Ah, ok, makes sense.. Thanks for the exmplanation! Markus -----Original Message----- From: Modeller Caretaker [mailto:modeller-care@salilab.org] Sent: Wednesday, September 28, 2016 12:05 PM To: Markus Heller Subject: Re: [modeller_usage] (no subject) On 9/28/16 10:43 AM, Markus Heller wrote: > 3. $ python calc_model.py > console_output.txt Modeller numbers residues starting from 1; it doesn't reset the counter to 1 at the start of a new chain, so your residues are numbered 1:A through 470:A and 471:B through 940:B (see the .ini file). If you want to also renumber the residues, use the renumber_residues argument to rename_segments(): https://salilab.org/modeller/9.17/manual/node191.html Ben Webb, Modeller Caretaker -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage