Presentation is loading. Please wait.

Presentation is loading. Please wait.

CCP4 from a user perspective

Published bySudomo Sugiarto Modified over 5 years ago

Similar presentations

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

4 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 Johan P. Turkenburg

5 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 Johan P. Turkenburg

6 ACA Meeting 2005 Johan P. Turkenburg
CCP4 Website Downloads Problem pages Documentation Meetings Jobs 10/11/2018 ACA Meeting Johan P. Turkenburg

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

8 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 Johan P. Turkenburg

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

10 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 Johan P. Turkenburg

11 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 Johan P. Turkenburg

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

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

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

15 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 Johan P. Turkenburg

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

17 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, 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

19 ACA Meeting 2005 Johan P. Turkenburg
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

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

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

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

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

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

27 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 Johan P. Turkenburg

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

29 ACA Meeting 2005 Johan P. Turkenburg
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

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

35 ACA Meeting 2005 Johan P. Turkenburg
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

38 ACA Meeting 2005 Johan P. Turkenburg
‘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

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

42 ACA Meeting 2005 Johan P. Turkenburg
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

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

50 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 Johan P. Turkenburg

Download ppt "CCP4 from a user perspective"

Similar presentations

CCP4 Molecular Graphics (CCP4MG)

CCP4 Molecular Graphics (CCP4MG)
Automated phase improvement and model building with Parrot and Buccaneer Kevin Cowtan

Automated phase improvement and model building with Parrot and Buccaneer Kevin Cowtan
Martyn Winn, STFC Daresbury Laboratory. 1. CCP4 as a suite 2. Overview of CCP4 functionality 3. Future directions.

Martyn Winn, STFC Daresbury Laboratory. 1. CCP4 as a suite 2. Overview of CCP4 functionality 3. Future directions.
M.I.R.(A.S.) S.M. Prince U.M.I.S.T.. The only generally applicable way of solving macromolecular crystal structure No reliance on homologous structure.

M.I.R.(A.S.) S.M. Prince U.M.I.S.T.. The only generally applicable way of solving macromolecular crystal structure No reliance on homologous structure.
M.I.R.(A.S.) S.M. Prince U.M.I.S.T.. The only generally applicable way of solving macromolecular crystal structure No reliance on homologous structure.

M.I.R.(A.S.) S.M. Prince U.M.I.S.T.. The only generally applicable way of solving macromolecular crystal structure No reliance on homologous structure.
Introduction CCP4i, Files and Utilities Martyn Winn CCP4, CCLRC Daresbury Laboratory

Introduction CCP4i, Files and Utilities Martyn Winn CCP4, CCLRC Daresbury Laboratory
Experimental Phasing stuff. Centric reflections |F P | |F PH | FHFH Isomorphous replacement F P + F H = F PH FPFP F PH FHFH.

Experimental Phasing stuff. Centric reflections |F P | |F PH | FHFH Isomorphous replacement F P + F H = F PH FPFP F PH FHFH.
Direct Methods and Many Site Se-Met MAD Problems using BnP Direct Methods and Many Site Se-Met MAD Problems using BnP W. Furey.

Direct Methods and Many Site Se-Met MAD Problems using BnP Direct Methods and Many Site Se-Met MAD Problems using BnP W. Furey.
Don't fffear the buccaneer Kevin Cowtan, York. ● Map simulation ⇨ A tool for building robust statistical methods ● 'Pirate' ⇨ A new statistical phase improvement.

Don't fffear the buccaneer Kevin Cowtan, York. ● Map simulation ⇨ A tool for building robust statistical methods ● 'Pirate' ⇨ A new statistical phase improvement.
In honor of Professor B.C. Wang receiving the 2008 Patterson Award In honor of Professor B.C. Wang receiving the 2008 Patterson Award Direct Methods and.

In honor of Professor B.C. Wang receiving the 2008 Patterson Award In honor of Professor B.C. Wang receiving the 2008 Patterson Award Direct Methods and.
Automated protein structure solution for weak SAD data Pavol Skubak and Navraj Pannu Automated protein structure solution for weak SAD data Pavol Skubak.

Automated protein structure solution for weak SAD data Pavol Skubak and Navraj Pannu Automated protein structure solution for weak SAD data Pavol Skubak.
Direct Methods By Fan Hai-fu, Institute of Physics, Beijing Direct Methods By Fan Hai-fu, Institute of Physics, Beijing

Direct Methods By Fan Hai-fu, Institute of Physics, Beijing Direct Methods By Fan Hai-fu, Institute of Physics, Beijing
Introduction to CCP4 and ccp4i Martyn Winn CCP4, STFC Daresbury Laboratory Bangalore, Feb 2008.

Introduction to CCP4 and ccp4i Martyn Winn CCP4, STFC Daresbury Laboratory Bangalore, Feb 2008.
CCP4 helpdesk: What’s New in CCP4 6.0? Martyn Winn CCP4 CCLRC Daresbury Laboratory Cheshire.

CCP4 helpdesk: What’s New in CCP4 6.0? Martyn Winn CCP4 CCLRC Daresbury Laboratory Cheshire.
23 rd August 2005CCP4 Workshop IUCr 2005 Florence Italy 1 N6: A Protein Crystallographic Toolbox: The CCP4 Software Suite and PDB Deposition Tools IUCr.

23 rd August 2005CCP4 Workshop IUCr 2005 Florence Italy 1 N6: A Protein Crystallographic Toolbox: The CCP4 Software Suite and PDB Deposition Tools IUCr.
CCP4 Study Weekend 3rd January 2003 CCP4i - “Tricks and Tools” Peter Briggs CCP4 Daresbury.

CCP4 Study Weekend 3rd January 2003 CCP4i - “Tricks and Tools” Peter Briggs CCP4 Daresbury.
28 th May 2005CCP4 Workshop, ACA Orlando 2005 1 An Introduction to the CCP4 Software Suite: CCP4i, Files and Utilities Peter Briggs CCP4, CCLRC Daresbury.

28 th May 2005CCP4 Workshop, ACA Orlando An Introduction to the CCP4 Software Suite: CCP4i, Files and Utilities Peter Briggs CCP4, CCLRC Daresbury.
Peter J. Briggs, Liz Potterton *, Pryank Patel, Alun Ashton, Charles Ballard, Martyn Winn CLRC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK *

Peter J. Briggs, Liz Potterton *, Pryank Patel, Alun Ashton, Charles Ballard, Martyn Winn CLRC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK *
23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 1 N6: A Protein Crystallographic Toolbox: The CCP4 Software Suite and RCSB PDB Deposition.

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 1 N6: A Protein Crystallographic Toolbox: The CCP4 Software Suite and RCSB PDB Deposition.
28 th March 2007 MrBUMP – Automated Molecular Replacement Ronan Keegan, Martyn Winn CCP4, Daresbury Laboratory.

28 th March 2007 MrBUMP – Automated Molecular Replacement Ronan Keegan, Martyn Winn CCP4, Daresbury Laboratory.

Similar presentations

Ads by Google