Sample Conformations

In this part, we will sample conformations along ANM modes.

In [1]: from prody import *

In [2]: from pylab import *

In [3]: ion()

Load results

First, we load results produced in the previous part. If you are in the same Python session, you don’t need to do this.

In [4]: p38 = loadAtoms('p38.ag.npz')

In [5]: p38_anm = loadModel('p38_ca.anm.npz')

In [6]: p38_anm_ext = loadModel('p38_ext.nma.npz')

Sampling

We will use the sampleModes() function:

In [7]: ens = sampleModes(p38_anm_ext, atoms=p38.protein, n_confs=40, rmsd=1.0)

In [8]: ens
Out[8]: <Ensemble: Conformations along NMA Extended ANM p38 ca (40 conformations; 2834 atoms)>

This will produce 40 (n_confs) conformations with have an average RMSD of 1.0 Å from the input structure.

We can write this ensemble in a .dcd for visualization in VMD:

In [9]: writeDCD('p38all.dcd', ens)

Analysis

Let’s analyze the Ensemble by plotting the RMSDs of all conformations relative to the input structure:

In [10]: rmsd = ens.getRMSDs()

In [11]: hist(rmsd, density=False);

In [12]: xlabel('RMSD');

This histogram might look like a flat distribution due to the small size of the ensemble. For larger numbers of conformations it will get closer to a normal distribution.

Let’s see the projection of these conformations in the ANM slow mode space:

In [13]: showProjection(ens, p38_anm_ext[:3], rmsd=True);

Write conformations

We will write them in p38_ensemble folder:

In [14]: mkdir -p p38_ensemble

Let’s add the conformations to the AtomGroup object and set beta values of Cα atoms to 1 and of other atoms to 0:

In [15]: p38.addCoordset(ens.getCoordsets())

In [16]: p38
Out[16]: <AtomGroup: p38 (2834 atoms; active #0 of 41 coordsets)>

In [17]: p38.all.setBetas(0)

In [18]: p38.ca.setBetas(1)

In the next step, we will optimise the atom positions with a harmonic constraint on atoms with beta values of 1. The optimization aims to refine covalent geometry of atoms.We do not want the new Cα to change much to keep the refined ensemble diverse. We can easily verify that only Cα atoms have beta values set to 1:

In [19]: p38.ca == p38.beta_1
Out[19]: True

Now we write these conformations out:

In [20]: import os

In [21]: for i in range(1, p38.numCoordsets()):  # skipping 0th coordinate set
   ....:     fn = os.path.join('p38_ensemble', 'p38_' + str(i) + '.pdb')
   ....:     writePDB(fn, p38, csets=i)
   ....: 

Visualization

You can visualize all of these conformations using VMD as follows:

$ vmd -m p38_ensemble/*pdb