The Programmer's Guide is under construction.
A working knowledge of Python is required for the Programmer's Guide to be useful. The Python Tutorial is recommended for programmers who want a quick introduction to Python. Non-programmers should consult the Beginner's Guide to Python for some suggestions on where to begin.
If all you want to do is loop through a series of data files and perform a series of Chimera commands on them (possibly including writing out results), this extremely basic primer covers how to do that. For anything more complicated please keep reading.
The Chimera Programmer's Guide main component is an Examples section demonstrating various useful Chimera programming interfaces. There are also example scripts for performing various tasks that you may be able to use as a jumping off point for developing your own script. We recommend starting with the Examples, and then either using an example script or examining the Chimera source code for an extension that does something similar to what you want to do and working from there. You can also use Chimera's IDLE programming shell with the dir(obj) and help(obj) functions to find out more about the attributes and methods of particular objects. The FAQ (below) can also be helpful and questions to the chimera-dev mailing list are usually quickly answered.
Please see the Chimera documentation index and Chimera home page for other types of information.