Do you imply that you want to license your own code under a non-GPL-compatible license? Why? Michael
Re: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (almost working)
On Thu, Dec 18, 2003 at 12:26:48AM +0100, Michael Banck wrote: On Wed, Dec 17, 2003 at 06:00:44PM -0500, Michael George Lerner wrote: I've gotten the code much closer to working. Also, I think it's factored well enough that most of it should be non-GPL-contaminated. After I actually get it working completely, I'll email the APBS folks to see if they care about licensing issues. What's the problem? Both PyMOL and APBS are licensed under the GPL so I see no problems there. Well, pymol isn't obviously. Note to self: Don't post about licensing stuff after an evening of mulled wine. Still, as long as the pymol license is GPL-compatible (which I believe it is, but I'm no lawyer), and the additional code is licensed under the same license, it should be alright, as I understand it. sorry, Michael
Re: [PyMOL] gtk+ gui
On Sun, Dec 14, 2003 at 10:27:35PM +, Ramanan Selvaratnam wrote: On Sun, 2003-12-14 at 19:49, Ben Cornett wrote: I'm not much of a graphic artist, so I will probably stay away from creating any custom button pixmaps. I will be happy to look into this although it is not clear what is meant by 'Gnome like'. Well, GNOME applications have a consistent set of icons for common stuff like 'save', 'load' 'copy', etc., but also for 'zoom' and stuff like that. What would be needed are icons in a similar style for molecular-related stuff. Like drawing bonds, picking atoms, and so on. Some/much of this could be shared along ghemical, gchempaint and pymol/gtk (but no work has been done yet; the custom icons provided by ghemical do not look GNOMEish at all) Michael
[PyMOL] pyopengl broken?
Hi, I've got a bug on pyopengl (http://bugs.debian.org/214026). Seems the immeadiate fix is --- pymol-0.90.orig/setup.py +++ pymol-0.90/setup.py @@ -32,7 +32,7 @@ else: inc_dirs=[layer0,layer1,layer2,layer3,layer4,layer5] libs=[GL,GLU,glut,png] - pyogl_libs = [] + pyogl_libs = [GL,GLU,glut,png] lib_dirs=[/usr/X11R6/lib] def_macros=[(_PYMOL_MODULE,None), # (_PYMOL_NUMPY,None), Is there a reason why these libraries are not defined in pyogl_libs? With that fix, examples/devel/gl01.py works fine. gl02.py gl03.py still fail though, with this error message: Executive: object gl02 created. Traceback (most recent call last): File gl02.py, line 39, in __call__ glVertexPointer(3,0,self.vert) NameError: global name 'glVertexPointer' is not defined Digging a bit into contrib/pyopengl[1], I found that glVertexPointer will only get exported when NUMERIC is defined. As you can see from the patch above, _PYMOL_NUMPY is not defined and thus neither will be NUMERIC. If I uncomment that line above, I get this error while trying to build pymol: building 'pymol.opengl.glu._glu_num' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -D_PYMOL_MODULE -D_PYMOL_NUMPY -D_HAVE_LIBPNG -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/python2.3 -c contrib/pyopengl/_glu_nummodule.c -o build/temp.linux-i686-2.3/contrib/pyopengl/_glu_nummodule.o In file included from contrib/pyopengl/_glu_nummodule.c:8: contrib/pyopengl/_glumodule.c:660:25: arrayobject.h: No such file or directory In file included from contrib/pyopengl/_glu_nummodule.c:8: contrib/pyopengl/_glumodule.c: In function `py_glu_Build2DMipmaps': contrib/pyopengl/_glumodule.c:737: error: `PyArrayObject' undeclared (first use in this function) contrib/pyopengl/_glumodule.c:737: error: (Each undeclared identifier is reported only once contrib/pyopengl/_glumodule.c:737: error: for each function it appears in.) contrib/pyopengl/_glumodule.c:737: error: `ap' undeclared (first use in this function) contrib/pyopengl/_glumodule.c:754: warning: implicit declaration of function `PyArray_Check' contrib/pyopengl/_glumodule.c:755: error: syntax error before ')' token contrib/pyopengl/_glumodule.c:758: error: syntax error before ')' token contrib/pyopengl/_glumodule.c: At top level: contrib/pyopengl/_glumodule.c:132: warning: `GLUquadricType' defined but not used error: command 'gcc' failed with exit status 1 make: *** [install] Error 1 Finally, when I add HAVE_NUMERIC_ARRAYOBJECT_H to the defines in setup.py, pymol compiles fine[2] but gl02.py still fails: Executive: object gl02 created. Traceback (most recent call last): File gl02.py, line 39, in __call__ glVertexPointer(3,0,self.vert) _opengl_num.error: Can't convert this type of array! That's where I stopped debugging stuff, can anybody help me? thanks, Michael [1] btw, is this the standard pyopengl module? Why is it shipped with pymol? If it's modified, can't the changes be sent upstream so that a fork is not necessary? (I haven't checked at all, these thoughts just occured to me now) [2] when byte-compiling, I get this warning with python2.3: /usr/lib/python2.3/site-packages/pymol/opengl/gl/glconst.py:438: FutureWarning: hex/oct constants sys.maxint will return positive values in Python 2.4 and up GL_CLIENT_ALL_ATTRIB_BITS = 0x
