Generating conformational ensembles

ENCoM can be used to generate a conformational ensemble for a protein of interest. To do so, you simply need to call the build_conf_ensemble() method on an ENCoM object:

from nrgten.encom import ENCoM

model = ENCoM("test_medium.pdb")
model.build_conf_ensemble([7,8,9], "conf_ensemble.pdb")

The first argument is the list of normal modes to use to generate the ensemble. In the example above, the first 3 modes are used. Note that 1 corresponds to the first normal mode, but the first 6 normal modes are trivial rotational/translational motions. Thus, index 7 is the first non-trivial normal mode.

The second argument is simply the name of the output for the conformational ensemble. The ensemble is outputted using the same convention as ensembles of solutions for NRM experiments, using MODEL and ENDMDL statements to separate the different conformations.

Here is the detailed documentation for the build_conf_ensemble() method:

nrgten.enm.ENM.build_conf_ensemble(self, modes_list, filename, step=0.5, max_displacement=2.0, max_conformations=10000, use_motion=False)

Creates a conformational ensemble as a multi-model PDB file.

The idea is to make every combination of the selected modes at every given rmsd step, up to a total deformation for each mode (and in both directions).

Note

The mode indices in the modes_list argument are assumed to start at 1, with the first nontrivial mode thus being at index 7.

Parameters:

  • modes_list (list) – list of integer indices of modes to use for the conformational ensemble. The first non-trivial mode is at index 7.

  • filename (str) – The filename where the conformational ensemble will be written.

  • step (optional, float) – The RMSD step between each grid point in the conformational ensemble.

  • max_displacement (float, optional) – The maximum RMSD displacement for each mode. Has to be a multiple of step.

  • max_conformations (int, optional) – The maximum number of conformations. Ensures that users do not accidentally generate huge PDB files.