Visualization

Synopsis

This example is continued from Plotting. The aim of this part is visual comparison of experimental and theoretical modes. We will generate molecular graphics that was presented in our paper [AB09].

Notes

To make a comparative visual analysis of PCA and ANM modes that were calculated in the previous parts, NMWiz needs to be installed. NMWiz is a VMD plugin designed to complement ProDy.

Load data

We start by importing everything from the ProDy package:

In [1]: from prody import *

In [2]: from pylab import *

In [3]: ion()

Then we load data saved in Calculations:

In [4]: pca = loadModel('p38_xray.pca.npz')

In [5]: anm = loadModel('1p38.anm.npz')

In [6]: ensemble = loadEnsemble('p38_X-ray.ens.npz')

In [7]: ref_chain = parsePDB('p38_ref_chain.pdb')

Write NMD files

We will save PCA and ANM data in NMD format. NMWiz can read and visualize multiple NMD files at once. Interested user is referred to NMWiz documentation for more information. NMD files are saved as follows using writeNMD() functions:

In [8]: writeNMD('p38_pca.nmd', pca[:3], ref_chain)
Out[8]: 'p38_pca.nmd'

In [9]: writeNMD('p38_anm.nmd', anm[:3], ref_chain)
Out[9]: 'p38_anm.nmd'

It is also possible to load VMD to visualize normal mode data from within an interactive Python session. For this to work, you need VMD and NMWiz plugin installed. Check if VMD path is correct using pathVMD():

In [10]: pathVMD()
Out[10]: '/usr/local/bin/vmd'

If this is not the correct path to your VMD executable you can change it using the same function.

In [11]: viewNMDinVMD('1p38_pca.nmd')