[phenixbb] maps and autobuild
Pavel Afonine
PAfonine at lbl.gov
Mon Apr 6 09:44:22 PDT 2009
Hi Charlie,
> Also from reading the manual, as I understand it, the phenix.refine
> command will automatically generate Coot compatible maps.
phenix.refine always outputs maps ready to visualize in Coot. The files
is called xxx_map_coeffs.mtz and it contains various columns with
Fourier map coefficients. When loading this file into Coot you need to
choose which map to display (which map coefficients to use).
> But if I take my autobuild.pdb file and the original mtz data file,
> how can I quickly obtain the same R/Rfree, what commands would I have
> to imput other than phenix.refine mtz pbd?
In addition to what Tom wrote, there is a specific command to do this:
phenix.model_vs_data model.pdb data.mtz
and it will give you complete model and data statistics, including
R-factors.
> Also, is it possible to make 3Fo-2Fc maps?
phenix.refine can create a map i*mFo-j*DFc or i*Fo-j*Fc, where i and j
are any user provided numbers. Example:
phenix.refine model.pdb data.hkl params.txt
where params.txt file contains these lines:
refinement.electron_density_maps {
map {
mtz_label_amplitudes = 3FO2FCWT
mtz_label_phases = PH3FO2FCWT
likelihood_weighted = True
obs_factor = 3
calc_factor = 2
kicked = False
fill_missing_f_obs_with_weighted_f_model = True
}
map {
mtz_label_amplitudes = 1.5FO1.2FCWT
mtz_label_phases = PH1.5FO1.2FCWT
likelihood_weighted = False
obs_factor = 1.5
calc_factor = 1.2
kicked = False
fill_missing_f_obs_with_weighted_f_model = True
}
}
Pavel.
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