Kinemage Home Page at The Richardson Laboratory

MolProbity (and also our other software) has been updated to work with the new PDB format v3.0 instituted August 1. MolProbity input files will be converted if necessary, and procedures run and output produced in the new format. [However, there is an option to "downgrade" to v2.3 format for output.]
Please report any problems to us. If you need to do bulk runs with our programs off-line, we'd be glad to help.

ribbon display from Mage

Kinemages: 3D interactive graphics

"The Mage Page" discusses the what, where, and how of kinemage; some popular kinemage files are available from our kinemage list, while more kinemages can be gotten browsing our download section  ...

All-atom Contact analysis in Mage

Software: Display & Contacts & Utilities

"Remediator" script (Perl or Python) is a fast and accurate converter of "new" and "old" formats. Two new programs are available: Suitename for RNA backbone conformer analysis; and, Dangle, a Java-based geometry calculator.

Portion of new Ramachandran contours

Databases: protein & nucleic acid compilations

Top500 angle dataset (click to download zip archive of rotamer librarytop500-angles.050606.zip 80MB) & README for Ramachandran contours and rotamer scoring distributions, Top500 proteins with optimized H atoms, rotamer libraries, RNA backbone rotamers,  ...

MolProbity Logo slice

MolProbity: structure validation

Web service for all-atom contact and geometrical analysis of your model.
Click this section's header, the image at left, or the MolProbity badge in any of the menus to go to the initial page of the MolProbity server.

Local backbone movements

Research: 3D structure of proteins & nucleic acids

All-atom contacts; structure validation & improvement; protein backbone motions; protein sidechain rotamers; RNA backbone rotamers, or view the RLab research index page.

Monoclinic SG bears in Mage

Teaching: Course materials

Duke courses: BCH222, BCH258, BCH291, & CHEM22L.
Off-site workshops: on-line tutorial on validation and rebuilding (updated from the 2005 ACA convention short course); CSH X-Ray Course, annual course; and others.

SOD drawing

Gallery: images

Take in our 2D images and 3D kinemages. View the on-line HTML version of the annotated Anatomy and Taxonomy of Protein Structure, or download the PDF pages.

Duke Chapel and cranes

About us: Lab Info

(very) Odds n' (no) Ends re. RLab: lab members, directions to the lab, select publications, lab wiki, lab links & partners in quality: PHENIX, ROC (RNA Ontology), SECSG, Duke Biochem. Dept., Duke SBB program

    "This page generated by:"
NIH Grant GM-073930  New Kind of Quality Management for X-ray & NMR Models
NIH Grant GM-074127  Inverse Kinematics, Sterics & Data - To Fit RNA Backbone
NIH Grant GM-073919  MolProbity Service & Related 3D-Analysis Resources
Program Grant (5P01)GM-063210  Protein Structure Initiative - "PHENIX: new methods for automated macromolecular crystallography (Project V)"
{NIH Grant GM-15000  Analysis & Design of Protein Structures (historically, long-term)}