3D protein structures are crucial for understanding biological function, yet experimental determination is often slow and complex. Computational tools such as AlphaFold now provide rapid predictions, but analyzing and comparing these models to experimental data can be challenging. UCSF ChimeraX offers powerful visualization and analysis features, but its complexity limits accessibility for new users and complicates workflows due to a complex syntax — even for advanced users. ChopChopMF addresses this issue by adding an intuitive graphical interface to ChimeraX. This interface enables both inexperienced and advanced users to quickly explore and analyze protein structures, with ChopChopMF tools covering topics such as: sequence alignments, AlphaMissense plots, Foldseek, PDBePisa plots, and more.
Full Documentation, Installation Guide and Usage you can find here in the: ChopChopMF Guide
After installing ChopChopMF, please close and restart ChimeraX. The full installation guide is within the ChopChopMF Guide
Everything the GUI does for single models is also available on the ChimeraX command line (and works with
chimerax --nogui --cmd): chopchop phospho, signalpeptide, tmhelix, healthcheck, report, interfacescores,
compare, domains, batch, guide, plus:
chopchop asymmetry #model A Ccompares two copies of a chain (homodimer subunits) through their C-alpha distance matrices, without superposition.chopchop glycosites #modellists N-X-S/T glycosylation sequons with their surface exposure.chopchop disulfides #model [maxDist 2.5]lists Cys pairs whose SG atoms are close enough for a disulfide bond.
glycosites and disulfides are also a toolbar tool: Glyco and Disulfide (Cell Biology).
Most of them take jsonFile <path> to write the result as JSON for scripts and AI assistants (see the guide).
From result to figure: FigureStyle (also on the ChimeraX Toolshed) applies a named style template to what you found and saves the image.
Version 1.5 — see the v1.5 release for what's new.
The PAE Analysis tool's Interface Scores (pDockQ, LIS/cLIS/iLIS) implement published methods — if you use them, please cite the original sources listed in Acknowledgements.