Using NMWiz in Chimera

This chapter provides an introduction to NMWiz in Chimera and its capabilities.

Main Window

NMWiz is located in Chimera Main ‣ Tools ‣ Structure Analysis menu and labeled as Normal Mode Wizard, as shown below:

../../_images/chimera_main_nmwiz.png

Location of NMWiz plugin in Chimera menus.

When you first open NMWiz, you will see the NMWiz 1.2 - Main window shown below:

../../_images/chimera_nmwiz_main.png

NMWiz Main window in Chimera.

NMWiz 1.2 - Main window offers options to load precalculated data or to generate data for molecules loaded in VMD:

  • Load NMD File lets you load precalculated data (.nmd files) for analysis.
  • ProDy interface facilitates ANM, GNM, and PCA/EDA calculations from VMD. This functionality is illustrated in the following chapters.

NMWiz Window

Now, let’s load 1dlo_anm.nmd file to introduced the NMWiz window:

../../_images/nmwiz_initial_chimera.png

NMWiz GUI

Changing and Editing Modes

The active mode is represented by arrows starting at the atom locations and pointing in the direction of motion. The top pane of the NMWiz window contains tools for changing some of the basic features of the displayed mode.

Active mode and color

The active mode can be changed using the drop down menu or incremented using the <= and => buttons. Changing the active mode will hide previously generated depictions, and the newly depicted mode will be assigned a distinct color.

Mode scale and direction

Mathematically, each mode’s sign is arbitrary. NMWiz depicts normal modes as they are read from the input file, but the +/- button changes the mode’s sign, inverting its direction. The size of the arrows can be adjusted using the Scale by or RMSD controls.

  • Scale by: The first number is the inverse of the mode frequency, and the second is a real-valued scaling factor that may be incremented or decremented using the adjacent buttons. The +/- button controls the sign of the scale factor. By default, NMWiz scales all modes to 2 Angstroms RMSD. * RMSD: Arrow length can be adjusted to show a specified displacement along the active mode. The sum of squares of the arrow lengths will be the square of the specified RMSD.

Animations

Clicking Animation ‣ Make will start an animation along the active mode. The animated motion changes the structure along the mode in both directions with an amplitude given by the RMSD displayed in top panel.

You can play/pause the movie from the movie dialog window in Chimera.

../../_images/nmwiz_movie_chimera.png

Plots and Heatmaps

You can generate plots and heatmaps that are linked to the protein display. Click Plot Mobility, for example. You will see a plot of the residue mean squared fluctuations for the active mode. Clicking the points on the plot will toggle labels for the corresponding atoms in the VMD molecular display.

Main Controls

Use the following controls for:

  • Main - Open the NMWiz main window, useful when it’s closed
  • Save - Save current dataset in NMWiz format
  • Remove - Remove current dataset and free memory
  • Help - Get some help