On Sep 21, 2011, at 10:48 AM, George Barbosa wrote: > Hello, I'm a newbie at Avogadro. I drew a molecule derived from an amino > acid, optimized its geometry with Avogadro, saved the file and closed it. But > then when I opened it briefly later some bonds were changed
Depending on the file format you used, bonding information may not be included. Avogadro uses CML as its native format, which will store bond orders. But if you save as a PDB or XYZ format, bond orders are not saved and Avogadro will have to work out the bond orders again. Also, keep in mind that Avogadro attempts to re-center a molecule when opening -- this may rotate the frame of reference so that atoms are not in the same place. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
