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
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