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Re: [modeller_usage] Loop modelling

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 mail list: https://salilab.org/mailman/listinfo/modeller_usage