CCP4 from a user perspective

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Presentation transcript:

CCP4 from a user perspective Johan P. Turkenburg York Structural Biology Laboratory University of York York, United Kingdom 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

York & York Structural Biology Laboratory 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Overview File formats CCP4 Website CCP4 Help CCP4BB CCP4 Program Suite CCP4 Interface Interaction with other programs Example(s) of Use 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg File formats Reflection files (mtz format) Coordinate files (pdb format) Provide ways in and out of CCP4 Suite 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg MTZ files Columns, columns, columns Labels Types Non-ascii Viewers PDB files ‘standard’ Ascii Widely used 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg CCP4 Website http://www.ccp4.ac.uk Downloads Problem pages Documentation Meetings Jobs 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg CCP4 Help Documentation General crystallography Help in interface 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg CCP4BB Members from all over the world Fast, expert help from colleagues Useful tips Non-CCP4 topics Heated (entertaining) discussions 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg CCP4 Program Suite Many programs from many authors All aspects of crystallography 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Overview Data processing Molecular Replacement Experimental Phasing Density Improvement Model Building & Refinement Validation, Analysis, Deposition 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Interface No more typos Import/Export Help Defaults Project Management !! Tasks (logical sequence) Graphs from log files 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Interface window 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Modules Picture of task list in interface 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Data Reduction 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg MOSFLM DENZO Two routes SCALA SCALEPACK TRUNCATE TRUNCATE MTZ file with structure factors etc. 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Experimental Phasing SHELXS and SHELXC/D/E CRANK & BP3 (Leiden) to come 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg ACORN Heavy atom substructures Locating secondary structure elements Density modification At high resolution, complete ‘density’ determination Foadi,J., Woolfson,M.M., Dodson,E.J., Wilson,K.S., Yao Jia-xing and Zheng Chao-de (2000) Acta. Cryst. D56, 1137-1147. 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg ACORN on a CBM Data to 1.0A on Se form at l = 0.87Å (SRS) Patterson shows Se very clearly ACORN gave excellent map in 18 min on SGI Ab initio structure determination and functional characterization of CBM36: A new family of calcium-dependent carbohydrate binding modules Jamal-Talabani S, Boraston AB, Turkenburg JP, Tarbouriech N, Ducros VMA, Davies GJ STRUCTURE 12 (7): 1177-1187 JUL 2004 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Patterson Demo 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

CBM ACORN map & final model 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

Molecular Replacement 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg MR programs Molrep AMoRe Phaser (Randy Read, Tuesday morning) Many utilities 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg MR Utilities 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Density Improvement 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Model Building 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Refinement 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg REFMAC Algorithms Scaling Restraints (geometric & NCS) TLS Combines with ARP/wARP Easy to use in interface 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

Monomer library sketcher 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Structure Analysis 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

Temperature factor analysis 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

Validation & Deposition 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Map & Mask Utilities 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

Reflection Data Utilities 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Convert from MTZ 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Coordinate Utilities 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

Graphics & Viewing Utilities 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Program List 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg ‘External’ Programs Arp/warp Shelx Mosflm Xtalview 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Example 1 Lyase Space group H32, unit cell 58.8 58.8 588.5 All programs used are runnable from interface Se MAD Shelxd to find sites MLPHARE, DM phasing/phase improvement ARP/wARP, REFMAC model building/refinement Input/output ‘chaining’ trivial (but not automatic) 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg LYASE SHELXD 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg LYASE SHELXE 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg LYASE ARP/wARP 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Example 2 Two esterases CE4 one crystal form (P41212 / P43212) Cd SIRAS SHELXD, MLPHARE, DM, ARP/WARP, REFMAC AXA with 2 crystal forms (P21 / P212121) Molecular Replacement 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg CE4 SHELX C/D/E 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

CE4 Phasing & Phase Improvement MLPhare with site from SHELXD DM 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

AXA P21 AMoRe Rotation function 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg AXA P212121 Analyse data 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

AXA P212121 Analyse data Results 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg AXA P212121 Solution MOLREP, two molecules Initial refinement REFMAC 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg

ACA Meeting 2005 Johan P. Turkenburg Acknowledgements Eleanor Dodson Keith Wilson Gideon Davies Ed Taylor Sam Hart Everyone else in YSBL 10/11/2018 ACA Meeting 2005 Johan P. Turkenburg