Use case "BEST"

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Summary

The main objective of BEST is to estimate the best strategy to collect the diffraction data. EDNA prototype will integrate the 3rd party programm raddose in order to take the radiation damage into account when calculating the strategy. see BEST documentation.

Here the BEST command line. It gives an idea of the mandatory parameters:

  • best -f {detector} -t {time} [OPTIONS] [FILES DENZO/HKL]
  • best -f {detector} -t {time} [OPTIONS] -mos [FILES/MOSFLM]
  • best -f {detector} -t {time} [OPTIONS] -xds [FILES/XDS]
Importance Very important
Priority High priority
Use Frequency Frequently used
Direct Actors Kernel / User
Pre-requirements Kernel running

Input

Required

  • General:
    • Detector Name: Detector name of the detector is in use. In addition to the type of detector, the name encodes unique properties of each device and/or data format
    • Exposure time: Exposure time of initial image(s) in seconds. (3)
  • Related to Radiation Damage:
    • Dose rate: X-ray dose rate in Gray/second. (Given by raddose)
    • Shape factor: Equals 1 if the crystal is smaller then the beam, or equals ratio of crystal size to the beam size (in the direction normal to the rotation axis) if beam is smaller then crystal. (1)
    • Crystal Susceptibility to radiation damage: The default value of 1 means that average decay rate as determined empirically on fairly large number of structures will be applied. Increase (up to 2) if you know that your samples are significantly more sensitive to radiation then others, or reduce (down to 0.5) for radiation-hard crystals (like trypsin).
  • MOSFLM, XDS specific: (ideally replaced by generic indexing and integration generic inputs):
    • if MOSFLM: .dat, .par and .hkl files (or content model?)
    • if XDS: .pck, .lp and .hkl files (2)


Optional

Output

Required

Optional

Main Success Scenario

Variations

Notes and Questions

Inputs

  • (1): the shape factor could be calculated automaically given the crystal size and the beam size
  • (2): For now, BEST needs to know whether the indexing AND the integration have been performed by MOSFLM or XDS. Ideally, it should be good if BEST could accept a generic inputs of both indexing and integration. For that we need to define them.
  • (3): If intensities are scaled by the scan speed, and the background by 1/exposure time, then we would not need the -t option (Gleb)