Mark, Thank you for attempting to troubleshoot the problem. Although I am still not certain as to what the underlying problem is, it appears to be specific to Python 2.5.1 and 64-bit. However, since sglite & ExtensionClass are no longer maintained in their present form and are thus liabilities, I have just replaced them with something simpler and more maintainable.
Please try attempting to compile from the subversion trunk via distutils: python setup.py build install python setup2.py install Cheers, Warren > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Mark Wehner > Sent: Sunday, January 13, 2008 9:13 AM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Problems with space group recognition > > Hi Warren, > > I used a small python script to reenact the steps of xray.py. > And the first problem occuring is: > > SgOps = sglite.SgOps(Symbols_Inp['Hall']) > TypeError: 'ExtensionClass' object is not callable > > Before that: > > Symbols_Inp = sglite.SgSymbolLookup(sgsymbol) print Symbols_Inp > > gives a reasonable output. > > Any idea what I'm doing wrong here? > > Regards, > Mark > > PS: The compiler isn't throwing any errors at compile time. I > downgraded one gcc version to test if it's my gcc version, > but still no sucess... Do you see any problematic flags here? > x86_64-pc-linux-gnu-gcc -pthread -fno-strict-aliasing > -march=nocona -Os -pipe -fPIC -DPythonTypes -Icontrib/sglite > -Icontrib/modules -I/usr/include/python2.5 -c > contrib/sglite/runtests.c -o > build/temp.linux-x86_64-2.5/contrib/sglite/runtests.o > > > On Saturday 12 January 2008, you wrote: > > Mark, > > > > It sounds like the sglite module may not have compiled correctly. > > > > Cheers, > > Warren > > > > -- > > DeLano Scientific LLC > > Subscriber Support Services > > mailto:del...@delsci.info > > > > > -----Original Message----- > > > From: pymol-users-boun...@lists.sourceforge.net > > > [mailto:pymol-users-boun...@lists.sourceforge.net] On > Behalf Of Mark > > > Wehner > > > Sent: Saturday, January 12, 2008 4:07 AM > > > To: pymol-users@lists.sourceforge.net > > > Subject: [PyMOL] Problems with space group recognition > > > > > > Dear Pymol users & staff, > > > > > > I'm facing a problem with the recognition of space groups > from (once > > > working) valid pdb files with the last three or maybe 4 > versions of > > > Pymol. If I load any (all space groups I tested failed!) pdb file > > > I'm able to use all features except those that are > symmetry-related; > > > especially I need to generate symmetry mates for certain > proteins. > > > The output is already pointing to an error, but I can't find the > > > error in the source code... > > > > > > Output: > > > 'ObjectMolecule: Read crystal symmetry information. > > > Symmetry-Error: Urecognized space group symbol 'C 1 2 1'. > > > Symmetry-Error: Unable to get matrices from sglite. > > > CmdLoad: "pdb/1f5n.pdb" loaded as "1f5n".' > > > > > > I'm using Gentoo Linux and compiled against Python 2.5 using > > > gcc-4.1.2 on a 64-bit architecture (not using too much > optimization > > > [-Os]). > > > > > > Any help on this would be greatly appreciated. Thanks in advance. > > > Mark Wehner > > > > > > -------------------------------------------------------------- > > > ----------- > > > Check out the new SourceForge.net Marketplace. > > > It's the best place to buy or sell services for just > about anything > > > Open Source. > > > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.n > > > > et/marketplace > > > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyMOL-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > -------------------------------------------------------------- > ----------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for just about > anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.n et/marketplace > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
