Dale E. Tronrud

Senior Research Associate

Howard Hughes Medical Institute

Institute of Molecular Biology

University of Oregon

Eugene, OR 97403

det101@uoxray.uoregon.edu

Welcome to my home page! Here you will find links to the TNT web site and hypertext versions of a number of my papers. You will also find some nice photos of Oregon.

TNT

TNT is a package of programs used to optimize the fit of a model of a protein/nucleic acid to X-ray diffraction data while maintaining quality bond lengths, angles, and other good things.

Papers

(html) (pdf) An Efficient General-Purpose Least-Squares Refinement Program for Macromolecular Structures. Acta Cryst. (1987). A43, 489-501
(html) (pdf) Conjugate-Direction Minimization - An Improved Method for the Refinement of Macromolecules. Acta Cryst. (1991). A48, 912-916
(html) (pdf) Methods of Minimization and their Implications. "Proceedings of the CCP4 Study Weekend", 1994
(html) (pdf) Knowledge-Based B-Factor Restraints for the Refinement of Proteins, J App Cryst. (1996). 29(2), 100-104
(html) (pdf) The Limits of Interpretation, "Proceedings of the CCP4 Study Weekend", 1996
(html) (pdf) The Joint Refinement of Inhibitors of Thermolysin ,"Proceedings of the Macromolecular Crystallographic Computing School", Eds Phil Bourne, and Keith Watenpaugh, 1996
(html) (pdf) The TNT Refinement Package. in Macromolecular Crystallography, Part B, Eds Charlie Carter, and Robert Sweet, Volume 277 in Methods in Enzymology, pp 306-319, 1997
(html) (pdf) The Efficient Calculation of the Normal Matrix in Least-Squares Refinement, Acta Cryst. (1999). A55, 700-703
(html) (pdf) Introduction to Macromolecular Refinement, "Proceedings of the CCP4 Study Weekend", Acta Cryst. (2004). D60, 2156-2168

PowerPoint Presentations

Introduction to Macromolecular Refinement, York Refinement Workshop, January 2001
Stereochemical Dictionaries, York Refinement Workshop, January 2001

Photos

Yapoha Crater (260Kb) is a small cinder cone located just north of the North Sister in the central Cascades.
Teardrop Pool (218Kb) is located in the summit crater of the South Sister.
Ft. Rock (262Kb) is a highly eroded volcanic crater located in the high desert of Central Oregon. This area was a shallow lake during the ice age when the eruption occurred.
View of the Central Cascades (213Kb) from the north slope of Mt. Jefferson. This photo was taken at dawn.
Mt. St. Helens (297Kb) as seen from near Spirit Lake.
Mt. St. Helens' dome (291Kb) as seen from the crater rim. Spirit Lake, partially covered by floating logs, is to the right with Mt. Rainier almost hidden in the clouds above it.