Re: [PyMOL] energy minimisation in python
On Thu, Sep 18, 2003 at 05:48:56PM +0100, Paulo Martel wrote: On Thu, 2003-09-18 at 14:36, Alan Wilter Sousa da Silva wrote: And about Ghemical project? Ghemical is not a Python project, it is a GNU GPL package written in C FWIW, ghemical is written in C++. using the Gtk toolkit, with the GtkGlarea widget providing OpenGl accelerated graphics in a Gtk window. It provides much the same functionality as Pymol (but can already do MD and QC calculations), so there wouldnt be much point in trying to interface with it. Yes. Michael
Re: [PyMOL] pymol problems with Mandrake 9.1
On Tue, Sep 09, 2003 at 06:40:37AM -0700, Warren L. DeLano wrote: RPM doesn't look at the file system (AFAIK), it looks in the RPM database for the names of (Redhat-specific) known dependency packages. AFAIK, rpms can also declare file-dependencies. Whether this is a good thing or not, I don't know. Michael
Re: [PyMOL] RE: PyMOL v0.88 Released
On Thu, Jun 05, 2003 at 02:35:24PM +0100, Andy Calder wrote: Well I'm fairly new to the fink / X11 way of using PyMOL on a Mac but I self updated fink to version: 0.13.0 (Distribution version: 0.5.2.cvs) Without a hitch and did an update-all but fink reports pymol remains at 0.86-3. Just like with Debian, I guess the new release needs to be integrated/packaged into/for fink before you can upgrade to it. I've never used fink though, so I could be mistaken. Michael
Re: [PyMOL] April PyMOL News: Kick-off, OpenGL Cards, Unix
Hi,
On Sat, Apr 19, 2003 at 12:11:12PM -0800, Warren L. DeLano wrote:
Mac, Linux, and Windows will remain the primary PyMOL platforms, but I
welcome your feedback on the following question: How important is it
that PyMOL run well (be tested and released for use) under traditional
Unix operating systems? Such as:
1) IRIX (6.5.x)
2) Solaris (7, 8, or 9)
3) Tru64 Unix (for the Alpha)
4) and any other Unix platforms (AIX?)
While PyMOL sponsorship will likely provide enough funding to cover
inexpensive Mac and PC hardware, Unix workstations are simply not
affordable for us, given our limited means. It is not just the cost of
the hardware (which can sometimes be found cheap), but those darn
compiler licenses and hardware support expenses which really get us!
AFAIK gcc is available for most if not all those Unices, too, isn't it?
Well, a quick google search seems to say yes.
And as long as you program POSIX/cross-platform, there should not be a
big problem. Perhaps using auto{conf,make} might help a bit, dunno.
Pymol at least *compiles* under a vast amount of processor
architectures, if only under Linux:
http://buildd.debian.org/build.php?arch=pkg=pymol
Nothing wrong with testing your code on as much platforms as possible of
course :)
cheers,
Michael
Re: [PyMOL] improving interoperability between python molecule toolkits
On Thu, Dec 12, 2002 at 10:33:47AM +, Jules Jacobsen wrote: I completely agree here, an integrated total platform would be immensely useful. I think that the problem is not necessarily all that far from a solution- currently there is a collaborative computing project for NMR (CCPN) http://www.bio.cam.ac.uk/nmr/ccp/ Looks interesting, but I couldn't find a License. What's the License for CCPN, please? thanks, Michael
Re: [PyMOL] improving interoperability between python molecule toolkits
Hi again, Ok, so the license is available at http://www.bio.cam.ac.uk/nmr/ccp/project/about_ccpn/licensing/licensing.html Unfortunately, this looks quite incompatible to the GPL: (2) Conditions for DISTRIBUTION of SOFTWARE to MEMBERS (2.1) An individual or ORGANISATION must be a MEMBER of CCPN in order to receive any SOFTWARE from CCPN, and must adheretotheMEMBERSHIP,DISTRIBUTIONand RE-DISTRIBUTION rules. Under these conditions, any previously DISTRIBUTED SOFTWARE may be used in for the lifetime of the SOFTWARE even if MEMBERSHIP of CCPN lapses. (4) Conditions for MEMBERSHIP of CCPN MEMBERSHIP for an individual or ORGANISATION shall be based on registration and payment of annual fee as required and detailed below. The annual fee may be reviewed from time to time. The current scale of fees are as follows: a. individuals and not for profit ORGANISATIONs - nil b. ORGANISATIONs with annual turnover less than 20 pounds Sterling - nil c. ORGANISATIONs with annual turnover between 20 pounds Sterling and 1 million pounds Sterling - 1000 pounds Sterling d. ORGANISATIONs with annual turnover larger than one million pounds Sterling - 7000 pounds Sterling This makes the software not freely distributable, IMHO Furthermore, it violates one of the definitions of Open-Source Software, namely 'No Discrimination Against Persons or Groups', see http://www.opensource.org/docs/definition.php. Please correct me if I'm wrong. thanks, Michael
