As you may be aware, it may not be a good idea to store chemical information in PDB files as you need to guess the structure from the 3D coordinates if you don't include bond orders and hydrogens.
If you open them both in Avogadro, you will see that Open Babel detects a double bond in one case but not the other. Or just do: obabel a.pdb b.pdb -O tmp.smi [N](CCO[P@@](=O)(O)OC[C@H](OC(=O)CCCCCCC/C=C\CCCCCCCC)COC(=O)CCCCCCCCCCC/C=C/CC)(C)(C)C a.pdb [N](CCO[P@@](=O)(O)OC[C@H](OC(=O)CCCCCCC/C=C\CCCCCCCC)COC(=O)CCCCCCCCCCCCCCC)(C)(C)C b.pdb So, different structure, different canonicalisation. - Noel On 25 April 2013 13:41, gromacs query <gromacsqu...@gmail.com> wrote: > Dear All, > > I have some query related to canonical option in babel and am new to babel > > I have two pdb files (a.pdb and b.pdb). These include just heavy atoms but > are pdbs for same structure. > > a.pdb and b.pdb have same atom names but different atom number and > coordinates. > > What I expect is canonical output should remain same. But both gives me > different canonical order. Is this bug or something I am missing. > > I use this command: > > babel --canonical -ipdb a.pdb -opdb a_cano.pdb > babel --canonical -ipdb b.pdb -opdb b_cano.pdb > > I get different canonical ouput in both pdbs. Should not be the order remain > same? > > Please suggest > > regards, > Jiom > > ------------------------------------------------------------------------------ > Try New Relic Now & We'll Send You this Cool Shirt > New Relic is the only SaaS-based application performance monitoring service > that delivers powerful full stack analytics. Optimize and monitor your > browser, app, & servers with just a few lines of code. Try New Relic > and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
