MolProbity is a web-based structure validation tool for macromolecular crystallography that evaluates the quality of protein and nucleic acid structures 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 assess model accuracy. MolProbity provides diagnostic charts and graphical outputs to guide manual rebuilding of structures. X-ray crystallography provides detailed atomic structures of proteins, nucleic acids, and complexes, but local errors such as Ramachandran outliers, flipped side chains, and incorrect sugar puckers are common, especially at low resolution. MolProbity helps identify and correct these errors, improving the accuracy of structures and their database entries. MolProbity allows users to upload coordinate files from PDB or NDB databases, add hydrogen atoms, and perform all-atom contact analysis. It evaluates torsion angles, Ramachandran plots, and rotamer analysis, and provides a MolProbity score that combines various validation metrics. It also includes automated correction of Asn/Gln/His flips and other local errors. For nucleic acids, it analyzes sugar puckers and backbone conformers, and provides tools for interface analysis and loop fitting. MolProbity is available as a web service and can be installed locally. It includes command-line tools for batch processing and integrates with other software like PHENIX. The tool has significantly improved the quality of crystallographic models, with a clear trend of improvement in clashscore and flip rates since its introduction. MolProbity is freely available and supports a wide range of users, including structural biologists, students, and researchers. It provides detailed validation results, including charts, graphics, and output files, to help users refine and improve their structures. MolProbity is an essential tool for ensuring the accuracy and reliability of crystallographic data.MolProbity is a web-based structure validation tool for macromolecular crystallography that evaluates the quality of protein and nucleic acid structures 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 assess model accuracy. MolProbity provides diagnostic charts and graphical outputs to guide manual rebuilding of structures. X-ray crystallography provides detailed atomic structures of proteins, nucleic acids, and complexes, but local errors such as Ramachandran outliers, flipped side chains, and incorrect sugar puckers are common, especially at low resolution. MolProbity helps identify and correct these errors, improving the accuracy of structures and their database entries. MolProbity allows users to upload coordinate files from PDB or NDB databases, add hydrogen atoms, and perform all-atom contact analysis. It evaluates torsion angles, Ramachandran plots, and rotamer analysis, and provides a MolProbity score that combines various validation metrics. It also includes automated correction of Asn/Gln/His flips and other local errors. For nucleic acids, it analyzes sugar puckers and backbone conformers, and provides tools for interface analysis and loop fitting. MolProbity is available as a web service and can be installed locally. It includes command-line tools for batch processing and integrates with other software like PHENIX. The tool has significantly improved the quality of crystallographic models, with a clear trend of improvement in clashscore and flip rates since its introduction. MolProbity is freely available and supports a wide range of users, including structural biologists, students, and researchers. It provides detailed validation results, including charts, graphics, and output files, to help users refine and improve their structures. MolProbity is an essential tool for ensuring the accuracy and reliability of crystallographic data.