Toolbar Buttons

The toolbar is a user interface component that appears in the main Chimera window, typically on the left-hand side. The purpose of the toolbar is to hold buttons that invoke commonly used functionality (e.g., displaying protein backbone) and sets of buttons that comprise the entire interface to an extension (e.g., playing molecular dynamics movies).

There are four items associated with the button: an icon,, a Python function, a short description, and an URL to a full description. The icon is displayed in the button, and determines the size of the button. The Python function is called when the button is pressed. The description appears as balloon help text. The full description is displayed when context help is invoked.

The code below illustrates how to a button on the toolbar. The code must be executed from a file (i.e., it cannot be typed in via the Python command line in the main Chimera window). The icon associated with the button is an image file named ToolbarButton.tiff in the same directory as the Python source code. The short description is ``Show Main Chain''. The Python function displays protein backbone and hides all other atoms and bonds, and the code in the body of the function is explained in greater detail in Molecular Editing Using Python.


Function mainchain sets the display status of atoms and requires no arguments. The body of the function is identical to the example described in Molecular Editing Using Python.
def mainchain():

Note that due to a fairly arcane Python behavior, we need to import modules used by a (script) function inside the function itself (the local scope) rather than outside the function (the global scope). This is because Chimera executes scripts in a temporary module so that names defined by the script don't conflict with those in Chimera's main namespace. When the temporary module is deleted, Python sets all names in the module's global namespace to None. Therefore, by the time this function is executed (by the toolbar button callback) any modules imported in the global namespace would have the value None instead of being a module object.

The regular expression module, re, is used for matching atom names.
import re

Import the object that tracks open models and the Molecule class from the chimera module.
from chimera import openModels, Molecule

mainChain = re.compile("^(N|CA|C)$", re.I)
for m in openModels.list(modelTypes=[Molecule]):

for a in m.atoms:
a.display = mainChain.match( != None

Need to import the chimera module to access the function to add the icon to the toolbar.
import chimera

Create a button in the toolbar. The first argument to is the icon, which is either the path to an image file, or the name of a standard Chimera icon (which is the base name of an image file found in the "share/chimera/images" directory in the Chimera installation directory). In this case, since ToolbarButton.tiff is not an absolute path, the icon will be looked for under that name in both the current directory and in the Chimera images directory. The second argument is the Python function to be called when the button is pressed (a.k.a., the "callback function"). The third argument is a short description of what the button does (used typically as balloon help). The fourth argument is the URL to a full description. For this example the icon name is ToolbarButton.tiff; the Python function is mainchain; the short description is "Show Main Chain"; and there is no URL for context help.'ToolbarButton.tiff', mainchain, 'Show Main Chain', None)

Code Notes

The code in this example consists of two portions: defining the actual functionality in function mainchain and presenting an user interface to the functionality. While the example is presented as a single Python source file, there are good reasons for dividing the code into multiple source files and using a Python package instead. The advantages of the latter approach is illustrated in Packaging an Extension.

Running the Example

You can execute the example code by downloading the linked Python script and opening it with the File→Open menu item or with the open command. Note that the .py extension is required for the open dialog/command to recognize that the file is a Python script. The icon tiff file must be saved to a file named 'ToolbarButton.tiff' in the same directory as the script.