Jayapal, Prabha wrote: > I am a new user of MODELLER 9. I got an appreciable model using > modeller and I would like to evaluate the model by the > model.energy(). But I got an error like, ... > transfe_507E> Number of residues in alignment different from that in MODEL: 60 120 > (Did you call clear_topology() before generate_topology() ?) ... > aln = alignment(env) > code = "nitro.B99990066" > mdl = model(env, file=code) > aln.append_model(mdl, atom_files=code, align_codes=code) > aln.append_model(mdl, atom_files=code+'.ini', align_codes=code+'-ini') > > mdl.generate_topology(aln[code+'-ini'])
Add the line mdl.clear_topology()
before the generate_topology() call, if you want to do this the "hard" way. Or look at the example at http://salilab.org/modeller/9v1/manual/node228.html for an easier way.
Ben Webb, Modeller Caretaker