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CCP4 Library Development

CCP4 Library Development. CCP4 Libraries. CCP4 5.0 released with : CMTZ, CMAP, etc. - for i/o, fine control of data, jiffy applications other C libraries - general CCP4 utilities MMDB - for coordinate applications and ccp4mg Clipper - for grown-up applications FFTw dna_output.

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CCP4 Library Development

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  1. CCP4 Library Development M.D.Winn, York, March 22nd/23rd 2005

  2. CCP4 Libraries • CCP4 5.0 released with: • CMTZ, CMAP, etc. - for i/o, fine control of data, jiffy applications • other C libraries - general CCP4 utilities • MMDB - for coordinate applications and ccp4mg • Clipper - for grown-up applications • FFTw • dna_output • CCP4 6.0 will have: • cctbx • errrr ... that’s it M.D.Winn, York, March 22nd/23rd 2005

  3. Libraries: future directions No definite plans ... ... possibilities: • Independent library distribution • Scripting interfaces (python for automation, tcl for ccp4i) • Re-write other libraries: • fftlib --> fftw • harvlib, libhtml • Include other libraries for general use, e.g. mmut More important: Extend library code as required by automation projects Re-write legacy applications in cleaner / simpler way M.D.Winn, York, March 22nd/23rd 2005

  4. Developer's Guide to Upgrading Programs to CCP4 5.0 Libraries http://www.ccp4.ac.uk/dev/releases/changes_for_developers_5.0.html • libccp4 --> libccp4f, libccp4c, libmmdb • library.h --> ccp4_sysdep.h, ccp4_errno.h • New crystal level in MTZ header (groups datasets) - autogenerated if not present • Column ordering by dataset • DCELL (present since 4.1) now used by CCP4 progs • symop.lib --> syminfo.lib • Library reads P2, ‘P 2’, ‘P 1 2 1’, 3 -- (CCP4 progs ) will write ‘P 2’ M.D.Winn, York, March 22nd/23rd 2005

  5. Use of new libraries Core library (CMTZ, CMAP, CSYM, utilities) mtz2sca, bp3/crank, mapslicer + other enquiries MMDB ccp4mg, coordinate utilities Clipper pirate, clipper utilities cctbx phaser, pointless M.D.Winn, York, March 22nd/23rd 2005

  6. Coordinate Utilities In response to user requests, and for automated MR: • ncont • pdbcur • summarise PDB contents • delete H atoms • keep only most probable conformation • delete atoms with occupancy < cut-off (def. 0.0) • coord_format • assign chain IDs when blank • pdb_merge • merge chains or keep separate • chainsaw • poly-Ser model based on input alignment M.D.Winn, York, March 22nd/23rd 2005

  7. Coordinate Utilities (2) • Most are simple wrappers to MMDB functionality: • This is as it should be .... • ... but user-accessibility still important. • Why old-fashioned keyworded application programs? • familiar • it works • python scripts not yet migrated from developer to user ?! At some point, migrate to use python interfaces to mmdb and mmut M.D.Winn, York, March 22nd/23rd 2005

  8. cctbx sourceforge.net/projects/cctbx M.D.Winn, York, March 22nd/23rd 2005

  9. Future Release Plans M.D.Winn, York, March 22nd/23rd 2005

  10. The shape of things to come ... • Lots in the pipeline: • ccp4mg • pirate, buccaneer • new Mosflm GUI • Coot • SSM • BP3, CRUNCH • Phaser • Phil’s OO point group scorer • + update to usual suspects • + stuff from automation project March 2004 M.D.Winn, York, March 22nd/23rd 2005

  11. The shape of things to come ... • Still in the pipeline: • ccp4mg 2.0 • buccaneer • new Mosflm GUI (“late summer 05”) • Phaser 2.0 • pointless (available now) • Acorn • + stuff from automation project • Medium term: • ccp4i back-end: database handler • replacement of legacy programs M.D.Winn, York, March 22nd/23rd 2005

  12. MDW’s hitlist • To re-write or junk: • act, angles, contact, distang • coordconv • mtz2various, xdldataman • mtzmnf, mtzMADmod, freerflag • restrain • surface/volume March 2004 M.D.Winn, York, March 22nd/23rd 2005

  13. Long-term issues Change of emphasis to modern tools. E.g. function objects accessed from applications, scripts, MG. What are boundaries to graphics, automation, traditional suite ?? Databases are great. Do we make this a dependency of CCP4? Simplify or expand GUI? Deal with different GUIs for automation .... Workflows. Flexibility vs. focus. March 2004 M.D.Winn, York, March 22nd/23rd 2005

  14. CCP4 Licence Status M.D.Winn, York, March 22nd/23rd 2005

  15. Academic licence Unlicenced users .... Expires on 31st March 2005 New licence available soon: Commercial licence New licence available soon: M.D.Winn, York, March 22nd/23rd 2005

  16. M.D.Winn, York, March 22nd/23rd 2005

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