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CCTBX, which powers this version of MolProbity (4.3), requires stricter adherence to PDB format. If you are having trouble with version 4.3 try using MolProbity4 legacy version 4.02 at Note that not all features are supported on legacy 4.02 and we suggest repairing your PDB format instead.

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Walkthroughs, tutorials, and usage FAQs:

Evaluate X-ray structure: Typical steps for a published X-ray crystal structure or one still undergoing refinement.

Evaluate NMR structure: Typical steps for a published NMR ensemble or one still undergoing refinement.

Fix up structure: Rebuild the model to remove outliers as part of the refinement cycle.

Work with kinemages: Create and view interactive 3-D graphics from your web browser.

Guide to Reduce options: Learn about adding hydrogens to a structure for all-atom contact analysis.

Guide to validation options: Choose validations appropriate to a structure.

What's new in 4.3:

  • New NQH coordinate regularization method after flips in Reduce: a three-step process attempting to match existing coordinates replaces cctbx-based optimization
  • Updates to Omegalyze kinemage output - markup defaults to 'off', separate colors for cis-pro (sea), cis-nonpro (lime), and all twisted (yellow).
  • Improved error catching, with 'how to fix it' notes for common formatting errors

What's new in 4.2:

  • Cis-peptide identification, markup and statistics now available.
  • CaBLAM Cα-based validation of protein backbone and secondary structure now available.
  • Rotamer validation now uses Top8000 rotamer distributions. Favored vs Allowed distinction introduced for rotamers.
  • New coloring scheme in multicriterion chart encodes outlier severity at a glance.
  • Online tutorial explaining markup and methods
  • We now use a conformation-dependent library (CDL) from Dunbrack and Karplus for geometry analysis if requested.

What's new in 4.1:

  • Validation analysis now powered by CCTBX. Also adds geometry regularization for N/Q/H flip corrections. Read more about this change here.
  • Alternate conformations now handled for validation analysis.

Citations, science, and technical FAQs:

Cite MolProbity: Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21.


Davis et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research 35:W375-W383.

Cite KiNG: Chen et al. (2009) KiNG (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program. Protein Science 18:2403-2409.

Cite CCTBX: Grosse-Kunstleve et al. (2002) The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework. J. Appl. Cryst. 35:126-136.

About hydrogens: Why have the hydrogen bondlengths changed?

Installing Java: how to make kinemage graphics work in your browser.

Download MolProbity: how can I run a private MolProbity server, or run from the command line?

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