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

[Kyle Dolan]

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 at uchicago.edu

On Mon, Aug 2, 2010 at 7:48 PM, Pavel Afonine <pafonine at 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 at 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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>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>
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