All-atom Contact Analysis Tutorial, Introduction

This three-part tutorial is intended as a self-paced (although we use the practicals for workshops), self-guided introduction to using all-atom contacts in macromolecule building and refinement. While you will be introduced to a powerful toolset, there are other tools available, and we invite you to explore them on our website (http://kinemage.biochem.duke.edu/).

Parts of the practical -- The tutorial lessons:

Add H, calculate contacts, and assess geometry by running the MolProbity web service.
Repair of problem sidechains using the interactive KiNG/Probe system
Local backbone adjustments using KiNG

The HTML pages, associated image files and datafiles (coordinate files, kinemage files, and maps) comprising this tutorial can be downloaded as a zip archive a-acaTutorial.zip.

Reprint PDFs

(296KB) 2000Lovell	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. New rotamer library (the one of stereochemduke.odb)
(790KB) 2003Lovell	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. updates Ramachandran plot contours and introduces the C-beta-deviation measure
(780KB) 2003Methods	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. All-atom contact methodology applied to crystallography; from Methods In Enzymology, Vol. 374
(368KB) 2005Arendall	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. Statistics showing large improvements using these tools.

Typographical conventions used in these worksheets:

filenames are in bold,
command-line inputs are in fixed-width, execution of the command is implied
command-line prompts are indicated as shell>
menu commands > menu-pulldowns are in italics, note the '>' separator to indicate sub-menues.
dialog-box inputs & selections are by context.

Suggestions for your own use later: Try MolProbity on your own structures

Upload your PDB-format file into MolProbity. Add hydrogens, check geometry, and look at the contacts, as done in Part 1 above. If the structure is not too big, try making a Multri-crit kinemage. (Check out your competitor's structures, too!)
As a minimum, any structure should have its Asn/Gln/His flips corrected before deposition. If the MolProbity statistics look good already, or if these correction procedures are used to make them so, those statistics can be reported as REMARK 42 in the PDB header, which will soon be available as an output from MolProbity.

Alternative procedures for running locally

To run the functionalities of Part 1 locally on your own system (Linux, Unix, Mac OSX, etc.) rather than on the web, download KiNG or Mage; and Prekin, Probe, Reduce, Flipkin, and Clashlist from our web site at http://kinemage.biochem.duke.edu/ and put them in your path. (Note: KiNG is the only program that requires JAVA. Mage is an older C program that will do everything here that KiNG does except the backbone corrections. So in the commands given here, either Mage or KiNG will do.)

Run them with the following commands:
To add and optimize H atoms,

shell> reduce -build 1xyz.pdb >1xyzH.pdb

To run an automated check for amide and His flips, and produce animated kinemages:

shell> flipkin 1xyzH.pdb >1xyzNQflip.kin
shell> flipkin -h 1xyzH.pdb >1xyzHisflip.kin

Look at it in Mage:

shell> mage 1xyzNQflip.kin

Make a kinemage graphics file of the structure by:

shell> prekin -lots 1xyzH.pdb >1xyzH.kin

Add all-atom contacts with:

shell> probe 1xyzH.pdb >>1xyzH.kin

Then look at it in Mage.

For a clustered list of clashes, and an overall clashscore, run

clashlist 1xyzH.pdb >1xyzHclcl.txt

All-atom contacts and rotamers in XtalView and O

Our "penultimate" rotamer library is available as a drop-in files from our web site for XtalView and O (also available from the O web site). XtalView and Mi-fit can invoke our all-atom clashes. Our Website has a macro for invoking all-atom contact dot display in O, and instructions for its use.

HTML README files for related software

Reduce	Probe	clashlist
flipkins	kincontours
O - probe	O - rotamers

For help, questions, or bug reports later, contact:
Dave or Jane Richardson
e-mail: dcrjsr AT kinemage.biochem.duke.edu

Structure Validation Workshop

Using All-Atom Contact Analysis for Model Diagnosis & Repair