Free, open-source tools for 3D visualization and structural validation of macromolecules. Most are also distributed with the PHENIX suite and available through MolProbity; source lives on GitHub.
Interactive Java viewer for kinemages: display, analyze, and rebuild structures on Mac, Windows, and Linux.
The original kinemage display program for building and viewing 3D molecular illustrations.
Adds and optimizes hydrogen atoms in PDB models, with automated correction of Asn/Gln/His flips.
Computes all-atom contacts and steric clashes with small-probe contact dots.
Assigns conformer names (“suites”) to RNA backbone and flags outliers.
Diagnoses protein and RNA backbone conformation, especially useful at low resolution.