Re: [PyMOL] Problem with open source pymol
Thanks, Lina. It worked beautifully. On Wed, Dec 21, 2011 at 8:14 AM, lina lina.lastn...@gmail.com wrote: If you have fink, you can have an alternative way of installation. fink install pymol-py27 It works well. On Wed, Dec 21, 2011 at 4:19 AM, Lauren Porter lauren.pers...@gmail.com wrote: Pymol 1.3 is still available online, but it doesn't work with any versions of python greater than 2.5. If I try to install Pymol 1.4 doesn't work when I install it (problems with the GLEW library). I don't understand that problem either. It looks like it can't find GLEW, but I know that its path is included (see code below). I have never tried compiling pymol from source before, so I have never gotten it to work. And I reinstalled my GLUT library and rebuilt, but that did not fix the crashing problem in my original post. Any more suggestions? Thanks! ~Lauren ... warning: implicit declaration of function ‘glewInit’ layer0/ShaderMgr.c:173: error: ‘GLEW_OK’ undeclared (first use in this function) layer0/ShaderMgr.c:173: error: (Each undeclared identifier is reported only once layer0/ShaderMgr.c:173: error: for each function it appears in.) layer0/ShaderMgr.c:174: error: ‘GLEW_VERSION_2_0’ undeclared (first use in this function) layer0/ShaderMgr.c:185: warning: implicit declaration of function ‘glewGetErrorString’ ... 2011/12/19 Troels Emtekær Linnet tlin...@gmail.com Ok, maybe I am not the right person to ask. But. How did you get Pymol 1.3 ? The one in the subversion repo is 1.4.1 And it looks like you have python 2.5 I dont know if PyMOL needs python 2.7 Have you compiled before, where it worked? Best T Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 2011/12/19 Lauren Porter lauren.pers...@gmail.com Yes, I have GLUT installed (I'm using the framework), and I rerouted everything to make sure it was pointing to the right path. After doing that, I rebuilt and got a new error: Python 2.5.4 (r254:67916, Aug 1 2011, 15:52:49) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type help, copyright, credits or license for more information. import pymol Traceback (most recent call last): File stdin, line 1, in module File /Library/Python/2.5/site-packages/pymol/__init__.py, line 473, in module import _cmd ImportError: dlopen(/Library/Python/2.5/site-packages/pymol/_cmd.so, 2): Symbol not found: _FT_Done_Face Referenced from: /Library/Python/2.5/site-packages/pymol/_cmd.so Expected in: flat namespace in /Library/Python/2.5/site-packages/pymol/_cmd.so I read that this is because of a problem with the freetype 2 library, but I included the library's path in the setup file, so I have no idea what else to do. Any ideas? Thanks! ~Lauren 2011/12/19 Troels Emtekær Linnet tlin...@gmail.com 2011-12-19 12:32:21.901 Python[243:5d03] *** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[GLUTApplication _setup:]: unrecognized -- Do you have glut installed ? http://www.pymolwiki.org/index.php/Linux_Install#Requirements freeglut3-dev Best Troels 2011/12/19 Lauren Porter lauren.pers...@gmail.com Hi Everyone, I've compiled and installed pymol 1.3 on my Mac (OS 10.6 running Snow Leopard), but pymol keeps crashing. The compilation looks clean, so I have no idea why it's giving me trouble. I have pasted the details below. Any help would be much appreciated. Thanks! ~Lauren Python 2.5.4 (r254:67916, Aug 1 2011, 15:52:49) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type help, copyright, credits or license for more information. import pymol pymol.finish_launching() 2011-12-19 12:32:21.895 Python[243:5d03] -[GLUTApplication _setup:]: unrecognized selector sent to instance 0x1805490 2011-12-19 12:32:21.898 Python[243:5d03] An uncaught exception was raised 2011-12-19 12:32:21.899 Python[243:5d03] -[GLUTApplication _setup:]: unrecognized selector sent to instance 0x1805490 selector sent to instance 0x1805490' *** Call stack at first throw: ( 0 CoreFoundation 0x906e36ca __raiseError + 410 1 libobjc.A.dylib 0x990c15a9 objc_exception_throw + 56 2 CoreFoundation 0x9073090b -[NSObject(NSObject) doesNotRecognizeSelector:] + 187 3 CoreFoundation 0x90689c06 ___forwarding___ + 950 4 CoreFoundation 0x906897d2 _CF_forwarding_prep_0 + 50 5 Tk 0x17e11ea8 TkpInit + 601 6 Tk 0x17d7d60a Tk_PkgInitStubsCheck + 2489 7 _tkinter.so 0x01d9afe8 Tcl_AppInit + 130 8 _tkinter.so 0x01d9af09
Re: [PyMOL] about super_all.py Plugin installation.
You can try the alignto command as an alternative, if you want. JPK On Mon, Dec 26, 2011 at 12:45 PM, PAVAN PAYGHAN pavana...@gmail.com wrote: Dear PyMol Users, I am using PyMol +v0.97 version on Windows XP .I have downloded super_all.py and tried to install the plugin by using install Plugin option menu. Then I got the message that the plugin was installed but after re-initialization I dont find the Plugin for the same in Plugin list,also was unable to run super command .So will you please help me to solve this problem.Is there any incompatibility issues for OS XP? Please help me in solving this problem.Or suggest the proper way of doing the same as I am new user . Pavan -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ 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 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ 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] about super_all.py Plugin installation.
Dear Pavan, On Tue, 27 Dec 2011 00:15:38 +0530, PAVAN PAYGHAN pavana...@gmail.com wrote: Dear PyMol Users, I am using PyMol +v0.97 version on Windows XP .I have downloded super_all.pyhttp://pldserver1.biochem.queensu.ca/~rlc/work/pymol/super_all.py and tried to install the plugin by using install Plugin option menu. Then I got the message that the plugin was installed but after re-initialization I dont find the Plugin for the same in Plugin list,also was unable to run super command .So will you please help me to solve this problem.Is there any incompatibility issues for OS XP? Please help me in solving this problem.Or suggest the proper way of doing the same as I am new user . This is not a plugin that needs installing, but simply a script that you run. To use it, you just store the super_all.py file somewhere on your computer (I have a directory/folder dedicated to PyMOL scripts) and you load the script's function by using the Run function from the File menu. This has to be done once each time PyMOL starts. I load my commonly used scripts automatically via my .pymolrc file. Once the script loaded, then you can call the super_all function from the command line within PyMOL. You can see the options by typing super_all ? and you can get more information by typing help super_all I hope this helps. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical Molecular Sciences, Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ 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] alignment by residue
dear pymol users, i have a homodimer, with two identical monomers. i would like to know the rmsd of each residue in the first monomer with respect to each residue in the second monomer. i guess pair_fit should give the rmsd. is there a better command to look at the per residue rmsd. thank you. sasi -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev___ 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
