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#449 Importing PDB files via web crashes

v_1.0.0
closed
nobody
Open Babel (66)
5
2012-09-12
2010-02-17
Michael Banck
No

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=570230

Greetings,

Avogadro crashes when importing (File->Import->Fetch from PDB) with
PDB code 3B75 (Crystal Structure of Glycated Human Haemoglobin
DOI:10.2210/pdb3b75/pdb).

The console only shows this:

QStackedLayout::setCurrentWidget: Widget 0x9e23de8 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
Segmentation fault (core dumped)

In fact, other PDB codes seem to crash as well, I tried with 1QNF, 1DNP and 1IQR, and all of them crashed. So far, I could not find a PDB code which loaded fine. Downloading and converting the .pdbs with OpenBabel works fine.

Discussion

  • Michael Banck

    Michael Banck - 2010-02-17

    Hrm, no idea why SF now sets the priority to 1 by default - I don't believe I changed then when entering the bug.

     

  • Konstantin Tokarev

    Konstantin Tokarev - 2010-02-17

    Reproducible.
    Backtrace:

    Program received signal SIGSEGV, Segmentation fault.
    [Switching to Thread 0xf581c6e0 (LWP 30650)]
    OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8, bond_idx=4324,
    atomState=@0xffd47438, bondState=@0xffd47420)
    at /mnt/storage/openbabel/trunk/include/openbabel/atom.h:223
    223 unsigned int GetIdx() const { return((int)_idx); }
    (gdb)
    (gdb) bt

    0 OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8, bond_idx=4324,

    atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/include/openbabel/atom.h:223

    1 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,

    bond_idx=4323, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438

    2 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,

    bond_idx=4322, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438

    3 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,

    bond_idx=4321, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438

    4 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,

    bond_idx=4320, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438

    5 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,

    bond_idx=4319, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438

    6 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,

    bond_idx=4318, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438

    7 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,

    bond_idx=4317, atomState=@0xffd47438, bondState=@0xffd47420)
     

  • Michael Banck

    Michael Banck - 2010-02-20

    From the backtrace, this appears to be #2841031 in openbabel.

    The question is why avogadro runs expand_kekulize() for PDB files loaded via the web, and not for those opened via File or the command-line.

     

  • Tim Vandermeersch

    Tim Vandermeersch - 2010-03-10

    This bug has been fixed in OB trunk.

     

  • Geoff Hutchison

    Geoff Hutchison - 2010-03-10

    I also can't reproduce this with Open Babel, but did crash the Mac 1.0 release of Avogadro. I'm building a full debug build to try to find the crash. I can attest that OB 2.2.3 seems immune, so I'm confused.

     

  • SourceForge Robot

    SourceForge Robot - 2010-03-25

    This Tracker item was closed automatically by the system. It was
    previously set to a Pending status, and the original submitter
    did not respond within 14 days (the time period specified by
    the administrator of this Tracker).