[CSHL Web Site]

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. All-atom Contacts Tools in Coot & O

Rebuilding with A-aCA along with rotamer selection in Coot and O.

All-atom contact dots

4. Optional exercises

Optional (more) Examples

More Info about All-atom Contacts Analysis


J. S. Richardson, W.B. Arendall III, and D. C. Richardson (2003) "New Tools and Data for Improving Structures, Using All-Atom Contacts. " Chapter in Methods in Enzymology: Macromolecular Crystallography, Part D, ed. C.W. Carter, Jr and R.M. Sweet. Academic Press (San Diego) 374: 385-412.


I.W. Davis, L.W. Murray, J.S. Richardson, and D.C. Richardson (2004) "MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes." Nucleic Acids Research 32(Web Server Issue):W615-619


S.C. Lovell, I.W. Davis, W.B. Arendall III, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, and D.C. Richardson (2003) "Structure Validation by Cα Geometry: φ,ψ and Cβ Deviation." Proteins: Structure, Function and Genetics 50: 437-450.


New rotamer library (the one of stereochemduke.odb)
S. C. Lovell, J. M. Word, J. S. Richardson, and D. C. Richardson (2000) "The Penultimate Rotamer Library." Proteins: Struct Function and Genetics 40: 389-408.


I.W. Davis, W.B. Arendall III, D.C. Richardson, and J.S. Richardson (2006) "The backrub motion: How protein backbone shrugs when a sidechain dances" Structure 14: 265-274


W.B. Arendall III, W. Tempel, J.S. Richardson, W. Zhou, S. Wang, I.W. Davis, Z.-J. Liu, J.P. Rose, W.M. Carson, M. Luo, D.C. Richardson, and B-C. Wang (2005) "A test of enhancing model accuracy in high-throughput crystallography." Journal of Structural and Functional Genomics 6:1-11.

A page with links to more info sources: including typographical conventions used in these pages, mouse key maps, and software "readme" pages.

Jane & Dave Richardson