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Visualization

1. nglview, VMD and PyMOL

In the previous notebooks, a relatively basic visualization of intermediate results was done with nglview. While nglview is convenient for a quick introspection inside a notebook, it only offers a fairly simple customization of the visual representation through its Python API.

More advanced biomolecular visualization tools are available, of which VMD and PyMOL are popular choices. Both tools are comparable in functionality (but obviously differ when going through the details). A major difference in practice is the distribution of both codes. VMD is free as in free beer, but not open source. One can download binaries and source code from its homepage. PyMol is in principle an open-source project, but binary packages (with several commercial enhancements) are sold for a mild price. For this tutorial, we will use VMD, so you can get you started without having to pay for a license.

2. Walk-through for VMD + good practices

This tutorial will show you how to make the following visualization of the final structure of the Villin headpiece molecular dynamics simulation, see 04_protein:

vmdscene

Note that the final geometry may be slightly different due to the random initialization of the atomic velocities. In any case, try to reproduce this image as well as possible. The instructions are based on good practices for making high-resolution publication-ready visualizations.

Load the trajectory (option 1, any operating system)

  • Start the VMD program.

  • Select the menu option File -> New Molecule... and load the file init.pdb from the directory 04_protein.

  • Click on the first line in the VMD Main window.

  • Select the menu option File -> Load Data Into Molecule..., select the file traj.dcd from the directory 04_protein and also select the option Load all at once. Then click the Load button and close the popup window.

Load the trajectory (option 2, Linux)

In the introductory part of this tutorial, VMD was installed in a separate conda environment because it would otherwise interfere with Jupyter. Hence, we first need to switch to the correct conda environment:

conda activate vmd

The easiest way to load a trajectory in VMD, is to provide the topology and trajectory inputs on the command line:

cd ../04_protein/
vmd init.pdb traj.dcd

Play the trajectory

After VMD has started, play the video (play button in the bottom-right of the main window) or skip to the last frame immediately. The default representation is not particularly clear or insightful. This choice is mainly motivated by the computational efficiency with which VMD can draw a lot of simple lines.

Change to the "NewCartoon" representation

In the main window, select the menu function Graphics -> Representations... and change the Drawing Method to NewCartoon and change Selected Atoms to protein. This will discard the water molecules and show the familiar cartoon with three curls for the alpha helices.

You can recenter the view on the visible parts by selecting the menu option Display -> Reset view.

All-atom visualization of a subsystem

Now add a new representation in the Representations window, by clicking on Create Rep. This will duplicate the currently selected representation, hence not showing any differences until you start modifying the new representation.

Set the Drawing Method to CPK and change the Selected Atoms to protein and (resid 4 or resid 7). This will only show all atoms of two residues whose side-chains interact electrostatically.

Finally, add a third drawing method and use the Drawing Method option HBonds.

An overview of the VMD atom selection language can be found here: http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html

Remove clutter and make the image print-friendly

  • Get rid of the frame axes (because it is fairly useless): select in the menu Display -> Axes -> Off.
  • Set the project to orthographic, unless you enjoy skewed perspective images: select in the menu Display -> Orthographic.
  • Change the background color to white (to save ink and to improve clarity): select in the menu Graphics -> Colors. In the Color Controls window, select Display and change BackgroundTop and BackgroundBot to 8 white. Also select in the menu: Display -> Background -> Gradient. This way, depth cueing uses dark shades while the background is white.
  • Change the curly cartoon color to something distinct from the color of the carbon atoms: in the Graphical Representation window, select the NewCartoon representation. Then select for Coloring Method the option ColorID and set the color to 3 orange.
  • Finally rotate the visual to clearly view the interacting side chains without hiding the essential parts of the protein. Also zoom in to efficiently use the display size.

Enable ambient occlusion

Ambient Occlusion is a 3D visualization technique that clarifies the shape of complex geometries by simulating realistic ambient lighting effects. Parts of a model buried inside will become darker as the simulated light cannot easily reach such places. For a small protein like the Villin headpiece, this will have little effect, mainly visible inside alpha helices. For larger systems, ambient occlusion has a major beneficial effect.

To enable ambient occlusion in VMD, several options need to be switched on. Keep in mind that you will only see the result in the next step and the visualization may at first look even worse.

  • Go through each representation and set the Material to AOShiny.
  • In the menu Display -> Display options. In the Display Settings window, under Ray Tracing Options, enable Shadows and Amb. Occl..

Ray-trace the image with Tachyon

Ray-tracing is an (expensive) 3D visualization technique to generate more realistic-looking images. Usually, such images are visually clearer. An additional advantage is that the image resolution can be easily controlled.

The first step is to select the menu option File -> Render. In the File Render Controls window, select the Tachyon option and click Start Rendering. This will render a the scene of interest, which takes a few seconds. The image is stored on disk as vmdscene.dat.tga. At the same time, also the scene file is written: vmdscene.dat. This file can be edited to adapt the resolution and to change other settings. After modifying the scene file, you can re-render by running the following command in a terminal:

${CONDA_PREFIX}/lib/tachyon_LINUXAMD64 vmdscene.dat -format TARGA -o vmdscene.dat.tga

This should work on Linux and MacOS. A slightly different command may be needed on Windows.