We present a novel design for managing competing user interests and privacy protection cooperation in a collaborative virtual environment for molecular modeling. Based on the user feedback, this design includes four levels of access control for collaborative sessions and provides dynamic action priority specification for manipulations on shared molecular models. Furthermore, we implement a messaging system that includes a text chatting tool and system broadcasting functions. Our design supports flexible user group formation and interaction. We have implemented our design on a set of Microsoft Windows PCs connected to a Linux molecule simulation server. A GUI interface developed in Python is also illustrated.