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== Step | == Step I: 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 | 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 | ||
Revision as of 21:46, 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 I: 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 to match with your experiments (you can leave other parameters with their default values - or just delete them from you .phil file). For this tutorial, we use parameters from our thermolysin data set.
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
Step 3: Post-refine and merge
Once you have the input .phil file, you can run prime by calling
prime.postrefine thermolysin.phil
Prime will post-refine and merge for reflection sets using three (default value) macrocycles. At the end of the run, you can obtain merging statistics in the last cycle - all other cycle statistics are also available in log.txt.
Advance settings
Now that you have your first trial merged data set, you can explore different parameter settings to merge or to obtain the Bijvoet pairs (I+/I-) for your anomalous data set.
Anomalous data:
target_anomalous_flag = True
In the last cycle, prime will output a reflection set with I+ and I-.
Indexing ambiguity
For space groups with indexing ambiguity, use the solutions from cctbx.xfel (see Tutorial for resolving indexing ambiguity) to merge the data set.
indexing_ambiguity { flag_on = True index_basis_in = /path/to/solution/pickle_file.pickle }
Number of micro- and macrocycles
n_postref_cycle = 3 n_postref_sub_cycle = 3
Number of bins for merging statistics
n_bins = 20
Help for input parameters
Most input parameters are self-explained. However, you can run -h switch to view help information for each parameter.
prime.postrefine -h