Coot Tools for Model Building and Validation

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Presentation transcript:

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) Xfit [XtalView] (D. McRee) Free Software GUI design considered important

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

Stuart McNicholas Alexei Vagin Eugene Krissinel Kevin Cowtan

Diamond, R. (1971). Acta Cryst. A 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

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

Some more Coot Tools…

Top500-based distribution

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

1plu vs. 1dab

Handling NCS…

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

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

Torsion-based Validation Ramachandran Plots Omega distortion Rotamer analysis

Nomenclature correction (fix-nomenclature-errors 1)

Ramachandran Plot for residues with CB

Ramachandran Plot for GLY

Ramachandran Plot for PRO

(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)

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

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