Re: [PyMOL] Problems with space group recognition

[DeLano S. <de...@de...>]

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  However, since sglite & ExtensionClass are no
longer maintained in their present form and are thus liabilities, I have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: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Mark Wehner
> Sent: Sunday, January 13, 2008 9:13 AM
> To: pym...@li...
> 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:de...@de...
> >
> > > -----Original Message-----
> > > From: pym...@li...
> > > [mailto:pym...@li...] On 
> Behalf Of Mark 
> > > Wehner
> > > Sent: Saturday, January 12, 2008 4:07 AM
> > > To: pym...@li...
> > > 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
> > >
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> 
> 
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