Abstract In silico methods have contributed greatly to our understanding of the molecular world. PyMOL, an open-source 3D molecular visualization software, produces high quality images and videos of proteins. Here, we discuss a plugin called ProMOL that augments PyMOL’s capabilities by adding a way to decipher unknown proteins using template-based structural alignment. Software is constantly updated to meet the demands of users. ProMOL fell behind in this regard and required a major overhaul in its code to work with older and newer versions of PyMOL. This included multiple API updates, Python language migration, and code optimizations. The result of the overhaul produced two versions of ProMOL. ProMOL 5.5 is a working version used with PyMOL 1.8 and ProMOL 6.0 partially works with PyMOL 2.4. Outdated software stymies scientific progress and innovation. The right tools in the right hands can lead to phenomenal discoveries.

Library of Congress Subject Headings

Proteins--Analysis--Data processing; Molecular structure--Data processing; Structural bioinformatics

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Paul A. Craig

Advisor/Committee Member

Gary Skuse

Advisor/Committee Member

Joe Geigel


RIT – Main Campus

Plan Codes