Automatic Software Pipelines

Automatic Software Pipeline

Strategy estimations are carried out on datasets with fewer than 20 images

 Data reduced using fast_dp and xia2

If a pdb file is provided, difference maps can be generated by DIMPLE

If a sequence file is provided, MrBUMP will run automatically to find a molecular replacement solution

If data integration highlights the possibility of anomalous signal and an anomalous scatterer is specified in ISPyB, experimental phasing is carried out with Fast ep and/or Big ep

Summary:

• Strategy Calculation with EDNA and MOSFLM
• Data reduction with fast_dp and XIA2
• Difference map calculation with DIMPLE
• Molecular replacement with MrBUMP
• Experimental phasing with fast_ep
• Experimental phasing with big_ep
• Identification of fluorescent elements with AutoPyMCA

Strategy calculation with EDNA and Mosflm

Strategy calculations are automatically carried out for every data collection of fewer than 20 images using Mosflm and EDNA Mxv1. EDNA MXv1 is run automatically with preset parameters 4 times, and will pick up the spacegroup specific for the sample in ISPyB (unless it is P1). It is possible to specify additional strategy preferences that will be run in addition to the standard 4. All results can be downloaded to the GDA.

Please ask your local contact for more details.

Data reduction with fast_dp and XIA2

Each sweep of data will be automatically reduced with fast_dp and XIA2 without any additional input. If you have set the spacegroup of the sample in ISPyB, it will be used in fast_dp.

You can re-run fast_dp and Xia2 though DAWN and Xia2 can also be used from the CCP4i GUI.

Click here for more information.

Please ask your local contact for more details.

Difference map calculation with DIMPLE

For DIMPLE to run automatically after data reduction with fast_dp, the model pdb (including cryst card) should be to a protein within ISPyB. When adding or editing a protein there is an additional section to upload a pdb file. Once defined, any sample that makes use of this protein will automatically invoke DIMPLE when data is collected. These only need to be defined once per proposal, and automatically works on any visit. PDB files must be stripped of ligands or DIMPLE will fail.

You can re-run DIMPLE through the CCP4 GUI or through DAWN.

 Examples:  Given a dataset with filename:

   SomeProject_crystal3_1_0001.cbf

then dimple will run for pdb files named:
    SomeProject.pdb
    crystal3.pdf
    Some.pdb
    cryst.pdb
    SomeProject.2ndcrystal.pdb
    SomeProject.2nd.crystal.pdb

but not for
    SomeProject_myOtherCrystal.pdb
    crystal3_otherSpacegroup.pdb
    crystal3-otherSpacegroup.pdb
(note underscores and dashes)

Alternative spacegroups can be requested like this:
    SomeProject.P3121.pdb
    SomeProject.P3221.pdb
    SomeProject.P321.pdb

Click here for more information.

Please report issues to your local contact.

Molecular replacement with MrBUMP

For MrBUMP to run automatically after data reduction with fast_dp, the sequence should be added in ISPyB. Once defined, any sample that makes use of this protein will automatically invoke MrBUMP when data is collected.

Experimental phasing with Fast EP

Fast_ep is a brute force experimental phasing pipeline using the fast_dp MTZ file and the SHELX suite to produce a map, if certain parameters are met in the dataset. No additional information is required.

Click here for more information.

Please ask your local contact for more details.

Experimental phasing with big EP

Big_ep is an advanced experimental phasing pipeline using the output of autoprocessed xia2 MTZ files. It assesses the quality of anomalous signal using the SHELX suite and automatically runs AUTOSHARP, AUTOSOL and CRANK2 to phase and build a model. It will do this without any prior information but if you provide a sequence and a heavy atom in ISPyB for your crystals this can improve success.

Your results can be found in the processed folders of your visit and summary info and map and model viewer are available in ISPyB. Note that these processes take some time to run following the xia2 jobs so it is worth periodically checking in ISPyB for new results.