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CCP4 Study Weekend 2013 “ Molecular Replacements ”

CCP4 Study Weekend 2013 “ Molecular Replacements ”. What’s new in CCP4. " What's new in CCP4 6.3.0 " Ronan Keegan, STFC Rutherford Appleton Laboratory " PiMS Update " Chris Morris, STFC Daresbury Laboratory " New features in Mosflm and iMosflm " Harry Powell, MRC Cambridge

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CCP4 Study Weekend 2013 “ Molecular Replacements ”

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  1. CCP4 Study Weekend 2013“Molecular Replacements”

  2. What’s new in CCP4 • "What's new in CCP4 6.3.0" • Ronan Keegan, STFC Rutherford Appleton Laboratory • "PiMS Update" • Chris Morris, STFC Daresbury Laboratory • "New features in Mosflm and iMosflm" • Harry Powell, MRC Cambridge • "What's new in Crank" • Pavol Skubak, Leiden University • "Modelling around 10Å resolution using ARP/wARP" • Philipp Heuser, EMBL Hamburg

  3. Lunchtime Bytes • Coot - P. Emsley/B. Lohkamp • CCP4mg - S. McNicholas • MrBUMP / AMPLE - R. Keegan/M. Winn • Xia2/Diamond - G. Winter/P. Hathaway • Aimless / Pointless - P. Evans • Mosflm / iMosflm - H. Powell/O. Johnson • Phaser - R. Oeffner • Buccaneer / Nautilus (5th of January only)  - K. Cowtan • Crank (4th of January only) - P. Skubak • PiMS - C. Morris • Balbes - F. Long • Refmac / ProSMART - G. Murshudov/R. Nicholls Bytes

  4. What’s new in CCP4 6.3.0 Ronan Keegan Research Complex at Harwell STFC Rutherford Appleton Laboratory

  5. About CCP4 • CCP4 stands for “Collaborative Computational Project Number 4” • One of several CCPs set up in the UK to advance and support scientific software development • CCP4 was set up in the late 1970’s to bring together the leading developers of software in the field of protein X-ray crystallography in the UK • The aim was to assemble a comprehensive collection of software to satisfy the computational requirements of the relevant UK groups

  6. Hosted by the Science and Technology Facilities Council (STFC) • Part of the Research Complex at Harwell (RCaH) next door to Diamond • CCP4 funded by: • Biotechnology and Biological Sciences Research Council (BBSRC) • Medical Research Council (MRC) • Industrial funding CCP4

  7. Core Group (Oxford): • Maintain and support software suite • Application and infrastructural software developments • Collaborate with Diamond on software deployment on the beamline • Educational outreach • Maintaining CCP4 resources such as the CCP4 bulletin board CCP4

  8. Core Group (Oxford): • Maintain and support software suite • Application and infrastructural software developments • Collaborate with Diamond on software deployment on the beamline • Educational outreach • Maintaining CCP4 resources such as the CCP4 bulletin board • Cambridge: • Laboratory of Medical Biology • Data processing software - Mosflm, Aimless • Refinement software – Refmac • Model building - Coot • University of Cambridge • Phaser group Cambridge CCP4

  9. Core Group (Oxford): • Maintain and support software suite • Application and infrastructural software developments • Collaborate with Diamond on software deployment on the beamline • Educational outreach • Maintaining CCP4 resources such as the CCP4 bulletin board • Cambridge: • Laboratory of Medical Biology • Data processing software - Mosflm, Aimless • Refinement software – Refmac • Model building - Coot • University of Cambridge • Phaser group • University of York: • Software development – CCP4mg, Buccaneer, Nautilus • CCP4 GUI2 development York Cambridge CCP4

  10. Core Group (Oxford): • Maintain and support software suite • Application and infrastructural software developments • Collaborate with Diamond on software deployment on the beamline • Educational outreach • Maintaining CCP4 resources such as the CCP4 bulletin board • Cambridge: • Laboratory of Medical Biology • Data processing software - Mosflm, Aimless • Refinement software – Refmac • Model building - Coot • University of Cambridge • Phaser group • University of York: • Software development – CCP4mg, Buccaneer, Nautilus • CCP4 GUI2 development • Others include the Crank group at Leiden in the Netherlands York Cambridge CCP4

  11. CCP4 Usage

  12. The CCP4 software suite • The CCP4 suite is a comprehensive suite of software for protein crystallography • New versions of the suite are released about every 18 months • New programs • Major updates to existing programs • Other new features such as changes to CCP4i interface • New - Revisions to the current release are made available through the CCP4 updates manager

  13. CCP4 Software Molecular Replacement Density Modification Data Processing and Reduction Structure Analysis Experimental Phasing Model Building Refinement Deposition Data Collection Crystallisation

