International Tables for Crystallography (2012). Vol. F, ch. 21.6, pp. 694-701
doi: 10.1107/97809553602060000884

Chapter 21.6. MolProbity: all-atom structure validation for macromolecular crystallography

Contents

  • 21.6. MolProbity : all-atom structure validation for macromolecular crystallography  (pp. 694-701) | html | pdf | chapter contents |
    • 21.6.1. Summary of MolProbity flow and user interactions  (p. 694) | html | pdf |
    • 21.6.2. Validation analyses  (pp. 694-697) | html | pdf |
      • 21.6.2.1. Addition of H atoms  (pp. 694-695) | html | pdf |
      • 21.6.2.2. All-atom contact analysis  (p. 695) | html | pdf |
      • 21.6.2.3. Torsion-angle combinations: updated Ramachandran and rotamer analyses  (pp. 695-697) | html | pdf |
      • 21.6.2.4. Covalent-geometry analyses  (p. 697) | html | pdf |
      • 21.6.2.5. Nucleic acid analyses  (p. 697) | html | pdf |
      • 21.6.2.6. The overall MolProbity score  (p. 697) | html | pdf |
    • 21.6.3. Correction of outliers  (pp. 698-699) | html | pdf |
      • 21.6.3.1. Manual rebuilding  (p. 698) | html | pdf |
      • 21.6.3.2. Automated corrections  (p. 699) | html | pdf |
    • 21.6.4. Other MolProbity utility functions  (pp. 699-700) | html | pdf |
      • 21.6.4.1. Interface analysis  (p. 699) | html | pdf |
      • 21.6.4.2. Protein loop fitting  (p. 699) | html | pdf |
      • 21.6.4.3. Kinemage construction and viewing  (p. 699) | html | pdf |
      • 21.6.4.4. Other file types and functions  (p. 699) | html | pdf |
      • 21.6.4.5. PDB-format interconversion  (pp. 699-700) | html | pdf |
    • 21.6.5. Discussion  (p. 700) | html | pdf |
      • 21.6.5.1. Global versus local, absolute versus comparative  (p. 700) | html | pdf |
      • 21.6.5.2. Impact on database quality  (p. 700) | html | pdf |
    • 21.6.6. MolProbity availability  (p. 701) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 21.6.1.1. An outlier legend, showing each symbol used in a MolProbity multi-criterion kinemage and illustrating the relationship of the three types of all-atom contact to the atomic van der Waals (vdW) surfaces (spheres of small grey dots)  (p. 694) | html | pdf |
      • Fig. 21.6.1.2. Two multi-criterion validation kinemages illustrating the successful outcome of an overall process of MolProbity diagnosis and structure improvement  (p. 695) | html | pdf |
      • Fig. 21.6.2.1. The simple `flip' correction of a Gln side-chain amide in the 2dq4 threonine 3-dehydrogenase structure  (p. 695) | html | pdf |
      • Fig. 21.6.2.2. A MolProbity results summary and sortable multi-criterion chart for the 1n78 Glu tRNA-synthetase complex at 2.1 Å resolution  (p. 696) | html | pdf |
      • Fig. 21.6.2.3. The general case Ramachandran kinemage and the C β deviation kinemage for file 2dq4   (p. 696) | html | pdf |
      • Fig. 21.6.2.4. Close-up of a ribose-pucker outlier in the multi-criterion kinemage for 1n78 , with backbone and bases turned on  (p. 698) | html | pdf |
      • Fig. 21.6.3.1. Rebuilding of a backward-fitted Leu side chain in KiNG off-line in the DNA polymerase 1xwl at 1.7 Å resolution  (p. 698) | html | pdf |
      • Fig. 21.6.5.1. MolProbity -relevant quality criteria as a function of time for all structures in the PDB at a middle range of resolution, separately fitted before and after introduction of the web site  (p. 700) | html | pdf |