CCP4 Study Weekend 2013 Molecular Replacements Whats new in CCP4 "What's new in CCP4 6.3.0" "PiMS Update"
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 10 resolution using ARP/wARP" Philipp Heuser, EMBL Hamburg Bytes 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 Research Complex at Harwell STFC Rutherford Appleton Laboratory
Whats new in CCP Ronan Keegan Research Complex at Harwell STFC Rutherford Appleton Laboratory 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 1970s 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 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 Core Group (Oxford): CCP4 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 Core Group (Oxford): Cambridge: Cambridge CCP4
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 Core Group (Oxford): Cambridge: University of York: York Cambridge
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 Core Group (Oxford): Cambridge: University of York:
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 CCP4 Usage 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 CCP4 Software Crystallisation Data Collection
Data Processing and Reduction Experimental Phasing Molecular Replacement Density Modification Model Building Refinement Structure Analysis Deposition 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 Data Processing and Reduction
Bytes iMosflm Pointless Determine point-group (& space group) Bytes Aimless (New) Scale-symmetry-related intensities together Produce statistics on data quality Replacement for Scala 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 Experimental Phasing Bytes 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 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 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 BALBES Webservice http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
or Google forBALBES 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 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, -helical proteins (