  14. CCP4 Releases • Current Release Version - CCP4 6.3.0 • Several new programs: • Aimless, Dimple, AMPLE, Zanuda, ProSMART, Nautilus, Ensembler, Sculptor, Jligand • In collaboration with the EMBL Hamburg, ARP/wARP is now rolled with the CCP4 suite • Updates to many of the major programs • Phaser, Refmac, Mosflm/iMosflm, Crank, MrBUMP • New infrastructure • Downloads manager and Updates Manager

  15. Data Processing and Reduction iMosflm Bytes Pointless Determine point-group (& space group) Bytes Aimless (New) Scale-symmetry-related intensities together Produce statistics on data quality Replacement for Scala

  16. Data Processing and Reduction Bytes • Automated data-reduction – from diffraction images to merged reflection file Dimple (New) • On-beamline rapid calculation of difference maps to ascertain success or failure of ligand binding

  17. Experimental Phasing Bytes Crank • Automated experimental phasing pipeline • Heavy atom location through to Model Building Bytes Phaser EP • Automated experimental phasing • SAD phasing • Combined MR and SAD Phasing

  18. Molecular Replacement Bytes Phaser MR • Automated Maximum Likelihood method for molecular replacement • Twining • Translational NCS Molrep • Molecular Replacement • Phased Rotation/Translation function • Multi-copy search

  19. Molecular Replacement - Automation Bytes MrBUMP • Automated molecular replacement • From model search and preparation through to initial refinement • Uses Phaser and Molrep • Now includes Model building options Bytes BALBES • Automated molecular replacement using Molrep and Refmac • Custom DB with search models monomer, domain and multimeric form

  20. BALBES Webservice http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp or Google for“BALBES”

  21. Molecular Replacement – Search model preparation Sculptor (New) • Multi-protocol search model preparation • weighted sequence similarity • accessible surface area Ensembler (New) • Ensemble search model generation tool from the developers of Phaser Molrep & Chainsaw • Search model preparation using internal sequence alignment or provided alignment

  22. Molecular Replacement – Ab initio search models Bytes AMPLE (beta version) • Generate and prepare ab initio or de novo models using Rosetta and other software for use as search models in molecular replacement • Works well for smaller, α-helical proteins (<120 residues) but has been known to work for larger targets • Requires installation of several third-party applications such as Rosetta

  23. Density Improvement Parrot • Uses maximum likelihood methods and builds on original DM program • Fast and fully automated Pirate • Statistical-based density modification • Better in some cases but slower than Parrot

  24. Model Building Buccaneer • Chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target • Low resolution model building Bytes Nautilus (New) • Automatic model building of nucleotide structures in electron density maps Bytes Sloop (New) • Loop building by finding gaps in the chain and using fragments from the Richardson's Top500 library of structures to fill the gaps

  25. Model Building ARP/wARP • Automated building of • proteins • RNA/DNA • secondary structure • side chains • loops • solvent • ligands • Now jointly distributed by CCP4 Bytes

  26. Model Building - Coot Bytes • Coot 0.7 • RCrane and Cootaneer for RNA building • Ligand Builder working in conjunction with ProDRG • Jligand interface • Wider Linux support

  27. Model Building: ligand building Jligand • Generate and regularise ligands • Link ligands together and generate link description

  28. Refinement Bytes Refmac 5.7 • SIRAS and jelly body refinement • refinement of multiple occupancies • More reliability at lower resolution • Restraints to reference structures • Regularised map sharpening • Automatic and local NCS restraints • New Monomer library • Much expanded and corrected library • More than 9000 structures in first case • Better conformation to PDB 3 format

  29. Refinement Refmac 5.7/5.8 – coming soon • Improved jelly body refinement • Improved use of restraint information (ProSMART) • DNA/RNA base pair restraints • Suger/pucker restraints • Simultaneous density modification and refinement (initially SAD, more general later) • Better anomalous difference maps • Beta ensemble refinement • Multi-imputation and averaging of structure factors to desired resolution • Sampling of conformational space – Gibbs sampling • Estimation of individual errors of atoms – less biased electron density calculation

  30. Refinement ProSMART (New) Bytes • Structure alignment • Generation of external restraints for use in refinement ProDrg • Generate restraints for ligands for use in refinement and model building Zanuda (New) • Analyse refinement results • Check correct space group

  31. Structure Analysis PISA • Automatic inference on multimeric states from crystal packing • Analysis of macromolecular interfaces and macromolecular interactions • QTPisa – new QT based interface

  32. Structure Analysis CCP4MG 2.7.0 Bytes Gesamt (New) • Replacement for Superpose • Improved secondary structure alignment

  33. Report Viewer - QTRview • Graphical log file viewer • View graphs, tables and job summary information • Launch Coot, CCP4mg and ViewHKL to view data files • Can still view original log file

  34. viewHKL • Provides detailed graphical interface to reflection data • Combines MTZDump with HKLView/HKLPlot • Default viewer for MTZ files under ccp4i

