Structure Validation Workshop
Using All-Atom Contact Analysis for Model Diagnosis & Repair
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/).
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.
(2000) "The Penultimate Rotamer Library." Proteins: Struct Function and Genetics 40, 389-408.
(2003) "Structure Validation by Cα Geometry: φ,ψ and Cβ Deviation." Proteins: Structure, Function and Genetics 50, 437-450.
(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.
(2005) "A test of enhancing model accuracy in high-throughput crystallography." Journal of Structural and Functional Genomics 6, 1-11.
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.
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,
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.
|O - probe||O - rotamers|
For help, questions, or bug reports later, contact:
Dave or Jane Richardson
e-mail: dcrjsr AT kinemage.biochem.duke.edu