[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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