Introduction to CCP4 and ccp4i Martyn Winn CCP4, STFC Daresbury Laboratory m.d.winn@dl.ac.uk Bangalore, Feb 2008

1. Introduction to CCP4 and ccp4i Martyn Winn CCP4, STFC Daresbury Laboratory m.d.winn@dl.ac.uk Bangalore, Feb 2008

2. Short History of CCP4 • CCP4 Project established in 1979 funded by UK Research Council now based at Daresbury (nr Manchester) • Project aims • Encourage collaborative development of software in macromolecular crystallography. • Provide software for the steps of macromolecular crystallography. • Promote the teaching of macromolecular crystallography • Provide a graphical user interface for organisation and guidance (CCP4i). • Most successful of the CCPs and provided inspiration to later ones such as CCPB

3. CCP4 today Working Group 1 Working Group 2 Executive Committee Core group at DL CCP4-funded developers Collaborators User community

4. Many contributors • Too many to list – Eleanor Dodson, Phil Evans, Andrew Leslie, Ian Tickle, Kim Henrick, Eugene Krissinel, Jia-Xing Yao, Haifu Fan, Randy Read, Airlie McCoy, Garib Murshudov, Kevin Cowtan, Paul Emsley, Liz Potterton, Alexei Vagin, Maria Turkenburg, Alun Ashton, Peter Briggs, Charles Ballard, Peter Keller, etc etc, • The USERS – especially those who complain.. • The UK Funding bodies, CCLRC/STFC, BBSRC, MRC, industrial contributors, EU grants

5. Conferences ...

6. Your tutors .... Martyn Winn Paul Emsley Eugene Krissenel Serge Cohen Garib Murshudov Frank von Delft Eleanor Dodson Guy Dodson

7. Quick look at web site .... Related projects Documentation and roadmaps Download pages Courses Bulletin Boards Problems pages Newsletters www.ccp4.ac.uk

8. CCP4 Software Suite • Scope: covers data processing through to refinement and validation • Modular: lots of individual programs sharing data via common file formats • Keywords control program function and provide additional data Version 6.0 was released in February 2006 Version 6.0.1 was released in June 2006 Version 6.0.2 released in December 2006 Version 6.1 to be released early 2008 Also: package updates intermediate releases releases from author web sites

9. Inclusive Philosophy • There may be several ways of doing a similar task – user is expected to choose. • e.g. Molecular Replacement Phaser/Molrep/Amore. • ~200 programs • Many common routines in libraries to avoid duplicating work. • Mixture of C++, C, Fortran, • Source code available so it can be modified, corrected or borrowed (with author’s consent!).

10. Running CCP4 • All programs can be run from command line or via shell scripts (almost) • most comprehensive functionality • example scripts in $CCP4/examples/unix/runnable • Most programs can be run via GUI (ccp4i) • easier • not all functionality included • Some more graphical programs • iMosflm, Topdraw, Coot, CCP4mg, etc. We will mostly use ccp4i here ...

11. Tour of ccp4i Layout of console window Modules and workflow Example task Utilities

12. Project Management Tools in CCP4i • CCP4i to run jobs ... • ... but also to organise jobs • Why Project Management? • Reminds you what you did six months ago • Helps keep track of multiple projects and associated data • Facilitates back-tracking (especially if things go wrong) • Helps when depositing results & writing your paper • Jobs are organised into 1 or more Projects

13. Setting up projects Projects Aliases

14. MTZ data hierarchy: crystals, datasets and columns MTZ file • Crystal: a physical crystal which was used to obtain data in one or more diffraction experiments • e.g. native, heavy atom derivative etc • Dataset: data derived from a single experiment on a particular crystal • e.g. different MAD wavelengths • Column: a particular type of data associated with a dataset • e.g. experimental quantities (measured intensities) and data derived at various levels (observed structure factors, phases) Title/history Spacegroup Crystal 1 Crystal 2 Crystal name Project name Cell dimensions Crystal name Project name Cell dimensions Dataset 1.1 Dataset 1.2 Dataset name Wavelength Dataset name Wavelength Column Column

15. Crystals Projects and Datasets in practice • Each crystal has an associated set of cell parameters • the crystal cell is used by most programs e.g. map created by FFT will have cell of crystal of chosen column • Each dataset has an associated wavelength • many datasets can be associated with one crystal • can be used automatically by some programs • Each crystal has an associated project name • used by data harvesting • IMPORTANT: Set up crystals, projects, datasets as early as possible: • in Mosflm • when importing the data into MTZ format • add or edit later on using appropriate utilities

16. The End

17. Friendly Discussion Amongst Developers??

18. Help Modules Tasks (includes 1 or more programs) Job Database Tools & Utilities CCP4i main window – quick tour • To start up • Unix: type ccp4i at the command prompt • Windows: launch using the CCP4 icon on the Desktop

19. Top level help • split into topics • “Greyed out” tasks • indicate that you need to install underlying software first e.g. SHELX Database Search/Sort Tool Quick switch between projects Custom job view colours New ccp4i features

