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Validation Of Structural Models

Tools for finding, and perhaps fixing, errors in models


Model Assessment  

 MolProbity Click the icon at left to see these tools in action. Submit your own coordinates or choose a PDB entry.

These tools assess the quality of a macromolecular model directly, using geometry and physics (but not electron density or energies). As well as global values, they give local assessments for each residue, with both graphical and numerical output.


All-Atom Contact Analysis Assessment and display of atomic overlaps or "clashes", including all H-atoms.
Asn / Gln / His Flips Analysis and correction of sidechain amide and imidazole orientations, using atomic clashes as well as H-bond networks.
Ramachandran Redux Updated assignment of core, allowed, and forbidden phi,psi values from 100,000 B-filtered high resolution data points.


Crystallographic (re)-Building

Tools for assessing and improving the model during the process of crystallographic structure solution.


The Issue of Hydrogens All-atom contacts (or any packing analysis) require explicit hydrogen atoms, which can be added by our program Reduce.
Scanning for Problem Areas Probe can be run on an entire structure to get a display, or a list, of all serious atomic clashes.
Using Probe within XtalView for interactive display of clashes while model-to-map fitting.
Using Probe within O scripts to show clashes while model-to-map fitting.
Side Chain Rotamer Library drop-in files for use of our improved rotamer library in O or XtalView
Displaying Explicit Hydrogens in O O parameter files for hydrogen atoms (not recommended for most uses).



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