Say , for a particular class say http://cctbx.sourceforge.net/current/python/iotbx.pdb.atom_selection.html, the documentation gives me a "cache" class __init__ method that says

__init__(self, root, wildcard_escape_char=r'\')

How do I find out what "root" is in this example. Should I be looking at the c++ code to find out the "types" of these arguments.

It is a iotbx.pdb.hierarchy.root instance in this case, mostly referred to as "pdb_hierarchy" or just "hierarchy". Yes, for some things you have to go into the code. The best approach is to insert print statements to see what the objects are, then run the associated tests (e.g. iotbx/pdb/tst_*.py).

In addition a few of the auto-generated documentation pages such as http://cctbx.sourceforge.net/current_cvs/python/iotbx.pdb.atom.html return an error page.

Thanks for pointing this out. I'll look into this next week, when I'm back home.

I just want to know a good way of understanding the varrious interfaces when writing code using cctbx in Python

Don't hesitate to ask. You may have many questions at first, but then they'll become fewer and far in between. I'll respond more promptly after the conference trip. Ralf