Creating Images for .nmd Files with Structure Information in VMD

You can make gorgeous images and gifs with the NMD structure information in VMD.

  1. Load in the NMD and structure, then align as described previously.
  2. Change the arrow color in the top right of the NMD Wizard pane. Trying to change it from the graphics menu will not work.
  3. Use the NMD Wizard Pane to modify the arrow settings. Some solid choices are Arrow cylinder radius: 0.1 and Arrow/porcupine cone radius: 0.4.
  4. Change the Graphics material to your choosing. If you want the default Hard Plastic, you may need to deselect it and reselect it to make the changes take effect!
  5. After modifying the arrows, then modify the graphic display. If you go back to the arrows later, you may need to redo your specifications for the default_name coordinates structure…
The NMWiz GUI for a loaded NMD in VMD. There are many rows of buttons.
NMWiz GUI with a loaded structure.T he top right box in black shows where to modify the arrow color. The options button in red on the Mode (2) line opens the Mode Graphics Options dropdown at the bottom of the GUI. In that section, the purple box highlights the checkbox for drawing atoms in both directions. The green dashed box shows where to set the arrow and cone properties. The brown dashed box highlights the button for the arrow material.
A protein structure with normal mode information.
Example rendering with normal mode arrows. The protein structure is lime (ColorID 12), a highlighted residue is yellow (ColorID 4), and the nucleic acid residues are magenta2 (ColorID 28). The arrows are shown in both directions in black.

Table: Graphical Representation of 1: default_name coordinates

Style Color Selection Modified Property Material
Tube ColorID 12 all Radius: 0.2 AOChalky
VDW ColorID 12 name CA and not resid 251 Sphere Scale: 0.4 AOChalky
VDW ColorID 4 name CA and resid 251 Sphere Scale: 0.4 AOChalky
VDW Color 28 name P C2 “C4’” Sphere Scale: 0.4 AOChalky