coot tools for model building and validation paul emsley aug 2005 firenze university of york

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