How to skip automatic loop modeling?
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.
Many thanks, YooChan
On 7/20/19 12:11 AM, Yoochan Myung wrote: > As mentioned in the title, is there any way to ignore/skip loop modeling > in MODELLER9v21?
To be clear, you're referring to Modeller's handling of insertions, i.e. regions of the model that don't align with a template, during comparative modeling. (Loop refinement is a separate protocol that uses a statistical potential rather than information from the alignment.)
Modeller builds a model for the sequence you give it. If you don't want to build a model for a given sequence range, remove that range from the alignment. If there's sequence on both sides of the removed region, you might want to put a chain break there ('/' residue type) to prevent Modeller from trying to make a peptide bond.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Yoochan Myung