ResiRuler: A Toolkit for Visualizing Residue-Residue Distances and Structural Changes in Biomolecular Models
Proteins and their associated complexes often adopt multiple conformations, with the transitions between these states playing a critical role in biological function. However, the resulting structural heterogeneity can be challenging to visualize and communicate, often requiring manual inspection and time-consuming annotation of biomolecular structures. To address this, we developed ResiRuler, a…
Proteins and their complexes can adopt multiple conformations, with transitions between these states being crucial for biological function. However, visualizing and communicating this structural diversity can be difficult, often requiring manual inspection and annotation of biomolecular structures. To tackle this issue, we created ResiRuler, a local, web-based tool that quantifies atomic displacements using inter-residue distance measurements.
By converting structural differences into residue-pair distance changes, ResiRuler enables quick identification of regions undergoing coordinated motion, local rearrangement, or large-scale conformational change. The tool exports visualizations as PyMOL and ChimeraX scripts, allowing users to explore conformational differences and create publication-quality figures using their preferred visualization software.
ResiRuler accepts atomic models in the Macromolecular Crystallographic Information File (mmCIF) format, aligns multiple structures, and measures structural variation across models to facilitate visualization and presentation of these differences. This enables rapid identification of which protein regions change among ensembles of structures.
The software is available for free download on macOS and Linux systems at https://github.com/tbaker67/ResiRuler.
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