28 mar 06automation1 overview of developments within ccp4 generation 1 ccp4i tasks generation 2...
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28 Mar 06 Automation 1
Overview of developments within CCP4
Generation 1• ccp4i tasks
Generation 2• isolated scripts / web service
Generation 3 • integrated environment
28 Mar 06 Automation 2
Molecular Replacement - Mr Bump
• Ronan Keegan and Martyn Winn (DL)• automated framework for Molecular Replacement• Paricular emphasis on generating variety of search models
• Wraps Phaser, Molrep and Amore (Norman Stein)• Uses a variety of helper applications (eg Chainsaw) and bioinformatics tools (eg FASTA, Mafft)• Uses on-line databases (eg PDB, Scop)
• In favourable cases, gives “one-button” solution• In unfavourable cases, suggests likely search models for manual investigation
28 Mar 06 Automation 3
Mr Bump in pictures
QuickTime™ and aTIFF (Uncompressed) decompressor
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QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
28 Mar 06 Automation 4
• Model generation- initial search for homologues based upon fasta search of PDB (can be run locally)- template list based upon single chains, domains and multimers- optional side chain pruning by Chainsaw or molrep
• MR engine- choice of Phaser, molrep or amore.
• Success or failure- based upon Rfree in refinement of solution
• Performance- July 05 testing on SPINE targets, worked well on straightforward solutions- brute force method, so compute power important
Mr Bump details and performance
28 Mar 06 Automation 5
Molecular Replacement - MMASS
• Authors: Garib Murshudov, Alexei Vagin, Fei Long (YSBL)
• Built around molrep MR and model preparation, refmac and sfcheck• Custom database• Manager control process• Protocols
– Simple molecular replacement– Domains iterated with refinement– Use of tertiary structure if available– Completion of MR using phased MR and refinement
• Extensive testing against PDB
• Good performance against SPINE test data
28 Mar 06 Automation 6
Experimenal Phasing - HAPPy
• Paul Emsley (York University), Daniel Rolfe (DL), Charles Ballard (DL)
QuickTime™ and aTIFF (Uncompressed) decompressor
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• son of CHART, written in python
- SAD implemented
- custom analysis for resolution
range from scala and fhscal
- initially uses shelxd for at location,
with acorn to follow (?)
- phasing using mlphare, bp3 or
phaser
28 Mar 06 Automation 7
HAPPy details
- outputs HL coefficients
- density modification using DM and pirate
• Test on ccp4cluster
• Experimental and synthetic test data
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
28 Mar 06 Automation 8
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Experimental Phasing - CRANK (assoc.)
• Steven Ness, Raj Pannu (Leiden University)- www.bfsc.leidenuniv.nl/software/crank/index.html– Contact authors for more information
• Written in TCL/TK and interface tightly with CCP4i.• SAD/MAD heavy atom phasing• Built around BP3 and maximum likelihood techniques
Unfortunately, the ccp4 versiondoes not include crunch2
28 Mar 06 Automation 9
Data processing - XIA-DPA (assoc.)
• Author Graeme Winter (DL)
• XIA-DPA is an automated system to process and analyse X-Ray diffractions data
• Designed to fill the gap between DNA and CCP4 (automation)• Produces output in standard format files• Includes 2D and 3D pipelines for processing,
via Mosflm/Scala and XDS/XSCALE(/Scala)QuickTime™ and a
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28 Mar 06 Automation 10
XIA-DPA - what does it do?
• Index• Integrate• Determine point group• Scale• Merge• Analyse
Using a variety of programs…
QuickTime™ and aTIFF (Uncompressed) decompressor
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28 Mar 06 Automation 11
CCP4i database backend
• Authors: Peter Briggs, Wendy Yang
• Implemented using SQLlite and python• Automation means lots of data
– Process tracking– Data tracking– persistence of data
• Collaborating closely with HAPPy and XIA-DPA• Integration with ccp4i database handler is
beginning
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.