[modeller_usage] N-terminal acetylation via 'automodel?' ?

["Niels Johan Christensen" <s991418 AT student.dtu.dk>]

Dear all,

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 ?

Thank you.

Best Regards,
Niels Johan Christensen