kinemage web site

MolProbity web site

ace of clubs

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 Tools in Coot and PHENIX

Rebuilding with all-atom contact analysis along with rotamer selection in Coot improves refinement in PHENIX

All-atom contact dots

4. Further Exercises

try one or more of these

More Info about All-atom Contact Analysis


Davis, Leaver-Fay, Chen, Block, Kapral, Wang, Murray, Arendall, Snoeyink, Richardson & Richardson (2007) "MolProbity: all-atom contacts and structure validation for proteins and nucleic acids" Nucleic Acids Research 35(Web Server Issue):W375-383


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." 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." JMB 285: 1735-47.
Jane & Dave Richardson