28 th march 2007 mrbump – automated molecular replacement ronan keegan, martyn winn ccp4,...
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28th March 2007
MrBUMP – Automated MrBUMP – Automated Molecular ReplacementMolecular Replacement
Ronan Keegan, Martyn Winn Ronan Keegan, Martyn Winn
CCP4, Daresbury LaboratoryCCP4, Daresbury Laboratory
28th March 2007
Aim of MrBUMPAim of MrBUMP
• Automated framework for Molecular Replacement• Particular emphasis on generating variety of search
models
• Wraps Phaser, Molrep and Acorn• 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
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PipelinePipeline
`
`
`
`Target MTZ
& Sequence
TargetDetails
TemplateSearch
ModelPreparation
Molecular Replacement& Refinement
Check scores and exit or select the next model
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Template SearchTemplate Search
• Sequence based search (FASTA)• Secondary structure based search
(SSM)• Domain search (SCOP)• Identification of possible multimers
(PQS & PISA)• Users can also enter their own
templates by ID or from locally held files.
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Model PreparationModel Preparation• Search models can be prepared for MR in several
ways– Chainsaw – non-conserved residues are pruned (sequence
provided)– Molrep – pruning of non-conserved side-chains (internal
sequence alignment)– Polyalanine – all side chain atoms are pruned beyond the CB
atom– PDBclip – models are not modified
• An ensemble of the best models is also created for Phaser
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Molecular Replacement & Molecular Replacement & RefinementRefinement
• For each search model, MR is done with Molrep or Phaser or both.
• MR programs run mostly with defaults
• MrBUMP provides LABIN columns, MW of target, sequence identity of search model, number of copies to search for, number of clashes tolerated
• Allow Molrep / Phaser to set resolution limits and weights
• After MR, models are passed to Refmac for restrained refinement
otherwise
final Rfree < 0.48 orfinal Rfree < 0.52 and dropped by 5%
final Rfree < 0.35 or final Rfree < 0.5 and dropped by 20%
“success”
“marginal”
“failure”
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MrBUMP on clustersMrBUMP on clusters
• MrBUMP is usually run on a desktop
• However, MrBUMP can take advantage of a compute cluster to farm out the Molecular Replacement jobs.
• Currently Sun Grid Engine enabled clusters are supported but support will be added for other types of queuing system (e.g. LSF, Condor) if there is enough demand.
• Job control: All nodes terminate when one finds a solution
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MrBUMP OutputMrBUMP Output
• Currently produces a long log file listing search results, model preparation steps, summaries from each MR and refinement job and relevant references for programs used.
• Not ideal, there’s a lot of
information to trawl through. Summary of results now provided at the end of log file.
• Future versions will provide results in marked-up web page format for more clarity.
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MrBUMP pre-releaseMrBUMP pre-release
• Beta version first released in Jan’ 06 (current version is 0.3.3)
• Currently supported on Linux and Mac OSX, Windows version will be available when included in suite.
• Will be included in next release of CCP4 (version 6.1)
• MrBUMP paper to be published in Acta Cryst. D in April ‘07
• First citations in Obiero et al., Acta Cryst. (2006). F62, 757-760; El Omari et al., Acta Cryst. (2006). F62, 949-953
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New featuresNew features• Run Acorn after refinement for phase
improvement (high resolution data)• Support for searching in enantiomorphic
spacegroups.• Users can now specify template models by
PDB ID or add local PDB files.• “Generate models only” option.• XML Output.• Additional multiple alignment programs
supported – Tcoffee and Probcons.
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New feartures: SmartieNew feartures: Smartie
• Peter Briggs’ “Smart” CCP4 log file browser. Robust method for reading and extracting information from log files.
• Parses log files and picks out tables, header information and various other pieces of information.
• Very useful when generating XML output from a automation wrapper script such as MrBUMP.
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Future versionsFuture versions
• Improvements to multimeric search models (using PISA)
• Supplement multiple alignment with additional sequences and/or structural information
• Model completion and/or re-building• Target complexes.
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ConclusionsConclusions
• Test cases and the examples demonstrated the utility of trying a range of search models, a protocol that can only be attempted adequately by automation.
• MrBUMP is not meant to compete with careful analysis of the data and model by an experienced crystallographer. However, it may succeed in difficult cases by finding a combination of models and protocols that would not otherwise have been tried.
• In more straight forward cases the advantage is simply one of convenience.
• CCP4 web server log files indicate that it’s being used at least 3-4 times a day.
28th March 2007
Some thoughts about automationSome thoughts about automation
• MrBUMP started out as a project to develop a one-button solution for MR (e-HTPX). It has evolved to be more interactive if required whilst retaining the one-button functionality.
• Users like to have the donkey work done automatically but prefer controlled/transparent automation with the ability to both stop and start the program as they please at given points in the pipeline.
• Also like to have a large degree of control of the input parameters.