[Debichem-devel] Bug#570230: Bug#570230: Bug#570230: avogadro: Segmentation fault upon importing PDB data from a PDB code

[Michael Banck]

On Wed, Feb 17, 2010 at 03:47:24PM +0100, Michael Banck wrote:
> On Wed, Feb 17, 2010 at 02:37:10PM +0100, Filippo Rusconi wrote:
> > Package: avogadro
> > Version: 1.0.0-2
> > Severity: important
> > 
> > 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)
> 
> Indeed, I can reproduce this.  In fact, it crashes for all the PDB codes
> I tried, did you only try this one, or others as well, and what were
> your observations?
> 
> I have forwarded the bug upstream.

Turns out this is an OpenBabel bug after all.

It has been fixed upstream in trunk (to-be openbabel-2.3) with commit
r3601, unfortunately, the 2.2 code is different at this place.  So a
backport is non-trivial (at least for me after looking at it for a
minute); if somebody wants to take a look, be our guest.


Michael