Re: [modeller_usage] How to skip automatic loop modeling?

[Modeller Caretaker <modeller-care@ucsf.edu>]

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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