custom scheme, color palette

Define Custom Color Scheme Dialog Box

Define a custom color scheme based on another scheme or on a property.

To open this dialog box, choose Define Custom Scheme from the Color by option menu in the reference, consensus, sequence coloring, color by, color carbons, transfer color, apply coloring.

  • Using
  • Features
  • Additional Resources

Using the Define Custom Color Scheme Dialog Box

This dialog allows you to create a single custom color scheme, which is saved in the MSV project. The scheme can be a modified version of an existing scheme, or it can be based on values or value ranges of residue properties. The property can be categorical (which includes integers in the range -1 to 10 inclusive) or numerical.

The custom color scheme applies to all tabs in the Multiple Sequence Viewer.

Define Custom Color Scheme Dialog Box Features

Start with options

Define the starting point for the scheme. The tools displayed below depend on the choice made.

  • Existing scheme—choose an existing scheme from the option menu as the basis for the custom scheme. You can revert the customizations to the existing scheme by clicking the Reset button to the right.

  • Residue property—choose a residue property as the basis for the custom scheme. Tools for setting up the mapping of property ranges onto colors are displayed below. The property can be numeric or categorical. Categorical properties have text values or integers from -1 to 10 inclusive.

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 sequences.

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 sequences and enters them in the Min and Max text boxes.

Color mapping table

This table displays the values of text or integer properties or the ranges of numeric properties that are mapped to a color. The color square (chip) displays the color and is also a button that opens a color selector.

Delete button

Delete the rows that are selected in the table. Residues whose properties belonged to the categories or ranges defined by the rows are given the default color.

Combine button

Combine the ranges for the rows that are selected in the table to define a single category. The rows do not need to be contiguous. The combination is done by setting the color for the selected rows to the color of the uppermost selected row in the table. The rows themselves are not merged, so it is easy to separate them out with different colors again. This is a convenient way of combining ranges or values to map to a single color without deleting rows and redefining ranges.

Save button

Save the color scheme in the MSV project. The scheme is named Custom and appears on the Color by option menu. Each new customization overwrites the previous one.

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