UCSF ChimeraX : Tools for structure building and analysis
Elaine C. Meng, Thomas D. Goddard, Eric F. Pettersen, Gregory S. Couch, Zachary Pearson, John H. Morris, Thomas E. Ferrin · Protein Science · 2023
Advances in computational tools for atomic model building are leading to accurate models of large molecular assemblies seen in electron microscopy, often at challenging resolutions of 3-4 Å. We describe new methods in the UCSF ChimeraX molecular modeling package that take advantage of machine-learning structure predictions, provide likelihood-based fitting in maps, and compute per-residue scores to identify modeling errors. Additional model-building tools assist analysis of mutations, post-translational modifications, and interactions with ligands. We present the latest ChimeraX model-building capabilities, including several community-developed extensions. ChimeraX is available free of charge for noncommercial use at https://www.rbvi.ucsf.edu/chimerax.