common coot fulica atra - mitweb.mit.edu/pmueller/www/aca2007/wk01/coot.pdf · 2007. 8. 1. ·...
TRANSCRIPT
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CommonCommon CootCoot
((Fulica atraFulica atra))
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Coot and SHELXCoot and SHELXHow Coot can expedite structure How Coot can expedite structure
refinement and validation with SHELXrefinement and validation with SHELX
Paul EmsleyPaul Emsley
University of OxfordUniversity of Oxford
July 2007July 2007
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CootCoot Molecular Graphics applicationMolecular Graphics application
Protein Crystallographic modelbuilding toolsProtein Crystallographic modelbuilding tools Aim: “Slick and powerful” interface to CCP4 Aim: “Slick and powerful” interface to CCP4
Interface to other programs: SHELXL, Refmac, Interface to other programs: SHELXL, Refmac, Libcheck, Probe&Reduce (Molprobity), EBI, Libcheck, Probe&Reduce (Molprobity), EBI, EDS, Povray, Raster3D… and others.EDS, Povray, Raster3D… and others.
Several modelbuilding and validation toolsSeveral modelbuilding and validation tools
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Feature IntegrationFeature Integration
InternalInternal
ValidationValidation
RefinementRefinement
InternalInternalExternalExternal
ExternalExternale.g.e.g. MolProbity MolProbity
e.g.e.g. REFMAC REFMAC
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Validation FeaturesValidation Features Geometry DistortionGeometry Distortion
Bonds, Angles, PlanesBonds, Angles, Planes Bfactor varianceBfactor variance Density FitDensity Fit Peptide Omega anglePeptide Omega angle Water check Water check
By distance/map density/BfactorBy distance/map density/Bfactor By difference map varianceBy difference map variance
Unmodelled density blobsUnmodelled density blobs [Richardson’s Validation tools][Richardson’s Validation tools]
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Coot SHELXCoot SHELX Coot can read SHELX Coot can read SHELX .res.res Coot can read SHELX Coot can read SHELX .fcf .fcf Coot can read SHELX Coot can read SHELX .lst.lst Coot can write SHEL Coot can write SHEL .ins .ins
(This could be better)(This could be better) Add in GUI elements and some scriptingAdd in GUI elements and some scripting Complete SHELX interface in a Coot sessionComplete SHELX interface in a Coot session
work in progress (work in progress (i.e.i.e. not today) not today)
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Raster3D The “renderimage” function provides
output for raster3d’d render … and then runs it… … and displays the final image…
(with the assistance of Ethan Merritt)
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Futures…Futures… Under DevelopmentUnder Development
There may be bugsThere may be bugs Aim: Aim:
Slick, easy to useSlick, easy to use PowerfulPowerful Smooth interface to external applicationsSmooth interface to external applications
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Eugene KrissinelEugene Krissinel Kevin CowtanKevin Cowtan
Alexei VaginAlexei Vagin
Stuart McNicholasStuart McNicholas
+Francois Remacle+Francois Remacle
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Thanks to...Thanks to... Bernhard Lohkamp, William Scott, Eleanor Dodson, Bernhard Lohkamp, William Scott, Eleanor Dodson,
Karen McLuskey, Charlie Bond, Miguel Ortiz Lombardia, Karen McLuskey, Charlie Bond, Miguel Ortiz Lombardia, Lieven Buts, Adrian Lapthorn, Constantina Foteinou, Lieven Buts, Adrian Lapthorn, Constantina Foteinou, Mike Hartshorn, Ezra Peisash, Dirk Kostrewa, Frank von Mike Hartshorn, Ezra Peisash, Dirk Kostrewa, Frank von Delft, Bob Nolte, George Sheldrick, Joel Bard, Randy Delft, Bob Nolte, George Sheldrick, Joel Bard, Randy Read, Roberto Steiner, Jan Dohnalek, Juergen Bosch, Read, Roberto Steiner, Jan Dohnalek, Juergen Bosch, Martin Noble, Judit Debreczeni, Gabor Bunkoczi, Ingo Martin Noble, Judit Debreczeni, Gabor Bunkoczi, Ingo Korndoerfer, Tadeusz Skarzynski, Artem Lyubimov, Korndoerfer, Tadeusz Skarzynski, Artem Lyubimov, Sabine Schneider, Claudia Schnick, Tim Guene, Phil Sabine Schneider, Claudia Schnick, Tim Guene, Phil Evans, Tassos Perrakis, Dug Kuntz, Gideon Davies, Evans, Tassos Perrakis, Dug Kuntz, Gideon Davies, Tracey Gloster, Martyn Winn, Gerard KleywegtTracey Gloster, Martyn Winn, Gerard Kleywegt
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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 Builders and TestersCoot Builders and Testers William Scott, Ezra Peisach, Bernhard LohkampWilliam Scott, Ezra Peisach, Bernhard Lohkamp York YSBL, Dundee, Glasgow (early adopters)York YSBL, Dundee, Glasgow (early adopters) Coot Mailing List subscribersCoot Mailing List subscribers
http://www.ysbl.york.ac.uk/~emsley/coothttp://www.ysbl.york.ac.uk/~emsley/coot
or or
Google: CootGoogle: Coot
http://www.ysbl.york.ac.uk/~emsley/coot