More linux woes! Pymol 0.98beta18 built from source gives the following
error on launch:
cm...@euclid cmoad $ pymol
Traceback (most recent call last):
File "/usr/local/lib/python2.3/site-packages/pymol/__init__.py", line
329, in ?
import _cmd
ImportError: /usr/local/lib/python2.3/site-packages/pymol/_cmd.so:
undefined symbol: TextureFree
Gentoo Linux
gcc-3.3.4
glibc-2.3.4
Has anyone else seen this? I will try cvs as well.
Thanks,
Charlie
On Sat, 2004-11-20 at 18:51 -0800, Warren DeLano wrote:
> Charles,
>
> Open-Source PyMOL source code is always available for anonymous CVS checkout
> from SourceForge:
>
> http://sourceforge.net/cvs/?group_id=4546
>
> However, that tends to be 24-hours out of date -- and, well, a lot happened
> yesterday (grin)...so I just posted a couple of new builds along with a
> source snapshot.
>
> Windows & Source at http://delsci.com/beta
> Mac at http://delsci.com/macbeta
>
> Feedback on the new mouse configuration has been uniformly positive, so
> here's another question that relates to this latest beta (0.98beta18):
>
> Do people want "animation" enabled by default or not? It looks & feels
> great on good hardware, but could prove annoying on slow systems. My
> conservative side says, "yes, disable it since it's something new, and
> mostly aesthetic" But on the other hand, I really like how it enhances
> viewing of existing sessions with multiple scenes & views, as well as
> actions such as center, zoom, orient, and the middle-click variants on the
> sequence browser. Again, your input is desired.
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080
> . 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
> > Charles Moad
> > Sent: Saturday, November 20, 2004 3:06 PM
> > To: <pymol-users@lists.sourceforge.net>
> > <pymol-users@lists.sourceforge.net>
> > Subject: Re: [PyMOL] cmd.read_pdbstr segfault
> >
> > Is there an estimated time release for 0.98 source
> > release? I think I recall that you only released binary
> > betas, and I add some python modules to my install for
> > development reasons.
> >
> > Thanks,
> > Charlie
> >
> > On Nov 20, 2004, at 5:53 PM, Warren DeLano wrote:
> >
> > > Tom & Charles,
> > >
> > > Tom, thanks for your attention to this issue -- actually,
> > the problem
> > > is more narrow...
> > >
> > > Charles was (only) seeing a segfault with the read_pdbstr
> > function and
> > > PDB file 1DT7, and indeed I have been able to reproduce
> > this on Linux
> > > with version 0.97. However, the latest 0.98 betas seem to
> > handle the
> > > read just fine.
> > >
> > > Much of the PDB loader code was re-engineed since 0.97 to
> > support some
> > > new scenarios (such as PDB files containing multiple independent
> > > objects).
> > > Thus, it seems that the problem has inadvertently been
> > fixed -- I've
> > > confirm function of the latest code on all 3 major
> > platforms without
> > > mishap.
> > >
> > > So, unless or until anyone can reproduce this crash with the latest
> > > beta, I'm going to view this as a non-issue.
> > >
> > > Cheers,
> > > Warren
> > >
> > > --
> > > Warren L. DeLano, Ph.D.
> > > Principal Scientist
> > >
> > > . DeLano Scientific LLC
> > > . 400 Oyster Point Blvd., Suite 213
> > > . South San Francisco, CA 94080
> > > . 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 Thomas
> > >> Stout
> > >> Sent: Saturday, November 20, 2004 2:31 PM
> > >> To: Charles Moad
> > >> Cc: pymol-users@lists.sourceforge.net
> > >> Subject: RE: [PyMOL] cmd.read_pdbstr segfault
> > >>
> > >>
> > >>
> > >> Ah - completely different situation....I found an installation of
> > >> v0.97 (WinXP) and 1DT7 also loads fine there
> > >> - so I guess it's not inherent to version 0.97 - at least not the
> > >> windows version....
