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

[Anonymous]

@jtmacd

thanks for the script! It works in PyRoseta v1.1 for 3/4 loops but brakes one (actually it’s missing) even when I don’t select it for relaxation. This loop is 18 aa long and was create with MODELLER and is removed from the relaxed loop models. It also doens’t work in PyRoseta v2b, I get this error message:

Traceback (most recent call last):
File “relax_loops.py”, line 20, in
pose = Pose(input_pdb)
Boost.Python.ArgumentError: Python argument types in
Pose.__init__(Pose, str)
did not match C++ signature:
__init__(_object*, core::pose::Pose src, unsigned long residue_begin, unsigned long residue_end)
__init__(_object*, core::pose::Pose src)
__init__(_object*)

Please contact me at my email adress: tevang@bioacademy.gr for more information about the structure because this discussion is off topic.

@smlewis

I used the flag -fix_residues_to_native but it doesn’t loop to have an effect on the conformation. I didn’t have time to do enough sampling so this I run the fast relax protocol: a) on the whole protein with no restraints, b) on the whole protein with -constrain_relax_to_start_coords, c) on the whole protein with -constrain_relax_to_start_coords and -ramp_constraints, d) on the whole protein with -fix_residues_to_native 1 330 480 1068, e) on the whole protein with -fix_residues_to_native 480 1068. The domain I created with comparative modeling spans from 331 to 479. So I measured the Ca RMSD of the common residues among all cases, namely 480-1068, and found the following values (in Angstroms): a) 1.099, b) 0.768, c) 0.710, d) 1.163, e) 1.059

As you see the RMSD in the cases where I used the -fix_residues_to_native flag (d,e) is comparable with the RMSD of the fully flexible structure (a). Of course I didn’t do enough sampling to support my findings from a first view it doesn’t seem to work. Is there any way to increase the weights on the constraints that -fix_residues_to_native flag imposes?

And with respect to Hayretin’s command line, I used this one instead: /home/thomas/Programs/Rosetta/rosetta_source/bin/relax.default.linuxgccrelease -database /home/thomas/Programs/Rosetta/rosetta_database @flags -fix_residues_to_native .... I guess it is correct.

@smlewis and jtmacd

The 18 aa long loop that is missing from the relaxed loop models is also missing from the relaxed decoys.