Re: [modeller_usage] Loop modelling

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

On 2/8/22 10:45 PM, Hocine EL KHAOUDI ENYOURY wrote:
> Im trying to refine some loops of my structure. I was wondering if it 
> was possible, with modeller, to force the loop to adapt an alpha helix 
> or beta stand motif while refining.

Loop modeling is not really designed to do this. I would instead do 
regular comparative modeling and either apply secondary structure 
restraints to the desired region, or perhaps align with a template that 
itself has an ideal helix/strand structure. See 
https://salilab.org/modeller/10.2/manual/node28.html

In either case, you may need to modify your alignment to ensure that the 
model is not aligned with anything else (as restraints from that 
alignment will likely conflict with the secondary structure restraints).

	Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage