Hi, 2010/9/23 Dmitry Osolodkin <divan...@rambler.ru>: > Hello OpenBabel developers and users, > > probably you could help me with a simple problem. I have two molecules > (attached) to compute all-atom RMSD between them; they are same at all > except the position in the space (docking result and a cocrystal > structure). The only problem is that they have different atom numbering, > so RMSD-computing tools using atom numbers such as VMD RMSD Calculator > plugin give unreasonable numbers (about 5 A in this case, which is > obviously wrong). > > The question is: is it possible to change only atom numbering in one or > both molecules to make it the same for them, e.g. canonical? Or one of > them can be used as a template? Manual correction is hardly acceptable > because I have a series of complexes, not one. I also don't need > translation or rotation of the molecules, just compute RMSD between the > given positions.
If you are willing to try the development version, you can canonicalize the atom order for any format using: babel --canonical somefile.mol2 somefile_can.mol2 Tim > Thanks in advance, > Dmitry Osolodkin > -- > Dmitry Osolodkin > Researcher > Group of Computational Molecular Design > Department of Chemistry > Moscow State University > Moscow 119991 Russia > e-mail: dmitr...@qsar.chem.msu.ru > Phone: +7-495-9393557 > Fax: +7-495-9390290 > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
