Dear All, I would like to export multiple 3D structures into PDB to use them as ensembles in docking. I get constitutions from databases in MOL format or as SMILEs and via pybel I use Open Babel's `make3D()` method to generate 3D. Then I export them one by one into PDB and subsequently I merge them.
My problem is that the order of atoms, which must be fix accross models in order to use the ensembles in docking, is not always the same. See here an example: http://www.ebi.ac.uk/~denes/54b510889336eb2591d8beff/00127_0a949dbfc5df14c6619e5acf726e0d11_16.pdb.txt As you see here the only P atom is either number 25 or 45 in the sequence. Important: these molecules are constitutional isomers only different in double bond positions on their aliphatic chains. Any suggestion would be appreciated. Best, Denes -- Sent from: http://forums.openbabel.org/General-discussion-f3090658.html ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
