Reply To: How to relax only one domain of a protein and keep the rest of them fixed

[Anonymous]

Hi Guys!

Indeed, the missing loop residues had zero occupancies, so I changed them to 1.00 using the “clean_pdb.py” script and the loop residues were included in the relaxed loop model. Yet the relaxed full-length structures still don’t have the 18 aa of the loop even in the complete absence of constraints.

As for whole-structure relaxation I switched -ramp_constraints to 0, modified the coordinate constraint weights (values 0.5, 1, 2, 100) and did a little bit of sampling. What I found was that the the Ca RMSD of the common residues among all cases, namely 480-1068, dropped the most when I set -constrain_relax_to_start_coords to 1 and weight to 2 (lowest RMSD 0.699 A.), and the very next parameterization that lowered the RMSD was when -fix_residues_to_native 480 1068 and weight = 2 (lowest RMSD 1041 A.). As you see the “fast relax” protocol perturbs the structure too much. Are there any flags that lower the cycles of refinement in “fast relax” mode?