[phenixbb] omit map

Maia Cherney chern at ualberta.ca
Thu May 13 16:53:50 PDT 2010


Hi Pavel, sorry to send you this letter again, as I did not get the answer.

I ran phenix.refine to produce a kicked map after deleting my ligand (to 
get an omit map).
I could not make the Average Kick mFo-DFc Map using phenix.refine or 
phenix.maps.

I got an error message. Sorry: Duplicate mtz_label_amplitudes:2FOFCWT


Here is part of my .def file: How should I change it?

map {
     mtz_label_amplitudes = None
     mtz_label_phases = None
     likelihood_weighted = None
     obs_factor = None
     calc_factor = None
     kicked = False
     fill_missing_f_obs_with_weighted_f_model = True
   }
   map {
     mtz_label_amplitudes = "2FOFCWT"
     mtz_label_phases = "PH2FOFCWT"
     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"
     mtz_label_phases = "PHFOFCWT"
     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
   }




Pavel Afonine wrote:
> Hi Maia,
>
> just a remark: probably the quickest and simplest option to see if 
> your ligand is there is to do these two steps:
>
> 1) physically remove the ligand from PDB file;
> 2) compute Average Kick mFo-DFc Map using phenix.refine or phenix.maps.
>
> Pavel.
>
>> I am wondering what is the difference between an omit map that is 
>> produced by the refinement without a ligand and an omit map produced 
>> by autobuild.
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>
>



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