Re: [PyMOL] Query variable value
PyExperts: When inside PyMOL, how do I find out the value of a variable without using 'set'? For example, I can type: set specular, 1 and then I know, specular = 1. But how do I find out specular's (or ANY variable's) value without changing it? Thanks, Olivier Hello Olivier, For PyMOL variables, defined with set variable_name,variable_value , you can get it with get variable_name For other variables (Python variables), defined like it: variable_name=variable_value you can get it with print variable_name or use it simply with variable_name I hope this will help you. -- Sébastien Moretti http://www.igs.cnrs-mrs.fr/ CNRS - IGS 31 chemin Joseph Aiguier 13402 Marseille cedex
Re: [PyMOL] PyMOL featured on Apple Store site?
Hi Warren and PyMol users, Warren DeLano wrote: They've got MacPyMOL two places on this site: http://www.apple.com/powermac/graphics.html Be sure to note the explicit mention of stereo 3D in a window down near the bottom. this is really great - stereo was the most missing features for me with Macs! But what about stereo support of the monitors? Would this already work with Apple's TFT screens? Are their refresh rates fast enough for that, or does one still has to buy a CRT monitor? Amazing! The Stereo 3D Matters to Me campaign actually worked. Apple really *is* serious about meeting our needs. Yes, apparently. Gives a good feeling with Apple. Cheers, Dirk. -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
Re: [PyMOL] PyMOL featured on Apple Store site?
Please, forget my questions about stereo-capable monitors - Warren has already answered my questions in another e-mail (that I read too late). Regards, Dirk. Dirk Kostrewa wrote: Hi Warren and PyMol users, Warren DeLano wrote: They've got MacPyMOL two places on this site: http://www.apple.com/powermac/graphics.html Be sure to note the explicit mention of stereo 3D in a window down near the bottom. this is really great - stereo was the most missing features for me with Macs! But what about stereo support of the monitors? Would this already work with Apple's TFT screens? Are their refresh rates fast enough for that, or does one still has to buy a CRT monitor? Amazing! The Stereo 3D Matters to Me campaign actually worked. Apple really *is* serious about meeting our needs. Yes, apparently. Gives a good feeling with Apple. Cheers, Dirk. -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
Re: [PyMOL] Query variable value
Olivier, But how do I find out specular's (or ANY variable's) value without changing it? I wrote a little extension called 'grepset' that does what you want and it is great for finding out about other settings. It is available at the pymol wiki site: http://www.pymolwiki.org/index.php/Grepset Cheers, Zac
[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.
[PyMOL] New plugin
Hi, I've develop a new extension (plug in) for PyMOL : dbSearch. It enable PyMOL to search a molecular structure (MDL mol format) by her name into a database (MySQL) and display it in PyMOL. You can find the archive there: http://pansanel.adlp.org/chemistry/resources/pymol_dbsearch.tgz Cheers, Jerome Pansanel
[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.
[PyMOL] Re: Apple's tk and pymol
I just fired up pymol installed via fink using Python compiled against a Framework build of Python that in turn is build against the TCL TK framework. your either get interaction with the GLUT GUI, or the Tcl/Tk user interface, but not both : (. I can't reproduce the problem, i.e., both guis work ok for me. Sorry if I am missing something obvious. Otherwise, it might work. Bill William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax) url: http://chemistry.ucsc.edu/~wgscott/
RE: [PyMOL] Re: Apple's tk and pymol
Bill, Are you using Framework GLUT or Fink/Xll GLUT? The latter might work because X11 actually runs as a separate process and has its own event queue which feeds into GLUT. If the former is working for you, then please provide some more specifics regarding OS version, etc. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of William Scott Sent: Thursday, October 20, 2005 4:28 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Re: Apple's tk and pymol I just fired up pymol installed via fink using Python compiled against a Framework build of Python that in turn is build against the TCL TK framework. your either get interaction with the GLUT GUI, or the Tcl/Tk user interface, but not both : (. I can't reproduce the problem, i.e., both guis work ok for me. Sorry if I am missing something obvious. Otherwise, it might work. Bill William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax) url: http://chemistry.ucsc.edu/~wgscott/ --- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Re: Apple's tk and pymol
Hi Warren: The display window is actually X so I assume it must be fink/X11 glut. Sorry I omitted that. Bill Are you using Framework GLUT or Fink/Xll GLUT? The latter might work
