Beamline Phone Number:
+44 (0) 1235 567406
Principal Beamline Scientist:
Armin Wagner
Tel: +44 (0) 1235 778560
E-mail: [email protected]
Email: [email protected]
Tel: +44 (0) 1235 778926
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, experimental phasing is carried out with fast_ep and/or big_ep
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.
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.
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 (in FASTA format) should be put in:
/dls/ixx/data/2013/VISITID/processing/seq
The sequence filename must include something from the image name e.g.
my_prot.seq with images called my_prot_MxSxx_00x.cbf
Your results can be found through the 'View Today's jpegs' Results page or can be found at:
your-visit/processed/AnySubDirectoriesTheSameAsDC/fileprefix/auto_mrbump
Please ask your local contact for more details.
You can re-run MrBUMP through the CCP4 GUI or through DAWN.
In addition to providing a seq file in the visit directory, it is now possible to add a sequence to a protein within ISPyB2. When adding or editing a protein there is an additionnal section to define a sequence. Once defined, any sample that makes use of this protein will automatically invoke MrBUMP when data is collected.
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.
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.
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