Main page - MolProbity Main page Main page About hydrogens Evaluate X-ray Evaluate NMR Fix up structure Work with kins View & download files Lab notebook Feedback & bugs Site map Save session Log out You are using 0% of your 200 Mb of disk space. File Upload/Retrieval (more options) PDB/NDB code: type: PDB coords PDB coords & xray data Biol. unit (PDB only) Biol. unit & xray data (PDB only) 2Fo-Fc map (EDS) Fo-Fc map (EDS) type: PDB coords xray data (mtz format) kinemage ED map het dict File is from CNS refinement Ignore segID field CCTBX, which powers this version of MolProbity (4.2), requires stricter adherence to PDB format. If you are having trouble with version 4.2 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: 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 validation options: Choose validations appropriate to a structure. 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. Common questions: 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? NB: the back button doesn't work inside MolProbity About MolProbity | Website for the Richardson Lab | Using ecloud x-H | Internal reference 4.2
