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Coot Tools for Coot Tools for Model Building Model Building
and and ValidationValidation
Paul EmsleyPaul Emsley
Aug 2005 FirenzeAug 2005 Firenze
University of YorkUniversity of York
CootCoot
Molecular Graphics applicationMolecular Graphics application Protein Crystallographic model-building toolsProtein Crystallographic model-building tools
An implementation of several of the ideas An implementation of several of the ideas in:in: OO (A. Jones) (A. Jones) QuantaQuanta (T. Oldfield) (T. Oldfield) Xfit [XtalView] (D. McRee)Xfit [XtalView] (D. McRee)
Free SoftwareFree Software
GUI design considered importantGUI design considered important
Components
• Clipper • Mmdb
– Eugene Krissinel’s coordinate library
• GTk+• GSL• Guile/python
– scripting
• GNU Auto tools– portability
• OpenGL
Eugene KrissinelEugene Krissinel Kevin CowtanKevin Cowtan
Alexei VaginAlexei Vagin
Stuart McNicholasStuart McNicholas
Major feature of CootMajor feature of Coot Gradient minimizer (BFGS derivative)Gradient minimizer (BFGS derivative) Based on mmCIF standard dictionaryBased on mmCIF standard dictionary Minimizing bonds, angles, planes, non-Minimizing bonds, angles, planes, non-
bonded contacts, torsions, [chiral bonded contacts, torsions, [chiral volumes]volumes]
Provides “interactive refinement”Provides “interactive refinement” Different minimizer to Refmac…Different minimizer to Refmac…
……means “nice & tight” geometrymeans “nice & tight” geometry Chi squaredsChi squareds
Real Space RefinementReal Space RefinementDiamond, R. (1971). Diamond, R. (1971). Acta CrystActa Cryst. A. A
27, 436-452.27, 436-452.
Refmac DictionaryRefmac Dictionary
CIF formatted organized storage of CIF formatted organized storage of chemical prior knowledgechemical prior knowledge
Alexei VaginAlexei Vagin
Some more Coot Tools…Some more Coot Tools…
Top500-based distributionTop500-based distribution
SSMSSM
SSM (Secondary Structure SSM (Secondary Structure Matching)Matching)
Made available as a web service Made available as a web service (MSDFold)(MSDFold)
Or as an application libraryOr as an application library Under the GNU LGPLUnder the GNU LGPL
by Eugene Krissinel at EBIby Eugene Krissinel at EBI
1plu vs. 1dab
Handling NCS…Handling NCS…
RefinementRefinement
ValidationValidationExternalExternal
e.g.e.g. REFMAC REFMAC
InternalInternal
InternalInternal
ExternalExternal
e.g.e.g. MolProbity MolProbity
Feature IntegrationFeature Integration
Validation ToolsValidation Tools Geometry DistortionGeometry Distortion
Bonds, Angles, PlanesBonds, Angles, Planes B-factor varianceB-factor variance Density FitDensity Fit Water check Water check
By distance/map density/B-factorBy distance/map density/B-factor By difference map varianceBy difference map variance
Un-modelled density blobsUn-modelled density blobs
Torsion-based ValidationTorsion-based Validation
Ramachandran PlotsRamachandran Plots Omega distortionOmega distortion Rotamer analysisRotamer analysis
Nomenclature correctionNomenclature correction
(fix-nomenclature-errors 1)(fix-nomenclature-errors 1)
Ramachandran Plot for residues with CB
Ramachandran Plot for GLY
Ramachandran Plot for PRO
Raster3DRaster3D
The The “render-image”“render-image” function provides function provides output for raster3d’d renderoutput for raster3d’d render
… … and then runs it…and then runs it… … … and displays the final image…and displays the final image…
(with the assistance of Ethan Merritt)
Moving towards….Moving towards….
……an intuitive and powerful toolan intuitive and powerful tool For analysis (validation)For analysis (validation) And correction (model-building)And correction (model-building)
I want Coot to be used productively I want Coot to be used productively And provide an enjoyable experienceAnd provide an enjoyable experience
Available for PC GNU/Linux, Windows, Available for PC GNU/Linux, Windows, Macintosh, sgi IRIXMacintosh, sgi IRIX
AcknowledgementsAcknowledgements Kevin CowtanKevin Cowtan Eleanor DodsonEleanor Dodson Keith WilsonKeith Wilson
Libraries, dictionariesLibraries, dictionaries Alexei Vagin, Eugene Krissinel, Stuart McNicholasAlexei Vagin, Eugene Krissinel, Stuart McNicholas Dunbrack, RichardsonsDunbrack, Richardsons
Coot testersCoot testers William Scott, Ezra Peisach, Bernhard LohkampWilliam Scott, Ezra Peisach, Bernhard Lohkamp York YSBL, Dundee, GlasgowYork YSBL, Dundee, Glasgow Coot Mailing List subscribersCoot Mailing List subscribers
http://www.ysbl.york.ac.uk/~emsley/coot
or or
Google: Emsley CootGoogle: Emsley Coot