Try instead: Align = openbabel.OBAlign(false, false) (see API docs for details).
I suspect the symmetry handling is running out of memory. This will simply - Noel On 17 July 2012 16:49, Чугунов Антон <batc...@yandex.ru> wrote: > Hello all! > I'm trying to calculate RMSD between two conformations of the same > alpha-helical peptides (just 706 atoms). What I do: > > Align = openbabel.OBAlign() > Align.SetRefMol(F2.OBMol) > Align.SetTargetMol(F1.OBMol) > Align.Align() > > and what I get: > > ============================== > *** Open Babel Error in operator() > memory limit exceeded... > ============================== > *** Open Babel Error in operator() > memory limit exceeded... > > What's the problem and how to handle this? > Thanks, > > Anton. > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
