Re: [modeller_usage] Modelling missing N-terminal residues

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

On 10/23/20 10:31 PM, Aathithya Diaz wrote:
> How to model the missing N-terminal residues (Residue number: 1-16) from 
> the protein structure?

This is straightforward; just add an insertion at the start of your 
alignment (i.e. add 16 residues to the model sequence, and 16 gaps to 
the template):

template  ----------------aaaaaaaaaaaaaa
target    bbbbbbbbbbbbbbbbbbbbbbbbbbbbbb

Note though that since Modeller has no template for this sequence, and 
only one end is constrained by known structure, most likely you'll get 
an extended chain. Since such a model is of little further use, it's 
usually better just to exclude these termini.

	Ben Webb, Modeller Caretaker
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