On 5/5/20 5:40 PM, Pedro Guillem wrote: > I'm using Modeller 9.24 to induce a couple of mutations into a PDB. > > I noticed that when I execute model.mutate() and export the PDB, the > residue indexes are completely different from the original file... ebery > residue looses its original position in the sequence and gets renumbered > to therever it lands. > > Is there a way I can force modeller to stick to the original numbering?
model.mutate() does not change the residue numbering, but likely you are doing something else in your script which does (by default Modeller numbers everything from 1). You can either renumber manually using rename_segments(): https://salilab.org/modeller/9.24/manual/node192.html
or you can transfer residue numbering from another PDB file with res_num_from(): https://salilab.org/modeller/9.24/manual/node191.html
See also the "mutate model" script which mutates and handles residue numbering: https://salilab.org/modeller/wiki/Mutate%20model
Ben Webb, Modeller Caretaker