Difference between revisions of "Cctbx.prime"
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run_no = None | run_no = None | ||
title = None | title = None | ||
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| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
scale { | scale { | ||
d_min = 0.1 | d_min = 0.1 | ||
| Line 37: | Line 31: | ||
== Step 2: Update input parameters == | == 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): | ||
| + | |||
| + | <pre> | ||
| + | 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 | ||
| + | </pre> | ||
Revision as of 21:17, 1 May 2015
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