> > >>
> > >> -Tom
> > >>
> > >>
> > >> -----Original Message-----
> > >> From: Charles Moad [mailto:cm...@indiana.edu]
> > >> Sent: Sat 11/20/2004 8:42 AM
> > >> To: Thomas Stout
> > >> Cc: pymol-users@lists.sourceforge.net
> > >> Subject: Re: [PyMOL] cmd.read_pdbstr segfault
> > >>
> > >> The application actually quits, hence the seg fault error.
> > >> This happens for quite a few files, and the only trend I
> > saw was file
> > >> size since the smaller ones had no troubles.
> > >>
> > >> - Charlie
> > >>
> > >> On Nov 19, 2004, at 6:21 PM, Thomas Stout wrote:
> > >>
> > >>>
> > >>> version 0.98 (beta 07 and beta 17) loads PDB IS 1DT7 just
> > >> fine. It's
> > >>> a little slow, but it works! Are you sure you don't have
> > >> "auto-zoom"
> > >>> off? I turn auto-zoom off by default and as a result
> > some entries
> > >>> (like 1DT7) load but are not visible. Clicking the "zoom" button
> > >>> brings it into the center of the graphics window.....
> > >>>
> > >>> -Tom
> > >>>
> > >>>
> > >>> -----Original Message-----
> > >>> From: pymol-users-ad...@lists.sourceforge.net
> > >>> [mailto:pymol-users-ad...@lists.sourceforge.net]on Behalf
> > >> Of Charles
> > >>> Moad
> > >>> Sent: Friday, November 19, 2004 5:18 AM
> > >>> To: pymol-users@lists.sourceforge.net
> > >>> Subject: [PyMOL] cmd.read_pdbstr segfault
> > >>>
> > >>>
> > >>> pymol-0.97 cmd.read_pdbstr is dieing for remotely
> > >> large pdb files.
> > >>> One
> > >>> for example is 1DT7. I don't get a descriptive error:
> > >>>
> > >>> /usr/local/bin/pymol: line 2: 10486 Segmentation fault
> > >> /usr/bin/python
> > >>> /usr/local/lib/python2.3/site-packages/pymol/__init__.py
> > >>> $*
> > >>>
> > >>> Thanks,
> > >>> Charlie
> > >>>
> > >>>
> > >>>
> > >>> -------------------------------------------------------
> > >>> This SF.Net email is sponsored by: InterSystems CACHE FREE OODBMS
> > >>> DOWNLOAD - A multidimensional database that combines robust
> > >> object and
> > >>> relational technologies, making it a perfect match for
> > >> Java, C++,COM,
> > >>> XML, ODBC and JDBC. www.intersystems.com/match8
> > >>> _______________________________________________
> > >>> PyMOL-users mailing list
> > >>> PyMOL-users@lists.sourceforge.net
> > >>> https://lists.sourceforge.net/lists/listinfo/pymol-users
> > >>>
> > >>>
> > >>> -------------------------------------------------------
> > >>> This SF.Net email is sponsored by: InterSystems CACHE FREE OODBMS
> > >>> DOWNLOAD - A multidimensional database that combines robust
> > >> object and
> > >>> relational technologies, making it a perfect match for
> > >> Java, C++,COM,
> > >>> XML, ODBC and JDBC. www.intersystems.com/match8
> > >>> _______________________________________________
> > >>> PyMOL-users mailing list
> > >>> PyMOL-users@lists.sourceforge.net
> > >>> https://lists.sourceforge.net/lists/listinfo/pymol-users
> > >>>
> > >>>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >
> > >
> > >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: InterSystems CACHE FREE
> > OODBMS DOWNLOAD - A multidimensional database that combines
> > robust object and relational technologies, making it a
> > perfect match for Java, C++,COM, XML, ODBC and JDBC.
> > www.intersystems.com/match8
> > _______________________________________________
> > PyMOL-users mailing list
> > PyMOL-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>
>
>
