Crank and Databases Steven Ness Leiden University The Netherlands.

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Presentation transcript:

Crank and Databases Steven Ness Leiden University The Netherlands

Crank Crank - Suite for automated structure solution Simple design – XML based –Input, Run, Output Designed to: –Teach beginners –Enable experts Variety of user interfaces Arbitrary user-designed pipelines Visualization and database storage of results High throughput tools for the individual scientist Working on adding Grid support to Crank

CRANK E/FA value calculation SHELXC DREAR AFRO ECALC Substructure Refinement and Phasing BP3 MLPHARE SHARP Substructure Determination SHELXD CRUNCH2 RANTAN SOLVE Density Modification SOLOMON DM SHELXE RESOLVE PIRATE User Interface XML Script CCP4i Web Model Building/ Refinement RESOLVE MAID FFFEAR REFMAC ARP/wARP* EmmaTruncate CAD SFTOOLSScaleit FHSCAL Tools PROCHECK SFCHECK ValidationViewing O CCP4mg Xfit PyMol

Required Parameters Experimental Data input Types of input data Pipeline of programs

Crank database 3_crank/workdb Stores all information needed by each step Currently a directory with files File name encodes –Program “step” –Type of data –e.g. “crank.out.3_BP3.mtz” or “crank.in.2_CRUNCH2.coords.xml”

MTZ column labels Symbolic column names All CCP4i user input column labels are renamed to avoid known problems (e.g. CAD/SFTOOLS) Examples –INPUT1_X1_D2_F_PLUS –1_AFRO_F_COLUMNS_F –3_BP3_PHASE_COLUMNS_PHIB This also works for other kinds of user input columns from the CCP4i interface

Other types of input data Sequence Substructure List of Substructures Protein Model List of Protein Models Map Rfree Column Many more to be added

Crank XML Generated either directly by programs or by wrappers to convert logfiles to XML Stores all information generated by programs Main purpose : Decisions –These are the way that the user can direct program/information frlow in their pipeline Secondary purpose : Data mining

Our Needs Way to access any given column in an MTZ file Storage of –Sequence, Substructure, Protein Models, Maps, Rfree columns, many more types. Access via –API (Python, Tcl, C, C++) –Filesystem

Acknowledgements and Program availability: Navraj Pannu RAG de Graaff Pavol Skubak Irakli Sikharulidze Jan Pieter Abrahams