Atom Energy Coloring Panel

Color atoms in the Workspace or entries using a color ramp based on a numeric property, such as an energy.

To open this panel: click the Tasks button and browse to Structure Analysis → Atom Energy Coloring.

  • Features
  • Additional Resources

Atom Energy Coloring Panel Features

Property option menu

Choose the property to use for the coloring from this option menu. The menu is not populated until you click Get Properties, and is repopulated each time you click Get Properties.

Get Properties button

Populate the property option menu with the properties that are present in the Workspace structures (included entries). If you change the included entries, click this button again to repopulate the menu.

Color scheme option menu

Choose the color ramp for the property. The color ramps are all taken from the red - white - blue spectrum. Two cover the full range from red through white to blue and the inverse; the other four cover red through white and blue through white and their inverses. The first named color on any menu item applies to the minimum value, the last applies to the maximum value of the property. These ramps provide choices for properties that have no limits on their range, and those that have a defined minimum or maximum (such as all positive, all negative).

Average results over option menu

Average the property values over the specified sets of atoms:

  • N Atoms— for each atom, average the property values over atoms within N-1 bonds
  • Residues—average the property values over entire residues
  • Molecules—average the property values over entire molecules.
United atom coloring option

Combine the property value for hydrogen atoms with the value for the atoms to which they are attached.

Always set middle of the range to be zero option

Ensure that the property value is zero at the middle of the color ramp. If any value is given in either the Minimum or Maximum text box, the range is determined by the maximum absolute value X of whatever was specified; oherwise the range is determined by the maximum absolute value X found in the project. The property value range represented by the ramp extends from −X to X.

Minimum text box

Set the minimum value of the property for the application of color. Atoms with values below the minimum will be colored with the value for the minimum.

Maximum text box

Set the maximum value of the property for the application of color. Atoms with values above the maximum will be colored with the value for the maximum.

Reset Min/Max button

Reset the minimum and maximum values to the minimum and maximum found in the project.

Apply coloring to buttons

Apply the color ramp to the atoms defined by the buttons:

  • All Entries—Color all entries in the project.
  • Selected Entries—Color the entries that are selected in the Project Table (Entry List).
  • Workspace—Color all atoms in the Workspace (the included entries).
  • Selected Atoms—Color the atoms that are selected in the Workspace.
Reset button

Reset the panel to its default settings.

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