[phenixbb] syntax for Averaged Kicked maps and maps.param

amadrona at uci.edu amadrona at uci.edu
Mon Aug 2 17:38:05 PDT 2010


Hello,

Disclaimer:  I am a newbie to both crystallagraphy and Phenix.

I am running phenix.refine (v1.6-289) in the command line

1.  I want to make averaged "kicked-maps" but I keep getting a syntax
error.  I tried renaming "maps.param" but this file was not recognized.

2.  When I enter Phenix.maps into the command line I get a message that
syas "not implemented"
I am trying to get the latest versiou of phenix installed.

The following is the syntax I put in my custom_params file
Thanks

-Yarrow

refinement.main.number_of_macro_cycles = 2
#refinement.main.fix_rotamers = True
refinement.refine.strategy = individual_sites+individual_adp
refinement.output.prefix = CIN4_refine_omit
refinement.output.serial = 12
refinement.output.write_def_file = True
refinement.target_weights_wxc.scale = 0.2
refinement.main.max_number_of_interations=15


refinement.electron_density_maps {
map {
  mtz_label_amplitudes = "2FOFCWT_kick"
  mtz_label_phases = "PH2FOFCWT_kick"
  likelihood_weighted = True
  obs_factor = 2
  calc_factor = 1
  kicked = True
  fill_missing_f_obs_with_weighted_f_model = True
}
map {
  mtz_label_amplitudes = "FOFCWT_kicked"
  mtz_label_phases = "PHFOFCWT_kicked"
  likelihood_weighted = True
  obs_factor = 1
  calc_factor = 1
  kicked = True
  fill_missing_f_obs_with_weighted_f_model = false
}




More information about the phenixbb mailing list