O Stuff

List originally compiled by Mitchell D. Miller for Rice University Crystallography Practicum.

WWW O - official WWW server for users of the O - (Aarhus)
http://www.bioxray.dk/~mok/o-files.html
Alwyn's Home page - links about distribution, recent versions, and new commands http://alpha2.bmc.uu.se/~alwyn/
Uppsala Software Factory - Gerards Kleywegts Software http://alpha2.bmc.uu.se/~gerard/manuals/
The O FAQ http://imsb.au.dk/~mok/o/ofaq/ofaq.html
Distribution of usefull O macro's with descriptions http://alpha2.bmc.uu.se/~gerard/manuals/omac_index.html
Official O FTP server for updates (registered O users only) ftp://alpha2.bmc.uu.se/pub/

Primary O reference

T.A. Jones, J.Y. Zou, S.W. Cowan & M. Kjeldgaard, "Improved methods for building protein models in electron density maps and the location of errors in these models", Acta Cryst. A47, 110-119 (1991).

Initial FRODO references

T.A. Jones, "A graphics model building and refinement system for macromolecules", J. Appl. Cryst. 11, 268-272 (1978).
Jones, T.A. (1985). Interactive computer graphics: FRODO. Meth Enzymol 115, 157-171.
Jones, T.A. (1982). ??? In "Computational Crystallography", edited by D. Sayre. Clarendon Press, Oxford, pp. 303 - 317.
Kleywegt, G.J. and Jones, T.A. (1997). Model-building and refinement practice. Meth Enzymol 277, 208-230. (Preprint HTML)
Jones, T.A. and Kjeldgaard, M. (1997). Electron-Density Map Interpretation. Meth Enzymol 277, 173-208.

Use of databases

Jones, T.A. and Thirup, S. (1986). Using known substructures in protein model building and crystallography. EMBO J 5, 819-822.

Use of real space refinement

Jones, T.A. and Liljas, L. (1984). Crystallographic refinement of macromolecules having non-crystallographic symmetry. Acta Cryst A40, 50-57.
Kleywegt, G.J. and Jones, T.A. (1996). Efficient rebuilding of Protein Structures. Acta Cryst D52, 829-833.
Zou, J.Y. and Jones, T.A. (1996). Towards the automatic interpretation of macromolecular electron-density maps: qualitative and quantitative matching of protein sequence to map. Acta Cryst D52, 833-841.
Jones, T.A. and Kjeldgaard, M. (1994). Making the first trace with O. In "From First Map to Final Model", edited by S. Bailey, R. Hubbard and D. Waller. SERC Daresbury Laboratory, Warrington, pp. 1-13.
Kleywegt, G.J. and Jones, T.A. (1994). Halloween ... masks and bones. In "From First Map to Final Model", edited by S. Bailey, R. Hubbard and D. Waller. SERC Daresbury Laboratory, Warrington, pp. 59-66.
Kleywegt, G.J. and Jones, T.A. (1997). Template convolution to enhance or detect structural features in macromolecular electron-density maps. Acta Cryst D53, 179-185

MISC References

Brändén, C.I. and Jones, T.A. (1990). Between objectivity and subjectivity. Nature 343, 687-689.
Kleywegt, G.J. and Jones, T.A. (1995). Where freedom is given, liberties are taken. Structure 3, 535-540.
Lattman, E.E. (1996). Why are Protein Crystallographic R-Values So High? PROTEINS: Struct. Funct. & Genetics 25, i-ii.
Hodgson, J. (1993) The Good, the Bad, and the Indifferent: A story of protein structure (mis)interpretation that unfolds with every new beta-turn. BIO/Technology 11, 36-37.
Hooft, R.W.W., Vriend, G., Sander, C. and Abola, E.E. (1996) Errors in protein structures. Nature 381, 272.
Kleywegt, G.J. and Jones, T.A. (1996). Phi/psi-chology: Ramachandran revisited. Structure 4, 1395-1400.
Zou, J.Y. and Mowbray, S.L. (1994). An evaluation of the use of databases in protein structure refinement. Acta Cryst D50, 237-249.
Dodson, E., Kleywegt, G.J. and Wilson, K.S. (1996). Report of a workshop on the use of statistical validators in protein X-ray crystallography. Acta Cryst D52, 228-234.
Kleywegt, G.J. and Brünger, A.T. (1996). Checking your imagination: applications of the free R value. Structure 4, 897-904.
Kleywegt, G.J. and Read, R.J. (1997). Not your average density. Structure 5, 1557-1569.