[phenixbb] [EXTERNAL] getting non-default values in phenix.refine

Edward A. Berry berrye at upstate.edu
Wed Dec 2 19:14:44 PST 2020

if you still have have the log file from the run that created that def,
there is a list of non-default parameters sandwiched between:
#phil __ON__
#phil __OFF__

awk \$2~/__ON__/,\$2~/__OFF__/ refine_nnn.log > ref.eff

or (csh)
alias log2eff 'awk \$2~/__ON__/,\$2~/__OFF__/ \!*'
log2eff refine_nnn.log > ref.eff

of course that will be parameters for that run, so you should increment .output.serial before running!


On 12/02/2020 09:38 AM, David A Case wrote:
> The top of .def files I have from (old?) phenix.refine runs says this:
> # Command to extract only non-defaults:
> #   phenix.refine --diff-params "cdl_002.def"
> But I can't get this to work:
> peano% phenix.refine --diff-params "cdl_002.def"
> Usage: phenix.refine [options] [reflection_file] [pdb_file] [parameter_file]
> refine.py: error: no such option: --diff-params
> Is there a way to get this functionality?
> ...thx...dac
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