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Coot Tools for Model Building and Validation

Aug 2005 Firenze. Coot Tools for Model Building and Validation. Paul Emsley. University of York. Coot. Molecular Graphics application Protein Crystallographic model-building tools An implementation of several of the ideas in: O (A. Jones) Quanta (T. Oldfield)

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Coot Tools for Model Building and Validation

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  1. Aug 2005 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 • Eugene Krissinel’s coordinate library • GTk+ • GSL • Guile/python • scripting • GNU Auto tools • portability • OpenGL

  4. Stuart McNicholas Alexei Vagin Eugene Krissinel Kevin Cowtan

  5. Real Space Refinement Diamond, R. (1971). Acta Cryst. A 27, 436-452. • 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

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

  7. Some more Coot Tools…

  8. Top500-based distribution

  9. 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

  10. 1plu vs. 1dab

  11. Handling NCS…

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

  13. 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

  14. Torsion-based Validation • Ramachandran Plots • Omega distortion • Rotamer analysis

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

  16. Ramachandran Plot for residues with CB

  17. Ramachandran Plot for GLY

  18. Ramachandran Plot for PRO

  19. 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)

  20. 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

  21. Acknowledgements http://www.ysbl.york.ac.uk/~emsley/coot or Google: Emsley Coot • 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

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