1. CCP4 Study Weekend 2013 “Molecular Replacements”

2. What’s 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 10Å resolution using ARP/wARP"
Philipp Heuser, EMBL Hamburg

3. 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

4. Research Complex at Harwell STFC Rutherford Appleton Laboratory
What’s new in CCP
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): 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

8. 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

9. 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

10. 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

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

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
Bytes
iMosflm
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 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 Bytes Bytes 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 Bytes 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 Bytes ProSMART (New) 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 Bytes CCP4MG 2.7.0 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 http://www.ccp4.ac.uk
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

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

40. Online Documentation & Resources
CCP4Wiki:
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

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
– Courses & Events

43. 2013 CCP4 Schools/Workshops
CeBEM/CCP4 South American Workshop: Montevideo, Uruguay April 9th – 17th 2013
APS/CCP4 Summer School: APS Synchrotron, Chicago, USA June 17th – 26th 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. 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

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