Re: [PyMOL] Re: macpymol beta 21 bug?
On Nov 4, 2005, at 12:38, Martin Montgomery wrote: Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB) with 10.4.2 and it works fine. After upgrading to 10.4.3 on that machine, everything is still fine. Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that still has a problem. I then booted into my back up clone which is at 10.4.2 and 99beta21 and 99beta25 work just fine. So the 64MB ATI cards look to be dodgy under 10.4.3 whilst the better spec ATI ones are OK. Will try and find a nVidia 64MB equipped mac for comparison. On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not noticed any change after updating to 10.4.3. I use a self-compiled PyMol 0.98. Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khin...@cea.fr -
[PyMOL] PyMol with MacOS 10.4
Are there other people out there who compile their own PyMol on the Mac and who have succeeded with MacOS 10.4 (Tiger)? After updating my Mac to Tiger, my PyMol installation doesn't work anymore: ~ pymol Traceback (most recent call last): File /usr/local/lib/pymol/modules/pymol/__init__.py, line 90, in ? import pymol File /usr/local/lib/pymol/modules/pymol/__init__.py, line 306, in ? import _cmd ImportError: Failure linking new module: /usr/local/lib/pymol/modules/ pymol/_cmd.so: Symbol not found: _gluCylinder Referenced from: /sw/lib/libglut.3.dylib Expected in: /usr/X11R6/lib/libGL.1.dylib I guess that something has changed in Apple's OpenGL libraries. My first reaction was to reinstall PyMol from sources in the same way as before (i.e. using the Distutils installation method and Fink's installation of Python 2.3). This fails pretty quickly due to some problem with the GLUT headers: In file included from layer0/os_gl.h:95, from layer2/RepNonbondedSphere.c:19: /sw/include/GL/glut.h:432: error: parse error before layer /sw/include/GL/glut.h:432: warning: function declaration isn't a prototype /sw/include/GL/glut.h:490: error: parse error before GLfloat /sw/include/GL/glut.h:490: warning: function declaration isn't a prototype ... This is perhaps not so surprising, because I didn't update Fink after updating to 10.4 - because that didn't work either. In fact, I am sufficiently fed up with the fragility of Fink that I would like to get rid of it entirely. So I thought I should try to use MacPython 2.4.1 (my everyday Python on the Mac) and Apple's OpenGL and GLUT frameworks. That required a few patches to the PyMol sources (the includes need to be changed from GL/... to OpenGL/...) and a bit of tweaking setup.py plus some manual intervention (Distutils doesn't handle -framework parameters), but I got an error-free compile pretty quickly. I can then even start PyMol, but it messes up my screen to the point that I need to go to sleep mode and then restart to get the Finder redrawn. And I am not even sure that my approach is reasonable, given that with MacPython I also use Aqua-Tk, and thus no X11 at all. Window handling ought to be different then. Does anyone have more ideas for getting this to work? I don't care which Python and which Tk I use, as long as I can add my own Python modules and get PyMol with NumPy support. Konrad.
Re: [PyMOL] Need testers for new MacPyMOL on Tiger
On Oct 14, 2005, at 17:50, Warren DeLano wrote: For cutting-edge Mac users, there is a new MacPyMOL for Tiger that integrates into a single window and links to the system Python instead of bringing its own copy (in part this is necessary preparation for Intel...). http://delsci.com/beta Please let me know how it works for you! It works fine on the few quick tests that I did. It looks fine as well, I much prefer the single window approach. Using the system Python is also a step in the right direction... now... if it also came with NumPy support compiled in... I might actually use it! Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khin...@cea.fr -
Re: [PyMOL] OSX: fink image libs, pymol and the command line
On Jun 13, 2005, at 16:42, Douglas Kojetin wrote: Thanks for the reply. Fink adds /sw/lib to the beginning of the DYLD_LIBRARY_PATH. Adding the following to the beginning of the shell script fixed the problem: DYLD_LIBRARY_PATH=/usr/local/lib It doesn't on my installation, which is about a year old and under 10.3. More importantly, it shouldn't. Meddling with DYLD_LIBRARY_PATH other than temporarily for debugging purposes is a good recipe to break a MacOS X system. Your problem with PyMOL is a perfect illustration. Did you consider submitting a bug report to the Fink team? Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khin...@cea.fr -
[PyMOL] Translating and rotating
Is it possible somehow to translate and rotate selections using the mouse? The translate and rotate commands are a bit cumbersome to do visual alignments. Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khin...@cea.fr -
