Hi Artem,
Quesiton 1 – is there a web site or some other form of a source for a complete cctbx documentation, most importantly with simple working examples?
There are a bunch of working examples in scitbx/examples, cctbx/examples, iotbx/examples, mmtbx/examples. A few of these go with newsletter articles or tutorials. -- I'm aware that this doesn't qualify as complete documentation, sorry, that would just take an enormous amount of time to write. The examples are meant to be starting points if you have a specific problem. Then ask questions via email. I'll help as much as I can. Also, use the many resources available for learning Python; this is essential.
Question 2 – is there anything inside cctbx that can compute elements of protein geometry – such as dihedral angles, planes, etc. (given selections of atoms)?
Assuming PDB input works for you, mmtbx/monomer_library/pdb_interpretation.py is probably the best entry point. To quickly see what it does, run the command: mmtbx.pdb_interpretation your.pdb This builds the geometry restraint objects as used in phenix.refine (and some other phenix tools). If you let me know what you want to do with these restraints, I'll try to work out specific examples showing how you could proceed. You are welcome to email me directly. Ralf