[phenixbb] about kick map generation

[Folmer Fredslund]

Dear ?? (qunqan?),

If I understand correctly, you get one mtz file with all the columns
needed to make the maps that correspond to your input file (which is
also clearly stated in the manual at
http://www.phenix-online.org/documentation/refinement.htm#anch70).

So, what you need to do is generate the maps with fft, or simply view
them (by defining the proper labels) in a program like COOT.

This should help.

Best regards,
Folmer Fredslund

2009/9/4 crystallogrphy <qunwan1 at gmail.com>:
> Hi,
> I am generating a averaged kick maps with the following script. According to
> the script, there should be both kick map and normal 2fofc maps. However,
> there is only one map files created. I am not sure it is kick map or routine
> 2fofc map. Does anyone knows?
>
> electron_density_maps {
>     map_format = *xplor
>     map_coefficients_format = *mtz phs
>     suppress = None
>     map {
>       mtz_label_amplitudes = "2FOFCWT"
>       mtz_label_phases = "PH2FOFCWT"
>       likelihood_weighted = True
>       obs_factor = 2
>       calc_factor = 1
>       kicked = False
>       fill_missing_f_obs_with_weighted_f_model = True
>     }
>     map {
>       mtz_label_amplitudes = "FOFCWT"
>       mtz_label_phases = "PHFOFCWT"
>       likelihood_weighted = True
>       obs_factor = 1
>       calc_factor = 1
>       kicked = False
>       fill_missing_f_obs_with_weighted_f_model = True
>     }
>     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_kick"
>       mtz_label_phases = "PHFOFCWT_kick"
>       likelihood_weighted = True
>       obs_factor = 1
>       calc_factor = 1
>       kicked = True
>       fill_missing_f_obs_with_weighted_f_model = False
>     }
>     map {
>       mtz_label_amplitudes = "2FOFCWT_no_fill"
>       mtz_label_phases = "PH2FOFCWT_no_fill"
>       likelihood_weighted = True
>       obs_factor = 2
>       calc_factor = 1
>       kicked = False
>       fill_missing_f_obs_with_weighted_f_model = False
>     }
>     map {
>       mtz_label_amplitudes = "FOFCWT_no_fill"
>       mtz_label_phases = "PHFOFCWT_no_fill"
>       likelihood_weighted = True
>       obs_factor = 1
>       calc_factor = 1
>       kicked = False
>       fill_missing_f_obs_with_weighted_f_model = False
>     }
>     anomalous_difference_map {
>       mtz_label_amplitudes = "ANOM"
>       mtz_label_phases = "PHANOM"
>     }
>     grid_resolution_factor = 0.25
>     region = *selection cell
>     atom_selection = None
>     atom_selection_buffer = 3
>     apply_sigma_scaling = True
>     apply_volume_scaling = False
>   }
>
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