Hi Pavel,

I am also trying to make kicked maps for the first time in order to improve density for a terminal helix and short loop that have been giving me problems in model building for an MR structure. On a similar note to Yarrow, I tried using his syntax in a maps.params file, like this:

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 = False
  }
  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
  }

But when I ran phenix.maps I received this message:

Unused parameter definitions:
  maps.map.mtz_label_amplitudes (file "maps.params", line 29)
  maps.map.mtz_label_phases (file "maps.params", line 30)
  maps.map.likelihood_weighted (file "maps.params", line 31)
  maps.map.obs_factor (file "maps.params", line 32)
  maps.map.calc_factor (file "maps.params", line 33)
  maps.map.fill_missing_f_obs_with_weighted_f_model (file "maps.params", line 35)
  maps.map.mtz_label_amplitudes (file "maps.params", line 38)
  maps.map.mtz_label_phases (file "maps.params", line 39)
  maps.map.likelihood_weighted (file "maps.params", line 40)
  maps.map.obs_factor (file "maps.params", line 41)
  maps.map.calc_factor (file "maps.params", line 42)
  maps.map.fill_missing_f_obs_with_weighted_f_model (file "maps.params", line 44)
*******************************************************************************

Sorry: Unused parameter definitions.

Next I tried using this in my .params file for phenix.refine:

refinement.electron_density_maps {
    map {
      map_type = "2mFo-DFc"
      format = *xplor ccp4
      file_name = None
      kicked = True
      fill_missing_f_obs = False
      grid_resolution_factor = 0.25
      scale = *sigma volume
      region = *selection cell
      atom_selection = None
      atom_selection_buffer = 3
      acentrics_scale = 2
      centrics_pre_scale = 1
      sharpening = False
      sharpening_b_factor = None
    }
    map {
      map_type = "mFo-DFc"
      format = *xplor ccp4
      file_name = None
      kicked = True
      fill_missing_f_obs = False
      grid_resolution_factor = 0.25
      scale = *sigma volume
      region = *selection cell
      atom_selection = None
      atom_selection_buffer = 3
      acentrics_scale = 2
      centrics_pre_scale = 1
      sharpening = False
      sharpening_b_factor = None
    }

When I opened the map_coeffs.mtz output file, it contains these columns
2FOFCWT_no_fill
PH2FOFCWT_no_fill
FOFCWT
PHFOFCWT

Are these the coefficients for the kicked maps?

Cheers,
Kyle

Kyle T. Dolan
Department of Biochemistry and Molecular Biology
The University of Chicago
ktd@uchicago.edu

On Mon, Aug 2, 2010 at 7:48 PM, Pavel Afonine <pafonine@lbl.gov> wrote:
 Hi Yarrow,

you can use GUI or the command line for doing this.

0) It would be best if you update to the latest version, although I believe it might work with the one you have too:

http://www.phenix-online.org/download/

1) GUI: launch PHENIX GUI and go to Maps -> Create Maps. then just add as many maps you want (or use pre-defined ones) and check a box for kick map.

2) From the command line type:

phenix.maps

and hit Enter (Return). That will create a file called something maps.params. Edit that file to add/remove the maps you need/ don't need and set

kicked = True

for the one you want to be "kicked", and then run

phenix.maps maps.params

Let me know if you have any questions or problems.

Good luck!
Pavel.



On 8/2/10 5:38 PM, amadrona@uci.edu wrote:
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
}

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