EZ-Viz, a tool for simplifying molecular viewing in PyMOL


  • This project was completed at Brookhaven National Laboratory and was supported by National Science Foundation Advanced Technological Education Grant 0402408.


PyMOL is a molecular modeling program that can be used in a wide range of studies within the scientific community. Its ability to produce informative, detailed, stereoscopic images makes it a very powerful tool both in the laboratory and in the classroom. However, the PyMOL user interface is difficult to use, and the PyMOL User's Manual readily admits that “development has been focused on capabilities, not on ease-of-use for new users.” To resolve this, we set out to develop a new interface for PyMOL that helps eliminate the need for command line interactions, making it a much more user-friendly interface. We have created a tabbed interface called EZ-Viz, which contains a series of buttons and entry fields that allow users to select given attributes of a molecule and make changes to it by clicking a button as opposed to issuing highly syntactical commands. Other features of the interface include a Chime/PyMOL command converter, nine preset molecular views, four molecular movies, and molecular sequence and hetero atom information, all at the click of a button. The ongoing and continued development of EZ-Viz could help to further the use of PyMOL, which we believe to be one of the most powerful molecular viewing programs currently available.