Cctbx.prime

Prime: post-refinement and merging

Step-by-step guidelines to post-refine and merge XFEL diffraction images. For more detail and citation, see Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals "DOI: http://dx.doi.org/10.7554/eLife.05421"

Step 1: Generating input file

Like most programs developed under cctbx framework, prime reads in input .phil file, which stores all the parameters needed to run post-refinement and merging steps. To generate the template .phil file, do the dry run by calling

$ prime.postrefine

An example of the template .phil file:

data = None
run_no = None
title = None
scale {
  d_min = 0.1
  d_max = 99
  sigma_min = 1.5
}
...

You can save the content of the output to any file name - in this tutorial, let's save it to thermolysin.phil.

Step 2: Update input parameters

For the first trial, set the required parameters as following (you can leave other parameters with their default values - or just delete them from you .phil file):

data = /path/to/your/integarion/result/pickle_files
run_no = 001
title = First trial for thermolysin
scale {
  d_min = 2.1
  d_max = 45
  sigma_min = 1.5
}
postref {
  scale {
    d_min = 2.1
    d_max = 45
    sigma_min = 1.5
    partiality_min = 0.1
  }
  crystal_orientation {
    flag_on = True
    d_min = 2.1
    d_max = 45
    sigma_min = 1.5
    partiality_min = 0.1
  }
  reflecting_range {
    flag_on = True
    d_min = 2.1
    d_max = 45
    sigma_min = 1.5
    partiality_min = 0.1
  }
  unit_cell {
    flag_on = True
    d_min = 2.1
    d_max = 45
    sigma_min = 1.5
    partiality_min = 0.1
    uc_tolerance = 3
  }
  allparams {
    flag_on = False
    d_min = 0.1
    d_max = 99
    sigma_min = 1.5
    partiality_min = 0.1
    uc_tolerance = 3
  }
}
merge {
  d_min = 2.1
  d_max = 45
  sigma_min = 1.5
  partiality_min = 0.1
  uc_tolerance = 3
}
target_unit_cell = 93.99,93.99,130.87,90,90,120
target_space_group = P 61 2 2
pixel_size_mm = 0.102