  35. Downloading the suite • Download CCP4 for Windows, Mac or Linux • New: Co-distribution of ARP/wARP • New: Package Manager – easy installation • New: 64-bit Linux version • Additional software dependencies also available • Download page accessible from • http://www.ccp4.ac.uk

  36. Package Manager • Easy installation mechanism for CCP4 and associated packages (Coot, ARP/wARP, CCP4mg) • Available on Linux, Mac and Windows • Sets up system variables automatically if you wish

  37. Package Manager • Easy installation mechanism for CCP4 and associated packages (Coot, ARP/wARP, CCP4mg) • Available on Linux, Mac and Windows • Sets up system variables automatically if you wish

  38. Package Manager • Easy installation mechanism for CCP4 and associated packages (Coot, ARP/wARP, CCP4mg) • Available on Linux, Mac and Windows • Sets up system variables automatically if you wish

  39. Update Manager • Automatically install latest fixes and new features • Allows for rolling back to previous versions • Updates made available once every two weeks or as and when they are needed • Available on Linux, Mac and Windows • Recent updates: • ARP/wARP • Phaser 2.5.2 • AMPLE • Ensembler interface • QTPisa • Refmac 5.7.0032

  40. Online Documentation & Resources • CCP4Wiki: • http://ccp4wiki.org • Documentation of programs and detailed guides on how to use the software to solve structures • General CCP4 Crystallography Wiki • Knowledge base for protein crystallographers • Linked to from the CCP4Wiki page • CCP4 Bulletin Board and ccp4 helpdesk (ccp4@ccp4.ac.uk)

  41. CCP4 Newsletter • Back after a 4 year hiatus • Detailed articles about many of the new software features and upcoming developments • Bi-annual • Archive of all previous newsletters now available online (since 1979)

  42. CCP4 Schools/Workshops • Main aim is to give education and expert help to researchers working with collected crystal data • Some schools also provide expert help with collecting crystal data (APS & Hamburg) • Applicants with challenging crystals and/or data are given strong consideration but this is not mandatory • Software developers from CCP4, Phenix (APS), Shelx, ARP/wARP, XDS and HKL as well as others give lectures, tutorials and are also available to help with data processing and structure solution throughout the meetings • http://www.ccp4.ac.uk– Courses & Events

  43. 2013 CCP4 Schools/Workshops • CeBEM/CCP4 South American Workshop: Montevideo, Uruguay April 9th – 17th 2013 • http://www.pasteur.edu.uy/mx2013 • APS/CCP4 Summer School: APS Synchrotron, Chicago, USA June 17th – 26th 2013 • http://www.ccp4.ac.uk/schools/APS-2013 • BCA Summer School • OIST/CCP4 School: Okinawa, Japan – November 2013 • ECM 28 - Introduction to Software Development for Crystallographers Warwick University, UK August 23rd-24th • Watch out for other CCP4 supported schools in the UK, Germany (Hamburg), India and China

  44. Lunchtime Bytes • Coot - P. Emsley/B. Lohkamp • CCP4mg - S. McNicholas • MrBUMP / AMPLE - R. Keegan/M. Winn • Xia2/Diamond - G. Winter/P. Hathaway • Aimless / Pointless - P. Evans • Mosflm / iMosflm - H. Powell/O. Johnson • Phaser - R. Oeffner • Buccaneer / Nautilus (5th of January only)  - K. Cowtan • Crank (4th of January only) - P. Skubak • PiMS - C. Morris • Balbes - F. Long • Refmac / ProSMART - G. Murshudov/R. Nicholls Bytes

  45. Acknowledgements • CCP4 Core group: Andrey Lebedev, Eugene Krissinel, Charles Ballard, David Waterman, Marcin Wojdyr, Ville Uski, Karen McIntyre, Martyn Winn • LMB/MRC: Andrew Leslie, Phil Evans, Garib Murshudov, Rob Nicholls, Harry Powell, Owen Johnson, Fei Long, Paul Emsley • Phaser Group: Airlie McCoy, Randy Read, Rob Oeffner, Gabor Bunkoczi • YSBL York: Keith Wilson, Kevin Cowtan, Liz Potterton, Stuart McNicholas, Eleanor Dodson • Leiden: Raj Pannu, Pavol Skubak • Others: Bernhard Lohkamp, Clemens Vonrhein, Ruslan Sanishvili, Frank Von Delft, Martin Noble, Jaclyn Bibby, Daniel Rigden, Graeme Winter, Alun Ashton, David Brown, Gwyndaf Evans, Arwen Pearson, Andrea Thorn, Tim Gruene, George Sheldrick and many more..

  46. AMPLE • Automated pipeline • Generates 100’s of possible “decoys” based on a target sequence • Decoys are clustered to determine most likely fold • Top cluster gives rise to a set of ensemble search models for use in molecular replacement • MrBUMP is used underneath to feed search models to Phaser and Molrep and on to refinement and model building

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