Residue Distance Map Panel

In this panel you can dispay a heat map of the distances between all pairs of a selected PDB atom type in a protein, and select points in the plot for highlighting and display of the distances in the Workspace.

To open this panel: click the Tasks button and browse to Structure Analysis → Residue Distance Map.

  • Features

Residue Distance Map Panel Features

Use structures from option menu

Select the source of the structure to display the distance map. The choices are

  • Workspace—Use the structure in the Workspace. There must be only one structure in the Workspace. Click the Load button to load the structure.
  • File—Read the structure from a file. Click the Browse button to locate the file. The file can be in Maestro or PDB format. Only the first structure in the file is read. When you click Open, the structure is imported into the project and displayed in the Workspace.
Structure loading button

Click this button to load the structure into the panel. It is labeled Load if you chose Workspace from the Use structures from option menu, or Browse if you chose File from the Use structures from option menu. The plot is automatically generated on loading the structure.

Plot option menu

Specify the type of atom between which distances are calculated and plotted. The choices are C-alpha (the default), C-beta,Closest atoms, for the shortest distance between any atoms in two residues, and Other (PDB name), for which you specify the PDB atom name in the associated text box, and click the check icon next to the box to update the plot. Otherwise, the plot is automatically updated when you change the type of atom used.

Label axes with option menu

Choose the quantity that is shown on the axes of the plot. The choices are Atom numbers, which displays the atom number for the chosen atom type, and Residue numbers, which displays the residue number. A warning is displayed if the protein has insertion codes, as there are duplicate residue numbers in this case.

Workspace Options option menu

Select options for

  • Show Distance Markers—display distance markers for the points that are selected in the plot.

  • Highlight Residues—highlight the pairs of residues for the points that are selected in the plot. The residues are highlighted by changing the carbon atom colors and using tube representation for the residues.

  • Clear Markers—Clear all the distance markers in the Workspace.

  • Clear Highlights—Clear all the highlighting of residues in the Workspace (return the representation to that used for the rest of the protein).

Plot area

This area displays the plot of the distance between all pairs of atoms of the selected typein the protein structure, as a heat map. The color scale is displayed to the right of the plot. Clicking on a point in the plot selects that point. When you do this, the pair of residues is highlighted in the Workspace if Highlight residues is selected, the distance between the atoms is displayed if Show Distance Markers is selected, and the Workspace view zooms in or out so that both residues of the pair are visible at the maximum possible size.

Message area

This area, below the plot area, displays a message identifying the data that is displayed when the pointer is not over the plot, and displays the identity of the alpha carbon atoms (residue and atom number) and the distance when the pointer is over a point in the plot.

Reset panel button

Reset the panel to its initial state, clearing all data.

Save Image button

Save an image of the plot. Opens a file selector in which you can navigate to a location and choose an image format.

Export Data button

Export the distances used to generate the map to a CSV file. Opens a file selector to name and save the file.