MrBUMP

MrBUMP is an automated molecular replacement pipeline, that streamlines the early stages of MX structure determination. MrBUMP takes a target amino acid sequence and uses known protein sturctures to generate search models. It then runs molecular replacement using these models to solve the phase problem and tests to see if the resulting solutions will refine successfully. The outcome of this is a strutural model that should serve as a good starting point for model building and refinement.

Running MrBUMP at Diamond

MrBump will run automatically upon the successful completion of any of the xia2 data-reduction pipelines, so long as a protein amino acid sequence has been uploaded to ISPyB for the given sample. MrBump will also use any protein structures (in pdb format) uploaded to ISPyB as an optional input to the pipeline. If protein structures have been uploaded, MrBUMP will run twice for each upstream pipeline, running once using just the amino acid sequence and once using the sequence and any uploaded pdb files as input. Note, uploading a sequence to ISPyB will trigger an automated run of AlphaFold and the protein strucutres from this will be automatically uploaded to ISPyB and will therefore be used by MrBUMP. A guide on how to upload protein sequences and structures to ISPyB can be found here.

Results in ISPyB

MrBUMP results will display in ISPyB under the downstream processing tab. A separate set of results is shown for each run of MrBUMP, which is typically run twice for each xia2 data reduction pipeline - once with and once without using uploaded pdb structures as an input. The results indicate which xia2 pipeline MrBump was triggered from. If you have more than one instance of a xia2 pipeline (e.g. from providing a space group or from reprocessing), the exact run of the upstream pipeline that the results correspond to can be found by clicking the "View Upstream" button. Currently there is no convenient way of distinguishing between MrBUMP runs that do and don't use uploaded pdb files as input but this can be determined by looking in the MRBUMP.log file via the "Logs & Files" button. If "Chain from local file to include in model search" is included in the "Keyword Input Summary" in the log, then the uploaded pdb files were used.

The ISPyB results tab for MrBUMP shows a graph of refinement, showing R factors vs refinement cycle. A good indicator of successful molecular replacement is if the R-factors decrease during the refinement steps and a Rfree < 0.5 is obtained.

The main results files from MrBUMP are the PostMRRefine.pdb and PostMRRefine.mtz files, which contain the refined model and density maps respectively. The files can be downloaded from the "Logs & Files" button or can be viewed in uglymol via the "Map / Model Viewer button".

The uglymol viewer shows the refined structural model along with the 2Fo - Fc map (calculated electron density) in blue and the Fo - Fc difference map in Green/Red, highlighting the differences between the model and the map.

Citation
Please remember to cite the appropriate autoprocessing pipeline used prior to MrBUMP, any programs used by MrBUMP (can be found from the MRBUMP.log file), as well as the following reference for MrBUMP iteself:

R.M. Keegan, S.J. McNicholas, J.M.H. Thomas, A.J. Simpkin, F. Simkovic, V. Uski, C.C. Ballard,
M.D. Winn, K.S. Wilson and D.J. Rigden (2018) Acta Cryst. D74, 167-182