Difference between revisions of "Cctbx.prime"
From cctbx_xfel
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| − | == | + | == 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 | 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 | ||
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$ prime.postrefine | $ prime.postrefine | ||
</pre> | </pre> | ||
| + | |||
| + | An example of the template .phil file: | ||
| + | |||
| + | <pre> | ||
| + | data = None | ||
| + | run_no = None | ||
| + | title = None | ||
| + | averaging_engine = both *python cpp | ||
| + | icering { | ||
| + | flag_on = False | ||
| + | d_upper = 3.9 | ||
| + | d_lower = 3.85 | ||
| + | } | ||
| + | scale { | ||
| + | d_min = 0.1 | ||
| + | d_max = 99 | ||
| + | sigma_min = 1.5 | ||
| + | } | ||
| + | ... | ||
| + | </pre> | ||
| + | |||
| + | You can se the content of the output here and save it to any file name - in this tutorial, let's save it to thermolysin.phil. | ||
| + | |||
| + | == Step 2: Update input parameters == | ||
Revision as of 21:03, 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
averaging_engine = both *python cpp
icering {
flag_on = False
d_upper = 3.9
d_lower = 3.85
}
scale {
d_min = 0.1
d_max = 99
sigma_min = 1.5
}
...
You can se the content of the output here and save it to any file name - in this tutorial, let's save it to thermolysin.phil.
