Designing a secure and dependable system is not just a technical issue, it involves also a deep analysis of the organizational and the social environment in which the system will operate. In this paper, we detail our experience in modeling and analyzing requirements for an industrial case (air traffic management system) using the Secure Tropos framework. Particularly, we focus on modeling and reasoning about trust and risk relations within the organizational structure; we discuss pros and cons of Secure Tropos stemming from our experience and lessons learned which might be general interests for RE methodologies.