ribbon display from Mage

Kinemages: 3D interactive graphics

"The Mage Page" discusses the history and of kinemages; some premade kinemage files are in kinemage list, or download section.   At the extremes, kinemages can be displayed in immersive virtual reality with Kinimmerse or on mobile-device Safari browsers with Magekinjas.


All-atom Contact analysis in Mage

Software: Display & Contacts & Utilities

For those working with RNA: Suitename reports on RNA backbone conformers either in MolProbity or standalone. See also links to collaborators' software, such as ERRASER, a thorough RNA backbone correction system.


Portion of new Ramachandran contours

Structural Informatics: datasets, libraries, etc.

Top8000 dataset (supersedes Top500)
HiQ54 dataset High Quality for critical methods-testing
Top500 dihedral distributions (click to download zip archive of rotamer librarytop500-angles.050606.zip 80MB) & README for Ramachandran contours and rotamer scoring, Top500 proteins with optimized H atoms, sidechain rotamer libraries,
RNA backbone rotamers vintage RNA05 (will be superseded by RNA11)


MolProbity Logo slice

MolProbity: structure validation, with new H parameters (March 2013)

Web service for all-atom contact, conformation, & geometry analysis of x-ray or NMR models, with automated correction of Asn/Gln/His flips. As a structure user, you can easily evaluate reliability of the parts you care about.

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 explore from the RLab research index page. [Caveat: seldom updated]


Monoclinic SG bears in Mage

Teaching: Course materials

Duke courses: BCH622, BCH681, BCH258 (old), BCH291 (old).
Workshop material: on-line tutorial on MolProbity validation and rebuilding; CSHL X-Ray course practical exercises; and others.


SOD drawing

Gallery: images, etc.

Visit Jane's WikiMedia Commons page for macromolecular & other images. View the on-line HTML version (or download PDFs) of the annotated Anatomy and Taxonomy of Protein Structure. Try a small selection of other 2D images.


Duke Chapel and cranes

About us: RLab info and links

Lab members; directions to the lab; publications: recent, classic, and dissertations; lab links & partners in quality: PHENIX, ROC (RNA Ontology), Duke Biochemistry Dept., SBB Pgm (Structural Biology & Biophysics), CBB Pgm (Computational Biology & Bioinformatics), WikiProject Biophysics.