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CCP4 from a user perspective

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Presentation on theme: "CCP4 from a user perspective"— Presentation transcript:

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

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

3 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 Johan P. Turkenburg

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

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

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CCP4 Website Downloads Problem pages Documentation Meetings Jobs 10/11/2018 ACA Meeting Johan P. Turkenburg

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

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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 Johan P. Turkenburg

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

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

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

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

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

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

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

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

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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, 10/11/2018 ACA Meeting Johan P. Turkenburg

18 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): JUL 2004 10/11/2018 ACA Meeting Johan P. Turkenburg

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

39 ACA Meeting 2005 Johan P. Turkenburg
Example Lyase Space group H32, unit cell 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 Johan P. Turkenburg

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

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

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

43 ACA Meeting 2005 Johan P. Turkenburg
Example 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 Johan P. Turkenburg

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

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

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

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

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

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

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

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