Colors and Color Wells

The color editor and color wells used in Chimera are not Chimera-specific interface components. They handle colors as simple red/green/blue/alpha tuples, whereas Chimera color objects have additional attributes (such as shininess). Since translating between the two representations of colors would be tedious, a ColorOption class is provided that encapsulates the use of a color well so that the programmer need only deal with Chimera color objects.

The example below demonstrates how to display a color well, and how to update the color of protein backbone atoms when the color of the well changes. The code in the graphical user interface submodule,, adds a button to the Chimera toolbar. When the user clicks the toolbar button, a window containing a color well is displayed. When the user changes the color in the well, the color of protein backbone atoms changes to match.

Example ColorWellUI/

This code is analogous to the code found in the "" modules in the Packaging an Extension and Extension-Specific User Interface examples. See Molecular Editing for a more detailed example on changing molecular attributes. Note that the mainchain function is expecting a color object as its argument (because the color is used to set an atomic attribute).
import chimera
import re

MAINCHAIN = re.compile("^(N|CA|C)$", re.I)
def mainchain(color):

for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for a in m.atoms:
if MAINCHAIN.match(
a.color = color

Example ColorWellUI/

Import the standard Python modules used by the example code.
import os
import Tkinter

Import the additional modules and classes needed. The ColorOption class facilitates interoperation between Chimera colors and color wells (which use rgba colors).
import chimera
from chimera.baseDialog import ModelessDialog
from chimera.tkoptions import ColorOption
import ColorWellUI

class ColorWellDialog(ModelessDialog):

ColorWellDialog is a "nameless" dialog. See the Extension-Specific User Interface example for a more detailed explanation of Chimera dialogs.

Set the title bar of the dialog to display Set Backbone Color.
title = 'Set Backbone Color'

def fillInUI(self, master):

Create a ColorOption instance. The ColorOption will contain a descriptive label and a color well. The arguments to the ColorOption constructor are:

master widget
row number to use when griding the ColorOption into the master widget. The default column is 0. The tkoptions module contains other options besides ColorOption (e.g. StringOption), which are generally intended to be put in vertical lists, and therefore a row number is specified in the constructor. In this example we are only using one option however.
option label. This will be positioned to the left of the color well and a ":" will be appended.
The default value for this option.
A callback function to call when the option is set by the user (e.g. a color dragged to the well, or the well color edited in the color editor)
An optional ballon-help message

coloropt = ColorOption(master, 0, 'Backbone Color', None, self._setBackboneColor, balloon='Protein backbone color')

Call _updateBackboneColor to make the color displayed in the color well reflect the current color of protein backbone atoms. While not strictly necessary, keeping the color in the well consistent with the color in the molecules enhances the extension usability.

Define _updateBackboneColor, which is used to make the color of a well reflect the color of protein backbone atoms.
def _updateBackboneColor(self, coloroption):

Loop through all atoms in all molecules, looking for protein backbone atoms. When one is found, its color is compared against the last color seen, theColor. The first time this comparison is made, theColor does not exist yet and a NameError exception is raised; this exception is caught, and theColor is assigned the color of the atom. All subsequent times, the comparison between atom color and theColor should work as expected. If the two colors are different, the color well is set to show that multiple colors are present and execution returns to the caller. If the two colors are the same, the next atom is examined. If only one color is found among all protein backbone atoms (or zero if no molecules are present), then execution continues.
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):

for a in m.atoms:
if ColorWellUI.MAINCHAIN.match(
if a.color != theColor:
except NameError:
theColor = a.color

Set the color of the well to match theColor. There are two possible cases:

theColor is not set (because there are no molecules),
theColor is None or a color object.

The set function will not result in a callback to _setBackboneColor.

Handle case 2. Set the color well to the proper color

except NameError:

Handle case 1. Set the color well to show that no color is present

Define _setBackboneColor, which is invoked each time the color in the well changes. When called by the ColorOption, _setBackboneColor receives a single argument coloropt, which is the ColorOption instance.
def _setBackboneColor(self, coloroption):

Call the mainchain function in the main package, with the color object corresponding to the color well color as its argument (which will be None if No Color is the current selection in the well), to set the color of backbone atoms.

Define the module variable dialog, which keeps track of the dialog window containing the color well. It is initialized to None, and is assigned a usable value when the dialog is created.
dialog = None

Define showColorWellUI, which is invoked when the Chimera toolbar button is pressed.
def showColorWellUI():

Declare that the name dialog refers to the global variable defined above.
global dialog

Check whether the dialog has already been created. If so, the dialog window is displayed by calling it's enter() function, and then the rest of the function is skipped by returning.
if dialog is not None:


Otherwise, create the dialog.
dialog = ColorWellDialog()

Create the Chimera toolbar button that invokes the showColorWellUI
dir, file = os.path.split(__file__)
icon = os.path.join(dir, 'ColorWellUI.tiff'), showColorWellUI, 'Set Main Chain Color', None)

Code Notes

This example registers a callback with the color well, so that any color change in the well results in the colors of protein backbone atoms being updated. An alternative style interface, similar to the one used in Extension-Specific User Interface, may be used by not registering the callback and adding an Apply button, which would invoke a function that fetches the color from the well and calls _setBackboneColor. For this example, since only one atomic attribute is being set, the immediate feedback seems more appropriate.

Note that there was no explicit mention of the color panel. Invocation of and interaction with the color panel is handled automatically by the color well.

The _updateBackboneColor function is used to synchronize the color displayed in the well with the color of the atoms. However, if the color of the atoms are altered through another agency (e.g., a different extension), then the well color and backbone color no longer match. The Trigger Notifications example shows how to keep the well color up-to-date.

Running the Example

The example code files must be saved in a directory named ColorWellUI. To run the example, start chimera, bring up the Tools preference category (via the Preferences entry in the Favorites menu; then choosing the "Tools" preference category) and use the Add button to add the directory above the ColorWellUI directory. Then type the following command into the IDLE command line:

import ColorWellUI.gui

This should display a button on the Chimera toolbar. Clicking the button should bring up a window with a color well inside. The color well may be used to manipulate the color of all protein backbone atoms.