CCP4 CSE. CCP for Protein Crystallography. Much of this talk prepared by Martyn Winn. Computational Science & Engineering Department

Transcription

1 CCP4 CCP for Protein Crystallography Much of this talk prepared by Martyn Winn CSE Computational Science & Engineering Department

2 Overview of Protein Crystallography Crystallisation e-htpx Data Collection Phasing PIMS CCP4 Protein Production Target Selection PDB (e.g. EBI) Protein Structure Structure analysis Deposition

3 Philosophy and sociology Collaboration going for > 25 years Large but disparate group of developers CCP4 provides centralised tools Support for/from large community well-established framework and practices (good thing/bad thing) End results: Deposition of refined model and (integrated) experimental data in PDB Data harvesting of metadata of structure solution

4 CCP4 - Very old stuff Originally a collection of Fortran programs (now ~200 applications in Fortran, C++, python) MTZ (reflection data) MAP (electron density) PDB (coordinates) Standard data files form main communication between different applications

5 CCP4 - Old stuff - Data harvesting Capture of metadata associated with structure solution process Released in CCP4 4.0 January 2000 Data Collection Data Reduction Phasing Refinement runtime creation of harvest files Data Harvesting data files (PDB, MTZ) upload harvest files at deposition PDB DEPOSITION

6 What do harvesting files look like? $HARVESTHOME/DepositFiles DepositFiles/<project_name>/< /<project_name>/<dataset_name.program> data_toxd[native] _entry.id TOXD _diffrn.id NATIVE _audit.creation_date T11:19:51+01:00 _software.classification phasing _software.contact_author 'Z.Otwinowski or E.Dodson _software.contact_author_ _software.description 'maximum likelihood heavy atom refinement & phase calculation' _software.name mlphare _software.version CCP4_3.5 loop phasing_mir_shell.d_res_high mmcif = macromolecular crystallographic information file Also used for: reflection data (input/output to PDB) refinement dictionaries (similar to force field parameters)

7 CCP4i job database: at the time (ca.2000), major step forward! Limitations simple flat-file (Not really a database!) handling functions are embedded within CCP4i Focus on job tracking, not crystallographic knowledge

8 New architecture Improved visualisation of project Applications have direct access to DB (via handler) Complete separation of GUI Single python process Flat files or relational DB

9 CCP4 XML Working Group Scope: Concerned with data exchange rather than storage May or may not be relevant for deposition - not the focus of this group. Many CCP4 programs already use or produce XML. Aim to draw together these efforts to produce "CCP4 XML". A recommendation rather than enforced standard. Provide or recommend XML tools for a variety of languages

10 CCP4 XML Working Group Martyn Winn (coordinator) Airlie McCoy Fei Long Graeme Winter Raj Pannu Charles Ballard Paul Emsley Ronan Keegan - CCP4 programs (Daresbury) - Phaser (Cambridge) - Balbes (York) - DNA/e-HTPX/XIA (Daresbury) - Crank (Utrecht) - CCP4 automation (Daresbury) - Coot (Oxford) - MrBUMP (Daresbury) Represent major packages and automation projects within CCP4 Most have some XML usage already.

11 XML: Where now? XML is being used by pipeline developers. Developers talk to each other, but otherwise independent. No major overlap yet in XML content. Variety of XML tools being used. Top-down imposition of data model may hinder progress Feeling that inter-package communication will not be difficult. Encourage sharing of tools and XML datatypes.

12 PIMS and CCP4 In long term, PIMS db will talk to CCP4 db: target sequence, bioinformatics results, ligands, heavy atoms, oxidised/reduced, ph success/failure of structure solution details of model built quality of model Data model co-developed with CCPN, e-htpx, EBI

13 Deposition of Data in PDB REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL

14 Populating the PDB Data captured at various stages: protein production, crystallisation (PIMS) data collection (e-htpx) structure solution (CCP4) Deposition of data (coordinates, reflections) and some meta-data (harvesting) well-established. We are working on capturing more metadata, with view to deposition.

15 Conclusions? CCP4 can t impose heavyweight data models / ontologies on developers Data exchange via lightweight messaging might be of interest. Systems biologists, Molecular dynamicists etc. would get data from the PDB. Major issue capturing uncertainty in structural details What do we deposit in the PDB?