Do you have nvidia drivers?
If so, may be you came across the same problem I have:
I have installed the latest version of Mandriva Linux on a AMD
Athlon(tm) MP 2400+ PC with
a Quadro4 900 XGL graphich card and the NVIDIA-Linux-x86-1.0-7174 driver
When I run pymol and load a pdb file, the program crashes with the
following message:
CmdLoad: "GLGA/sup_models/pdb1rzu.ent" loaded as "pdb1rzu".
*** glibc detected *** double free or corruption (!prev): 0x08a76ba0 ***
/usr/local/pymol-0.98-precompiled/pymol.com: line 14: 16877
Aborted (core dumped) $PYMOL_PATH/pymol.exe $*
However, if I set auto_show_lines=off and auto_show_nonbonded=off BEFORE
loading the molecule, the program loads the PDB file without crashing
(and without showing any graphical object, of course). Then, I can use
the "show" command/button for any type of representation (ribbons,
nonbonded, sticks, ...) EXCEPT the "lines" representation, which causes
a program crash.
This happens with both distributed binary and self compiled PyMol
versions. I have tried version 0.97 and 0.98 with the same results.
Then, browsing the internet, I came across the following message from
Warren:
http://sourceforge.net/mailarchive/message.php?msg_id=11735911
and I decided to try the 0_99beta01 version
(http://delsci.com/beta/pymol-0_99beta01-bin-linux-x86-nvidia-test.tgz),
which seems to solve my problem for the moment.
gerwald jogl wrote:
Hi everyone,
Just wanted to send in a description of the following situation:
I was using pymol 0.98 precompiled on FC3 today and did an automatic
update during the day (therefore, sorry but I don't know which
packages where upgraded :-(
Afterwards, pymol would start up, but core dump immediately after
loading a pdb file.
The same is happening with the 0.97 precompiled version and with my
own compile of the 0.98 source code.
This is what I get:
/xsoft/pymol-0.97precompiled/pymol.com: line 14: 19692 Segmentation
fault (core dumped) $PYMOL_PATH/pymol.exe $*
or my compile:
/xsoft/pymol-0.98/pymol.com: line 2: 19785 Segmentation fault
(core dumped) /usr/bin/python
/usr/lib/python2.3/site-packages/pymol/__init__.py $*
Any comments on this would be greatly appreciated...
Gerwald
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Laboratoire de Virologie Moleculaire & Structurale
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