1. Coot Tools for Model Building and Validation
Aug Firenze
Coot Tools for Model Building and Validation
Paul Emsley
University of York

2. Coot Molecular Graphics application
Protein Crystallographic model-building tools
An implementation of several of the ideas in:
O (A. Jones)
Quanta (T. Oldfield)
Xfit [XtalView] (D. McRee)
Free Software
GUI design considered important

3. Components Clipper Mmdb GTk+ GSL Guile/python GNU Auto tools OpenGL
Eugene Krissinel’s coordinate library
GTk+
GSL
Guile/python
scripting
GNU Auto tools
portability
OpenGL

4. Stuart McNicholas
Alexei Vagin
Eugene Krissinel
Kevin Cowtan

6. Diamond, R. (1971). Acta Cryst. A
Real Space Refinement
Diamond, R. (1971). Acta Cryst. A
27,
Major feature of Coot
Gradient minimizer (BFGS derivative)
Based on mmCIF standard dictionary
Minimizing bonds, angles, planes, non-bonded contacts, torsions, [chiral volumes]
Provides “interactive refinement”
Different minimizer to Refmac…
…means “nice & tight” geometry
Chi squareds

7. Refmac Dictionary
CIF formatted organized storage of chemical prior knowledge
Alexei Vagin

8. Some more Coot Tools…

15. Top500-based distribution

17. SSM SSM (Secondary Structure Matching)
Made available as a web service (MSDFold)
Or as an application library
Under the GNU LGPL
by Eugene Krissinel at EBI

20. 1plu vs. 1dab

21. Handling NCS…

25. Feature Integration Refinement Validation External Internal
e.g. REFMAC
Internal
External
e.g. MolProbity

26. Validation Tools Geometry Distortion Bonds, Angles, Planes
B-factor variance
Density Fit
Water check
By distance/map density/B-factor
By difference map variance
Un-modelled density blobs

28. Torsion-based Validation
Ramachandran Plots
Omega distortion
Rotamer analysis

31. Nomenclature correction
(fix-nomenclature-errors 1)

33. Ramachandran Plot for residues with CB

34. Ramachandran Plot for GLY

35. Ramachandran Plot for PRO

36. (with the assistance of Ethan Merritt)
Raster3D
The “render-image” function provides output for raster3d’d render
… and then runs it…
… and displays the final image…
(with the assistance of Ethan Merritt)

39. Moving towards…. …an intuitive and powerful tool
For analysis (validation)
And correction (model-building)
I want Coot to be used productively
And provide an enjoyable experience
Available for PC GNU/Linux, Windows, Macintosh, sgi IRIX

40. Acknowledgements Kevin Cowtan Eleanor Dodson Keith Wilson
Libraries, dictionaries
Alexei Vagin, Eugene Krissinel, Stuart McNicholas
Dunbrack, Richardsons
Coot testers
William Scott, Ezra Peisach, Bernhard Lohkamp
York YSBL, Dundee, Glasgow
Coot Mailing List subscribers or
Google: Emsley Coot