MolProbity is a web-based structure validation tool for macromolecular crystallography that evaluates the quality of protein and nucleic acid models at both global and local levels. It uses optimized hydrogen placement and all-atom contact analysis, along with updated covalent-geometry and torsion-angle criteria, to identify and correct errors in structures. These errors, such as Ramachandran outliers, flipped side chains, and incorrect sugar puckers, can affect biological interpretation, especially in low-resolution or high-resolution structures. MolProbity provides diagnostic charts and graphical outputs to guide manual rebuilding, and its results are beneficial for improving the global database of structures. The tool allows users to upload coordinate files from PDB or NDB databases, add hydrogen atoms, and perform all-atom contact analysis using programs like PROBE. It also evaluates torsion angles, including updated Ramachandran and rotamer analyses, and assesses covalent-geometry parameters such as bond-length and bond-angle outliers. For nucleic acids, MolProbity analyzes all-atom contacts, clash scores, and ribose pucker issues. It also includes automated correction tools like RNABC and AUTOFIX for RNA-suite and side-chain errors, respectively. MolProbity generates a MolProbity score, a log-weighted combination of clashscore, Ramachandran not favored, and bad rotamers, which reflects the quality of a structure at a given resolution. The tool is freely available for download and can be used as a local server, with command-line tools for batch processing. It is also integrated into the PHENIX crystallography system. MolProbity has significantly improved the quality of crystallographic models, as evidenced by reduced error rates and better structural accuracy over time. It is widely used by structural biologists, educators, and researchers for validation, teaching, and structural analysis.MolProbity is a web-based structure validation tool for macromolecular crystallography that evaluates the quality of protein and nucleic acid models at both global and local levels. It uses optimized hydrogen placement and all-atom contact analysis, along with updated covalent-geometry and torsion-angle criteria, to identify and correct errors in structures. These errors, such as Ramachandran outliers, flipped side chains, and incorrect sugar puckers, can affect biological interpretation, especially in low-resolution or high-resolution structures. MolProbity provides diagnostic charts and graphical outputs to guide manual rebuilding, and its results are beneficial for improving the global database of structures. The tool allows users to upload coordinate files from PDB or NDB databases, add hydrogen atoms, and perform all-atom contact analysis using programs like PROBE. It also evaluates torsion angles, including updated Ramachandran and rotamer analyses, and assesses covalent-geometry parameters such as bond-length and bond-angle outliers. For nucleic acids, MolProbity analyzes all-atom contacts, clash scores, and ribose pucker issues. It also includes automated correction tools like RNABC and AUTOFIX for RNA-suite and side-chain errors, respectively. MolProbity generates a MolProbity score, a log-weighted combination of clashscore, Ramachandran not favored, and bad rotamers, which reflects the quality of a structure at a given resolution. The tool is freely available for download and can be used as a local server, with command-line tools for batch processing. It is also integrated into the PHENIX crystallography system. MolProbity has significantly improved the quality of crystallographic models, as evidenced by reduced error rates and better structural accuracy over time. It is widely used by structural biologists, educators, and researchers for validation, teaching, and structural analysis.