Note: this feature requires a 'running' notebook, connected to a live kernel. It will not work with a staticly rendered display. For an introduction to the IPython interactive widget system and its capabilities, see this talk by Brian Granger http://player.vimeo.com/video/79832657#t=30m
Let's start by just loading up a PDB file from the RCSB
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from __future__ import print_function
import mdtraj as md
traj = md.load_pdb('http://www.rcsb.org/pdb/files/2M6K.pdb')
print(traj)
To enable these features, we first need to run enable_notebook to initialize
the required javascript.
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from mdtraj.html import TrajectoryView, enable_notebook
enable_notebook()
The WebGL viewer engine is called iview, and is introduced in the following paper: Li, Hongjian, et al. "iview: an interactive WebGL visualizer for protein-ligand complex." BMC Bioinformatics 15.1 (2014): 56.
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# Controls:
# - default mouse to rotate.
# - ctrl to translate
# - shift to zoom (or use wheel)
# - shift+ctrl to change the fog
# - double click to toggle full screen
widget = TrajectoryView(traj, secondaryStructure='ribbon')
widget
We can even animate through the trajectory simply by updating the widget's frame attribute
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import time
for i in range(traj.n_frames):
widget.frame = i
time.sleep(0.1)
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