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MolProbity4 structure validation now provides many of its validation metrics through CCTBX, the open-source component of the Phenix crystallographic package. CCTBX allows for consistent validation results with Phenix, as well as added functionality, such as geometry regularization of NQH flips. Read more about this change here.

We have updated Reduce to add hydrogens at a length more consistent with electron-cloud positions, and accordingly adjusted the Van der Waals radii in Probe to compensate for the change. This will affect comparison of results calculated with older versions of MolProbity, but generally results in lower clashscores. For analyses using nuclear-position hydrogens, you have the option of selecting nuclear x-H positions when adding hydrogens. Read more about this change here.

Ramachandran scoring has also been updated to use new six-category distributions, derived from a larger Top8000 dataset of high quality PDB files.

Please don't hesitate to report any bugs you may encounter.

If for some reason you need to use MolProbity4 version 4.02, which is now a retired legacy version, please go to

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.
  • 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.
  • 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?

NB: the back button doesn't work inside MolProbity