%load_ext autoreload
%autoreload 2
import molsysmt as msm
Set dihedral angles#
The geometry of a peptide or protein can be changed setting new values to a given dihedral angle (or a set of them). Lets see in the following lines how this can be done with the help of the method molsysmt.set_dihedral_angles. First of all a demo molecular system is loaded to play with it:
molecular_system = msm.systems['Met-enkephalin']['met_enkephalin.h5msm']
molecular_system = msm.convert(molecular_system)
msm.info(molecular_system)
| form | n_atoms | n_groups | n_components | n_chains | n_molecules | n_entities | n_peptides | n_structures |
|---|---|---|---|---|---|---|---|---|
| molsysmt.MolSys | 72 | 5 | 1 | 1 | 1 | 1 | 1 | 1 |
Lets get, before changing its value, the second \(\phi\) angle in the current conformation of the system:
phi_chains = msm.topology.get_dihedral_quartets(molecular_system, phi=True)
msm.structure.get_dihedral_angles(molecular_system, quartets=phi_chains[2])
| Magnitude | [[-179.99976916196186]] |
|---|---|
| Units | degree |
view = msm.view(molecular_system, viewer='NGLView')
view.clear()
selection_quartet = msm.select(molecular_system, selection=phi_chains[2], to_syntax='NGLView')
view.add_ball_and_stick('all', color='white')
view.add_ball_and_stick(selection_quartet, color='orange')
view
Now we can rotate this angle in order to have the desired value:
molecular_system = msm.structure.set_dihedral_angles(molecular_system, quartets=phi_chains[2],
angles='0.0 degrees', pbc=False)
msm.structure.get_dihedral_angles(molecular_system, quartets=phi_chains[2])
| Magnitude | [[0.0]] |
|---|---|
| Units | degree |
view = msm.view(molecular_system, viewer='NGLView')
view.clear()
selection_quartet = msm.select(molecular_system, selection=phi_chains[2], to_syntax='NGLView')
view.add_ball_and_stick('all', color='white')
view.add_ball_and_stick(selection_quartet, color='orange')
view