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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 http://rutile.biochem.duke.edu. Note that not all features are supported on legacy 4.02 and we suggest repairing your PDB format instead.

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.

and/or

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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