17th March 2008

MrBUMP progress reportRonan Keegan & Martyn Winn

Daresbury Laboratory

17th March 2008

About MrBUMP

• Molecular Replacement with Bulk Model Preparation• Given an initial sequence and the structure factor data it

seeks out the best search models for use in Molecular Replacement and tries as many as possible in order to find the best solution.

• In simple case the pipeline replicates what crystallographers might do and its value is simply one of convenience.

• In more difficult cases, the pipeline aims to discover the particular template structure and model edits required to produce a viable search model and may succeed in finding an efficacious combination that would be missed otherwise.

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About MrBUMP• MrBUMP CCP4i interface.• Users can control many of the

parameters in the pipeline but most options come with sensible default values.

• MrBUMP can make use of both Phaser and Molrep for the MR stage.

• Refmac also used to refine output models from MR.

• Other programs used: Chainsaw, Pdbcur, Pdbset, Acorn, PISA.

• MrBUMP to be included in CCP4 6.1.

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• DBhandler and Viewer– Working in collaboration with Wendy and Peter. – MrBUMP act as a testbed for trial release of

DBhandler and to help in its development.– Through the DBhandler python client API MrBUMP

deposits its job data in the handler database. – Users can then use the DBviewer to view the

progress of the MrBUMP job – Viewer allows for quick and easy access to any input,

output or log files generated. – Aids user in coming to a decision about the best result

from MR and refinement.

Integration with CCP4i DBhandler

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• DBhandler and Viewer

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• Model generation only mode– This option allows users to just generate models

without running the molecular replacement step.– Users can then pick and choose which models they

want to put through MR.

• MR only mode– Picks up models from a previously run “Models Only”

job.

– Idea is to allow for manual inspection and altering of the models should the user desire.

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• Complexes:– Users can enter pre-

determined fixed component(s) for the MR step. This is then passed into Phaser and/or Molrep.

– This is a first step towards a fully automated mechanism for handling complexes.

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• Downloading of PDB files.– Some users, particularly those with slow internet

connections found that it was taking a long time to retrieve PDB files from the internet.

– Some changes have been made to minimize this problem.

– Search to automatically determine the closest PDB server (EBI, RCSB, Japan)

– Users can specify a local directory where PDB files can be found.

– Any files downloaded are saved so that future runs can use them.

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• Other new features:– MrBUMP now runs on Windows. There is a

separate installer available for Windows on the downloads site.

– Users can enter a proxy server if they require one to access the internet.

– Internet connectivity test added.– RMS values for input PDB files can be

specified.

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• Testing– CCP4 Cluster is used to run a set of tests on the

latest CVS version of MrBUMP each week.– Set of examples (known structures) are used to test

each component of the pipeline.– Results are reported by email each week. – Currently success or failure is pointed out. – Future versions will give more detail.– Mechanism can also be used for parameter space

testing to help improve the success rate of the pipeline.

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Future Plans• Switch from PQS to using PISA for generating multimer

models.• Fully automated complex search.• Incorporate Pirate/Buccaneer. Make use of

ccp4_pipeline_simple to cycle Buccaneer and Refmac for model building.

• Allow for unlimited number of ensembles to be used as search models in MR.

• Look at using Rapper for creating ensembles and rebuilding.

• Improved model preparation, e.g. removal of flexible loops from search models

• Automatic update mechanism.• Tie-in with Balbes.

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• Primary reference:– R.M.Keegan and M.D.Winn, Acta Cryst. D63, 447 -

457 (2007) - "Automated search-model discovery and preparation for structure solution by molecular replacement“

• Other references:– Bahar, M. et al. (2006) "SPINE workshop on

automated X-ray analysis: a progress report" Acta Cryst. D62, 1170-1183

– Keegan, R.M. and Winn, M.D. Acta Cryst. D64, 119-124 (2008) - "MrBUMP: An automated pipeline for molecular replacement"

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• Number of citations for MrBUMP– J.Obiero, S.A.Bonderoff, M.M.Goertzen and D.A.R.Sanders, (2006),

Acta Cryst F62 757-760. – K.El Omari, B.Dhaliwal, M.Lockyer, I.Charles, A.R.Hawkins and

D.K.Stammers (2006), Acta Cryst F62 949-953 (PDB code 2j41). – Izhar Karbat, Michael Turkov, Lior Cohen, Roy Kahn, Dalia Gordon,

Michael Gurevitz and Felix Frolow (2007) J. Mol. Biol. 366 586-601 (PDB code 2i61).

– L.Lehtio et al, to be published (PDB code 2pa9) – M.A. Stead, C.H. Trinh, J.A. Garnett, S.B. Carr, A.J. Baron, T.A.

Edwards and S.C. Wright (2007) J. Mol. Biol. 373, 820-826 (see Supplementary Data) (PDB code 2q81)

– E. Kiyota, S. M. de Sousa, M. L. dos Santos, A. da Costa Lima, M. Menossi, J. A. Yunes and R. Aparicio (2007) Acta Cryst F63 990-992

– Van Straaten, K.E., Hoffort, A., Palmer, D.R.J., and Sanders, D.A.R., (2008), Acta Cryst F64 98-101.

– E.K. Millers, Structural investigations of Textilinin-1, a potent serine protease inhibitor from the Australian Brown snake, Pseudonaja textilis and ACII-4, a PLA2 with low phospholipase activity and high anti-coagulant activity, from Mulga, Pseudechis australis (2008) Phd Thesis.

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Acknowledgements

• Peter Briggs & Wanjuan Yang, DBhandler and Viewer• Randy Read & Airlie McCoy, Phaser• Alexei Vagin, Molrep• Garib Murshudov, Refmac• Norman Stein, Chainsaw• Eleanor Dodson, Lucas Bleicher, Derek Logan, Felix

Frolow, Mike Guliano, Pietro Roversi, Bernard Santarsiero and many more for their useful feedback.

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• External collaborations:– D. Ridgen, University of Liverpool – looking at using

mrbump to test results for use of ab initio modelling in molecular replacement.

– A. Buckle, Monash University – looking at using the Mustang_MR program as an additional method for generating search models and ensembles for molecular replacement.