[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 

> 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


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