When deleting an amino acid residue from a protein structure to reduce the loop size, it's important to consider the impact on the overall structure and stability of the protein. Deleting a residue can disrupt the local folding and interactions within the loop, potentially affecting the structural integrity of the protein. However, if you still want to proceed with deleting the residue and connect the loose ends without inserting another residue, one approach you can try is loop modeling. Here's a suggested procedure using PyMOL and MODELLER:

Keep in mind that loop modeling is a computationally intensive process, and the results may vary depending on the complexity of the loop and the accuracy of the modeling algorithm. It's always a good idea to validate the modeled loop using structural analysis tools, such as energy minimization, molecular dynamics simulations, or validation software (e.g., PROCHECK, MolProbity).

Additionally, consider that reducing the loop size may affect the protein's function and stability. It's important to carefully evaluate the potential consequences and consult with experts in the field before making significant modifications to a protein structure.

Ok, I understand the problem, thanks for replying. But in this case, the objective is really to make the structure more rigid with a reduction of loops or mutations that increase the hydrogen interactions in the moving parts. I intend to increase the thermal stability.