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Keywords: phi(), psi(), energies(), residue_total_energies()
!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()
from pyrosetta import *
from pyrosetta.teaching import *
init()
Begin by moving to the directory with your pdb files and loading cetuximab from 1YY8.clean.pdb used in previous workshops.
cd google_drive/MyDrive/student-notebooks/
pose = pose_from_pdb("1YY8.clean.pdb")
start_pose = Pose()
start_pose.assign(pose)
pose = pose_from_pdb("inputs/1YY8.clean.pdb")
start_pose = Pose()
start_pose.assign(pose)
Question: What are the φ, ψ, and χ angles of residue K49?
print(pose.residue(49).name())
print("Phi: %.5f\nPsi: %.5f\n" %(pose.phi(49), pose.psi(49)))
print("Chi 1: %.5f\nChi 2: %.5f\nChi 3: %.5f\nChi 4: %.5f" %(pose.chi(1, 49), pose.chi(2, 49), pose.chi(3, 49), pose.chi(4, 49)))
Score your pose with the standard full-atom score function. What is the energy of K49? Note the Dunbrack energy component (fa_dun
), which represents the side-chain conformational probability given phi/psi (Ie backbone-dependant).
Any energy can be converted to a probability. Use this energy (E) to calculate the approximate probability of the rotamer (p): p=e^(-E)
scorefxn = get_fa_scorefxn()
scorefxn(pose)
energies = pose.energies()
print(energies.residue_total_energies(49))
print(energies.residue_total_energies(49)[pyrosetta.rosetta.core.scoring.fa_dun])
YOUR-CODE-HERE
Use pose.set_chi(<i>, <res_num>, <chi>)
to set the side chain of residue 49 to the all-anti conformation. (Here, i
is the χ index, and chi
is the new torsion angle in degrees.) Re-score the pose and note the Dunbrack energy.
for i in range(1, 5):
pose.set_chi(i, 49, 180)
YOUR-CODE-HERE
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