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MolProbity will be updating very soon! Please try MolProbity 4.2 beta here.
CCTBX, which powers this version of MolProbity (4.1), requires stricter adherence to PDB format. If you are having trouble with version 4.1 try using MolProbity4 legacy version 4.02 at

Walk-thrus & tutorials:

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.

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.

What's new in 4.0:

  • Updated Reduce-added hydrogen lengths to be more consistent with other crystallography software.
  • New Top8000 Ramachandran validation information.
  • Allows use of both electron cloud and nuclear x-H bond-lengths. Read more about this change here.
  • Full support for 2-character CHAINIDs added. 4-character SEGIDs also supported in place of CHAINIDs.

Common questions:

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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