Dear all, I have a mol2 file and I would like to generate an input for an external program using chimera. For a great ease in practicability, I would like the mol2 order to be kept. I used the following artefact to get to what I want: def input(molecule): ##for compatibility with mol2 atom ordering I use the doble loop as follow ##makes the writing substantially slower, but yet the compatibility with mol2 format seems absolute. for i in range(len(molecule.atoms)): for atoms in molecule.atoms: if atoms.serialNumber == i: text=str(atoms.element)+"-"+str(atoms.gaffType)+"-"+str(atoms.charge)+" "+str(atoms.flex)+" "+str(atoms.coord()) +"\n" filename.write(text) i=i+1 I think I could order directly the writing in function of the serialNumber (which is preserved regarding the mol2) file. But how could I do this? Best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es