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Overview of developments within CCP4

Overview of developments within CCP4. Generation 1 ccp4i tasks Generation 2 isolated scripts / web service Generation 3 integrated environment. Molecular Replacement - Mr Bump. Ronan Keegan and Martyn Winn (DL) automated framework for Molecular Replacement

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Overview of developments within CCP4

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  1. Overview of developments within CCP4 Generation 1 ccp4i tasks Generation 2 isolated scripts / web service Generation 3 integrated environment 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 Automation

  3. Mr Bump in pictures Automation

  4. Mr Bump details and performance • 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 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 Automation

  6. Experimenal Phasing - HAPPy • Paul Emsley (York University), Daniel Rolfe (DL), Charles Ballard (DL) • 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 Automation

  7. HAPPy details • outputs HL coefficients • density modification using DM and pirate • Test on ccp4cluster • Experimental and synthetic test data Automation

  8. 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 Experimental Phasing - CRANK (assoc.) Unfortunately, the ccp4 version does not include crunch2 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) Automation

  10. XIA-DPA - what does it do? • Index • Integrate • Determine point group • Scale • Merge • Analyse Using a variety of programs… 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 Automation

  12. Future Challenges • Model Building • Buccaneer (KC) • Ligands (PE) • Generation 3 • Integration of automation efforts • Communication • Customisation • Feedback and Display Automation

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