Yes Konda Mani Saravanan I actually already have CMView installed on my ubuntu machine;

But I am not talking about visualisation of conatct maps of PDB structures.

I am talking about how to decipher predicted protein contact maps to infer where loops and where helix-loop contacts are; and potentially identify sub domains of domains etc etc. Are there any characteristic regions or features of contact maps that aren't realistically seen in known protein structures?

You could use RQA, it is a very simple and effective methodology for this task (see attached)

here the paper

Hi Alessandro Giuliani , I can't find your RQA tool online, is it available to download open source at all please?

Look at Norbert Marwan website where you can freely download the program

http://www.recurrence-plot.tk/