I am a MODELLER newbie, modelling a synthetic peptide (3 chains * 30 AAs) from the 1COI.PDB entry.
The results produced by the 'automodel' class are in many ways satisfactory, however I cannot figure out how to acetylate the amino terminus of the peptide. I acknowledge that this problem is adressed in the MODELLER FAQ, however the solution provided there does not seem to be designed for use with a simple 'automodel' script such as:
from modeller.automodel import *
env = environ() a = automodel(env, alnfile='vald-tril16c-hand.pir', knowns='merged.pdb', sequence='TRIL16C') a.starting_model = 1 a.ending_model = 5 a.make()
Hence my question is: Will I have to abandon the use of the 'automodel' class and gain more insight into MODELLERs "fine structure" in order to change the default terminus patching ?
Best Regards, Niels Johan Christensen