Color by Atom Property Dialog Box

Color atoms by values of a chosen atom property with colors from a color ramp.

To open this dialog box, open the Style toolbox, click the arrow on the Color Atoms button, and choose Other Schemes → Choose Atom Property.

  • Using
  • Features
  • Additional Resources

Using the Color by Atom Property Dialog Box

This dialog box provides the ability to fairly quickly apply a color scheme based on an atom property. The scheme can be applied only once, or it can be saved as a custom color scheme, in the same ways as when you create custom color schemes in the Color Schemes settings section of the Preferences Panel.

Color by Atom Property Dialog Box Features

Choose the atom property to use search bar, Settings button and list

Choose an atom property from the list, which shows the atom properties available in the Workspace structure. The properties can be of any type: integer, real, or string.

Use the search bar to find specific properties. Use the Settings button to list colors by default or alphabetically.

Color palette option menu

Choose the color ramp to use for the different ranges or values of the property.

# values/ranges text box and Update button

Specify the number of values or value ranges to use for coloring the properties. When the value is changed, the Update button is activated: click this button to update the value ranges and colors in the table.

For categorical properties, such as text-valued properties, the number of values is predetermined. The number is entered in the text box and the text box is disabled.

Min and Max value report

The minimum and maximum values used for the color range is reported here. The text is bold if the values have been changed from the range in the Workspace structure.

Edit button


This button opens a pane in which you can set the minimum and maximum values, between which the color ramp is applied. Click the check icon to close the pane and apply the values. The Detect link detects the range of property values in the Workspace structure and enters them in the Min and Max text boxes.

Value to color mapping table

This table lists the property values or property ranges and the color assigned to them from the chosen color palette.

Atoms that do not have a property value are assigned a color by default. You can delete this row by clicking the X icon, and these atoms will be treated as if the property value was zero. To restore this row, click the Update button, which is activated when you delete the row.

You can change any color by clicking on the color square and selecting a new color in the color selector that opens. The Color palette setting changes to Custom. If you increase the number of values or ranges, the additional colors are set to gray, and you will have to change them manually.

Use CA value for entire residue option

Use the color for the CA atom in each residue for all selected atoms in the residue. If atoms on a residue are selected but the CA atom is not, the atoms are treated as having no property value. This option cannot be saved with the color scheme.

Save Scheme button

Save the color scheme that you have set up as a custom color scheme. Opens the Save Color Scheme dialog box, in which you can specify a scheme name. By default, the scheme is added to the list in the Style toolbox. The default name is the property name.

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