Dihedral Angle Visualization
ProteinShop contains a feature to visualize the distribution of backbone dihedral angles in selected regions of the current protein. The "Ramachandran Plot Window" shows a 2D scatter plot of the backbone dihedral angles of the selected secondary structure and all active coil regions, overlayed over a pre-computed map of the Ramachandran energy calculated for each possible combination of (phi, psi) dihedral angles, see Figure 1. The Ramachandran Plot Window can be shown by selecting the "Show Ramachandran Plot Window" toggle in the Windows Menu.

Figure 1:Visualization of backbone dihedral angles in the Ramachandran Plot Window. Dihedral angles of the selected secondary structure are shown as white dots; dihedral angles of all active coil regions are shown as black dots; dihedral angles of the selected residue are shown as a large blue dot. Phi angles are mapped on the horizontal axis (from -pi to pi); psi angles are mapped on the vertical axis (from -pi to pi).



Dihedral Angle Scatter Plot
ProteinShop visualizes backbone dihedral angles by mapping each residue's phi angle along the scatter plot's horizontal axis, from -pi to pi (left to right), and each residue's psi angle along the vertical axis, from -pi to pi (bottom to top). All angles are measured in radians. The (phi, psi) coordinate frame, with its origin in the center of the scatter plot, is visualized as a white cross.

The Ramachandran Plot Window only visualizes dihedral angles of residues contained in either the currently selected secondary structure or in any of the active coil regions. Dihedral angles from the currently selected secondary structure are visualized as white dots; dihedral angles from the active coil regions are visualized as black dots, dihedral angles of the selected residue are shown as a large white dot. The white dot of the selected residue will turn into blue color when the mouse enters the plot. Dragging the blue dot and moving around inside the plot will change the dihedral angles of the selected residue. The 3D structure of the protein will change accordingly.

Ramachandran Energy Map
The Ramachandran energy map underneath the dihedral angle scatter plot is not maintained by ProteinShop, but loaded from a provided image file at program startup. In the energy map provided with ProteinShop, energies are visualized as colors ranging from blue (low energy) to red (high energy).

The used energy map is stored in an image file in binary PPM format in the ProteinShop main directory. Users can supply their own energy maps by replacing the Ramachandran64.ppm file with another color image. The image must have width and height of a power of two (the image is used as a texture map), and must be stored in binary (or raw) PPM format (with exactly one comment line in the PPM header). The definition of the PPM image file format can be found on the World Wide Web; alternatively, many commercial and open-source image manipulation programs, e.g., the Gimp, can write PPM files of the correct format.