kinemage web site

MolProbity web site

part 1

part 2

part 3

part 4

multi-crit kinemage

1. MolProbity Analysis

Add H, calculate contacts, and assess geometry by running the MolProbity web service

backrub for main chain

2. Rebuilding in KiNG

Local backbone adjustments using KiNG

rotamers & contact dots in O

3. MolProbity-style Validation in PHENIX and Coot

PHENIX has built-in MolProbity tools, and can interactively call Coot, which in turn can show all-atom-contacts

All-atom contact dots

4. Further Exercises

try one or more of these

More Info about All-atom Contact Analysis


Read, Adams, Arendall, Brunger, Emsley, Joosten, Kleywegt, Krissinel, Lütteke, Otwinowski, Perrakis, Richardson, Sheffler, Smith, Tickle, Vriend, & Zwart (2011) "A New Generation of Crystallographic Validation Tools for the Protein Data Bank" Structure 19: 1395-1412.


Chen, Arendall, Headd, Keedy, Immormino, Kapral, Murray, Richardson, & Richardson (2010) "MolProbity: all-atom structure validation for macromolecular crystallography" Acta Cryst D66:12-21.


Davis, Arendall, Richardson, & Richardson (2006) "The backrub motion: How protein backbone shrugs when a sidechain dances" Structure 14: 265-274.


Arendall, Tempel, Richardson, Zhou, Wang, Davis, Liu, Rose, Carson, Luo, Richardson, & Wang (2005) "A test of enhancing model accuracy in high-throughput crystallography." J Struct Funct Genomics 6: 1-11.


Lovell, Davis, Arendall, de Bakker, Word, Prisant, Richardson, & Richardson (2003) "Structure Validation by Cα Geometry: φ,ψ and Deviation." Proteins: Struct Funct Genetics 50: 437-450.


Lovell, Word, Richardson, & Richardson (2000) "The Penultimate Rotamer Library." Proteins: Struct Funct Genetics 40: 389-408.


Word, Lovell, Richardson, & Richardson (1999) "Asparagine and Glutamine: Using Hydrogen Atom Contacts in the Choice of Side-chain Amide Orientation." J Mol Biol 285: 1735-47.
Jane & Dave Richardson