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UCSF ChimeraX — next-generation molecular visualization and analysis tool for structural biology. Provides interactive 3D visualization of proteins, nucleic acids, cryo-EM density maps, and molecular
Use with AI
Install the MCP server or CLI to instantly fetch UCSF ChimeraX documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/chimerax
cryoSPARC — cryo-EM single particle analysis platform for high-resolution 3D structure determination. Provides motion correction, CTF estimation, particle picking (blob, template, Topaz), 2D classific
1 shared topic • 2 shared operations
ISOLDE — interactive molecular dynamics plugin for UCSF ChimeraX that enables real-time model building into low-to-medium resolution cryo-EM and crystallographic maps. Uses GPU-accelerated OpenMM with
1 shared topic • 2 shared operations
Use when working with OmegaFold to predict 3D protein structures from amino acid sequences without multiple sequence alignments (MSA-free). Covers single-sequence structure prediction, batch FASTA pro
1 shared topic • 2 shared operations
Phenix — comprehensive macromolecular structure determination from X-ray crystallography, cryo-EM, and neutron diffraction data. Provides automated molecular replacement (Phaser), structure refinement
1 shared topic • 2 shared operations
PyMOL — molecular visualization system for rendering publication-quality 3D images of protein structures, nucleic acids, small molecules, electron density maps, and volumetric data. Provides interacti
1 shared topic • 2 shared operations