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 Outdated software stymies scientific progress and innovation.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
Department, Program, or Center
Thomas H. Gosnell School of Life Sciences (COS)
Paul A. Craig
Robertson, Mariah, "ProMOL: Updating the Template Based Structural Alignment Plugin" (2021). Thesis. Rochester Institute of Technology. Accessed from
RIT – Main Campus