I am happy to announce, that I have finished working on a script that fetches the pKa values of your protein.
The script contacts, download results, processes the files, and write a pymol command that make pka atoms, labels,
colors, bonds, distances and such.
See more here: http://pymolwiki.org/index.php/Propka
The script contacts and gets the results from the propka server, which is one of the fastest and most used pka prediction methods available on "the market".
Any bugs, which is not already commented, I would be happy to hear about.