Plotting a Ramachandran map with matplotlib

In [1]:
%matplotlib inline
from __future__ import print_function
import mdtraj as md

Lets load up the trajectory that we simulated in a previous example

In [2]:
traj = md.load('ala2.h5')
atoms, bonds = traj.topology.to_dataframe()
atoms
Out[2]:
serial name element resSeq resName chainID segmentID
0 None H1 H 1 ACE 0
1 None CH3 C 1 ACE 0
2 None H2 H 1 ACE 0
3 None H3 H 1 ACE 0
4 None C C 1 ACE 0
5 None O O 1 ACE 0
6 None N N 2 ALA 0
7 None H H 2 ALA 0
8 None CA C 2 ALA 0
9 None HA H 2 ALA 0
10 None CB C 2 ALA 0
11 None HB1 H 2 ALA 0
12 None HB2 H 2 ALA 0
13 None HB3 H 2 ALA 0
14 None C C 2 ALA 0
15 None O O 2 ALA 0
16 None N N 3 NME 0
17 None H H 3 NME 0
18 None C C 3 NME 0
19 None H1 H 3 NME 0
20 None H2 H 3 NME 0
21 None H3 H 3 NME 0

Because alanine dipeptide is a little nonstandard in the sense that it's basically dominated by the ACE and NME capping residues, we need to find the indicies of the atoms involved in the phi and psi angles somewhat manually. For standard cases, see compute_phi() and compute_psi() for easier solutions that don't require you to manually find the indices of each dihedral angle.

In this case, we're just specifying the four atoms that together parameterize the phi and psi dihedral angles.

In [3]:
psi_indices, phi_indices = [6, 8, 14, 16], [4, 6, 8, 14]
angles = md.compute_dihedrals(traj, [phi_indices, psi_indices])

Lets plot our dihedral angles in a scatter plot using matplotlib. What conformational states of Alanine dipeptide did we sample?

In [4]:
from pylab import *
from math import pi

figure()
title('Dihedral Map: Alanine dipeptide')
scatter(angles[:, 0], angles[:, 1], marker='x', c=traj.time)
cbar = colorbar()
cbar.set_label('Time [ps]')
xlabel(r'$\Phi$ Angle [radians]')
xlim(-pi, pi)
ylabel(r'$\Psi$ Angle [radians]')
ylim(-pi, pi)
Out[4]:
(-3.141592653589793, 3.141592653589793)

(ramachandran-plot.ipynb; ramachandran-plot_evaluated.ipynb; ramachandran-plot.py)

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