UCSF Chimera & ChimeraX

Extensible interactive visualization and analysis suite for atomic structures, cryo-EM density maps, and AlphaFold predictions.

Specifications & Metrics

type: Structural Biology & Cryo-EM Visualization
language: Python and C++
license: Free for academic and noncommercial research use
developer: Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco

Developed by the NIH-supported Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF, Chimera and its next-generation successor UCSF ChimeraX combine atomic coordinate analysis with volumetric density map fitting.
ChimeraX is the standard structural biology platform for fitting atomic models into three-dimensional cryogenic electron microscopy (cryo-EM) maps from the Electron Microscopy Data Bank (EMDB) and inspecting AlphaFold predicted aligned error (PAE) plots.
Built-in structural tools perform automatic hydrogen-bond and steric-clash detection, amino-acid rotamer library sampling, Ramachandran plot validation, and molecular dynamics trajectory playback.