Zhiqiang Ye wrote: > I have a homodimer protein structure, it has two chains: A and B, > both of whcih start from 2. I want to get the structure of the > mutant K2S. So I modified the provided example: mutate_model.py to > do this job, the mainly modified part is: (I want to mutate both > chains) > > > mdl.pick_atoms(aln, selection_segment=("2:A", "2:A"), > selection_status='INITIALIZE', selection_search='SEGMENT', > selection_from='ALL') > > mdl.pick_atoms(aln, selection_segment=("2:B", "2:B"), > selection_status='ADD', selection_search='SEGMENT', > selection_from='ALL') > > But in the output model, the two chains are connected as one single > chain, and the residue number has changed start from 1, but I want the > mutant keep the original chain ID and number. How can I get this kind > of results?

Modeller always renumbers residues from 1, and puts everything into one chain, since we cannot rely on PDB numbering. You can restore the numbering from your original model, given an alignment between the two, using the res_num_from() command: http://salilab.org/modeller/8v2/manual/node131.html

P.S. You can find a more full-featured mutate-model example in the Modeller wiki at http://salilab.org/modeller/wiki/Mutate_model

Ben Webb, Modeller Caretaker