20. Protocol folder Make the key decisions File folder Set input and output file names Open folders Parameters that should be checked by the user Highlights indicate compulsory input WORK FROM THE TOP DOWN Closed folders Advanced/infrequently used Example of a CCP4i task interface Always add a title to distinguish different runs of the same task Save/restore parameters Run task Defaults - “If it’s not visible then it’s not important”

21. Brings up relevant documentation in browser General help from main window Help for a particular task Online help within CCP4i Help with a particular option: Right hand mouse button click over that option Bubble help Switch off in Configure Interface

22. One word alias ... … for project directory containing data files Setting up projects in CCP4i • All data files relating to one crystallographic project should be in a single project directory

23. Job database & Project History current project quick change • One job database per project • Stores parameters used to run each task • Records date, status & input, output and logfiles for each job (project history)

24. View files from any job in the database Remove failed/unwanted jobs from the database and archive important data Rerun any job in the database (with the option of changing the parameters first) • Use this to review parameters used in an earlier run Keep the database up-to-date • Record changes e.g. of file locations • Add runs of “external” programs Job database utilities

25. 1. Preferences • Default viewers for PDB files and map files • Data harvesting defaults • 2. Configure Interface • Maximum column lengths for menus • Switch bubble help on or off • Set name of web browser • Explicitly define paths for programs • 3. Edit Modules File • Create new modules • Add new references to existing tasks • Requires some understanding of how tasksare referenced in CCP4i • 4. Install Tasks • Used e.g. by ARP/wARP, Phaser • Tracks tasks that are installed & lets you review/uninstall Customising the behaviour of CCP4i Configuring and customising CCP4i

26. Overview of CCP4 file formats • Working Formats • MTZ:reflection data • See following slides • PDB:coordinate data - based on PDB version 2.1 draft • Officially for atomic position data • Also used semi-unofficially for storing other coordinate-based data • CCP4 map:electron density, pattersons, difference maps, masks • Binary format so use mapdump to view header information • Or can use mapslicer to view sections • Or import into CCP4mg or Coot • Map files can be large but are easily (re)generated from the original data • Other Formats • CCIF:harvest information, Refmac monomer dictionary • - subset of the IUCr mmCIF dictionary • XML:(currently developmental) markup logfile information • See FILE FORMATS section in documentation http://www.ccp4.ac.uk/dist/html/INDEX.html

27. CCP4 Data File Formats: MTZ files • Store reflection data, e.g: • Intensities • Structure factor amplitudes (observed/calculated) • Anomalous differences/Friedel pairs • Free-R flags (for cross-validation) • Phases, Figures-of-Merit etc • Binary format • files are more compact & faster to read/write • need to use utilities to view and manipulate • Batch MTZ files are produced after integration e.g. from Mosflm • also referred to as multi-record files • contain multiple observations of the same reflection (“record”) • (simplistically) each batch corresponds to a diffraction image • perform data reduction steps to get standard MTZ file

28. MTZ file: tabular view • MTZ file can be thought of as a “table” of data • columns = intensities, structure factors etc • rows = values of each column associated with a reflection Multiple Crystals within same file Multiple Datasets within each dataset Rows=reflections (Miller indices) Columns=quantities associated with reflections e.g. intensities, structure factors, phases, FOM etc Reference columns via their names (“labels”)

29. In ccp4i, need to select columns to be used from an input MTZ file: You may also need to add or change crystals / datasets:

30. * Title: Dendrotoxin from green mamba (1dtx) - Tadeusz Skarzynski 1992... * Number of Datasets = 4 * Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength: 1 TOXD / NATIVE 73.5820 38.7330 23.1890 90.0000 90.0000 90.0000 * Number of Columns = 14 * Column Labels : H K L FTOXD3 SIGFTOXD3 ANAU20 SIGANAU20 FAU20 SIGFAU20 … FreeR_flag * Column Types : H H H F Q D Q F Q F Q F Q I * Associated datasets : 1 1 1 1 1 2 2 2 2 3 3 4 4 1 * Cell Dimensions : 73.5820 38.7330 23.1890 90.0000 90.0000 90.0000 * Resolution Range : 0.00074 0.18900 ( 36.761 - 2.300 A ) * Space group = P212121 (number 19) User-supplied descriptive title Dataset information (names, associated cell & wavelength) Column information (labels, data types, which dataset they belong to) Additional information CCP4 Data File Formats: MTZ file header • Use the mtzdmp/mtzdump program to view MTZ information • Or simply View in ccp4i • Sample output from MTZ header: • Other information not shown here includes: number of reflections, history etc

31. AstexViewer: Java-based map-and-coordinate viewer Loggraph: For graphs in CCP4 formatted logfiles • MapSlicer: 2-d contoured sections through CCP4 maps Utilities: graphical viewers • XtalView/Xfit launcher: available for those who prefer to use XtalView - in CCP4i “Model Building” module