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).