Experiment Types

Summary of experiment kinds

Experiment kind Protocol Samples/hr (without screening) Samples/hr (with screening)
Native Prioritises completeness/resolution and collects 2 x 360° sweeps, 1st at chi=0 and 2nd at chi=30  20  15
Phasing Two 360° sweeps are collected using different chi/phi values at your chosen energy, using a lower transmission to maximise anomalous multiplicity and completeness.  20  15
Ligand Prioritises speed of data collection and collects a single sweep, 360° dataset  25  18
Stepped Prioritises resolution and conducts a stepped transmission scan (see below)  10  7


Exposure times, transmission and resolution

The philosophy of UDC is to collect a dataset suited to a particular experimental goal. Exposure settings are tuned to give maximum resolution while avoiding significant radiation damage (the aim is to have final I = 0.85 I0). This avoids the need for manual reprocessing in most cases. 

Radiation damage is first observed in the higher resolution shells. We use the choice of diffraction resolution to scale the total dataset exposure to compensate for this. Collections with a high resolution cut off will be collected with shorter exposure times than low resolution. This also avoids underexposing weakly diffracting crystals.

Below is an example plot showing the total exposure times for the UDC Ligand, Native and Phasing recipes that would be collected on I03 at the standard beamline energy (12700eV) with the 100 micron aperture and using 100% transmission. Exposure times and transmission values are adjusted for different energies.

Stepped transmission data collection

This is a method for collecting complete data in the absence of any prior information. It exploits the photon counting nature of the Pilatus and Eiger detectors and comprises a series of 360° data collection sweeps that increase in dose with each sweep. Post collection, the point at which radiation damage becomes apparent can be manually identified and all data prior to this point combined to yield a complete, minimal radiation damage dataset at the best achievable resolution.
The approach is described in detail in this paper: How best to use photons.
The implementation of this on I03 uses 4 x 360° sweeps with exposure settings for 1, 2, 3 & 4 Å. These transmissions are automatically adjusted based on the energy used.
The initial parameters were chosen based on the expected lifetime of a typical crystal that matches the beam size. It is expected that radiation damage will occur at some point during the collection, particularly in the final sweep.
Currently, the automatic processing software makes no attempt to truncate sweeps when radiation damage becomes apparent. It is therefore important that you manually assess the processed sweeps and combine all data prior to your choice of radiation damage cutoff – failure to do so may result in a weak dataset or one containing significant radiation damage.

Grouped Data Collections

Synchweb will only show one entry on the main page for the data collection group and the results displayed here will be for the first sweep collected. You can see the results from all sweeps by clicking on the link in the “Group” box to the right (underneath the beamsize).

grouped data collections in synchweb

This link will open a page with all sweeps individually listed. From here you can check the processing status and trigger reprocessing in the same way you would from the main page. By default, the automatic pipelines will try and combine whole sweeps, but will not add part of a sweep.
You might find some sweeps refuse to process automatically due to the weakness of the reflections. In this case you will have to process manually and you may find stacking the images for indexing to be of help (MERGE2CBF can be used for this).

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