Hello everyone,
As mentioned in the title, is there any way to ignore/skip loop modeling in MODELLER9v21? My script is as follows:
==========[script]============
env = environ()
a = automodel(env, alnfile='HM_1KTZ-202_het.ali',
knowns='202_het', sequence='TGFbeta1_HM_1KTZ',
assess_methods=(assess.DOPE,
#soap_protein_od.Scorer(),
assess.GA341))
a.starting_model = 1
a.ending_model = 3
a.make()
==========[script]============
My template has a missing loop (13 amino acids long) but MODELLER automatically links before/after the loop region for the modeled structures, which looked quite unreasonable.
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Yoochan Myung
PhD student | Ascher Lab
Department of Biochemistry and Molecular Biology
The University of Melbourne
30 Flemington Road, Parkville VIC 3010, Australia