laue_dials.integrate

Introduction

This script generates integrated MTZ files from refined data with predictions.

The program takes a refined geometry experiment file along with a predicted reflection table, and uses those to integrate intensities in the data set. The output is an MTZ file containing integrated intensities suitable for merging and scaling.

The algorithm applied here is a variable elliptical summation algorithm inspired by the VariableElliptical mode in Precognition. Elliptical profiles are modeled for each strong reflection, with weak reflections using an average of the k nearest strong spots, and then the pixel intensities within are summed to generate integrated intensities per reflection.

Examples:

laue.integrate [options] poly_refined.expt predicted.refl

Basic parameters

output {
  filename = 'integrated.mtz'
  log = 'laue.integrate.log'
}
nproc = 1
isigi_cutoff = 2.0

Full parameter definitions

output {
  filename = 'integrated.mtz'
    .help = "The output MTZ filename."
    .type = str
  log = 'laue.integrate.log'
    .help = "The log filename."
    .type = str
}
nproc = 1
  .help = "Number of parallel integrations to do"
  .type = int(allow_none=True)
isigi_cutoff = 2.0
  .help = "I/SIGI threshold to use for marking strong spots."
  .type = float(allow_none=True)