Crank and Databases
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Transcript of Crank and Databases
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Crank and Databases
Steven NessLeiden University
The Netherlands
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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
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CRANKCRANKE/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*
Emma Truncate
CAD
SFTOOLSScaleit
FHSCAL
Tools
PROCHECK
SFCHECK
Validation Viewing
O
CCP4mg
Xfit
PyMol
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Required Parameters
Experimental Data input
Types of input data
Pipeline of programs
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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”
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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
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Other types of input data
• Sequence• Substructure• List of Substructures• Protein Model• List of Protein Models• Map• Rfree Column• Many more to be added
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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
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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
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Acknowledgements and Program availability:
http://www.bfsc.leidenuniv.nl/software/crank
Navraj PannuRAG de GraaffPavol SkubakIrakli SikharulidzeJan Pieter Abrahams