[phenixbb] map output by phenix.refine

Pavel Afonine PAfonine at lbl.gov
Wed Jul 1 18:05:12 PDT 2009

Hi dream830106,

- the MTZ file with map coefficients "_map_coeffs.mtz" contains
coefficients for fours maps. What COOT decides to show you by default
obviously does not mean that the MTZ file contains only these maps. In
fact, COOT shows you 2mFo-DFc and mFo-DFc maps if you use automatic map
loading option. However, you can tell specifically which map to load
(this is what I always do): consult COOT manual for details.

- to get maps with custom coefficients, like 3Fo-2Fc, you need to ask
phenix.refine to compute these maps. This is explained in phenix.refine

- to see what's inside of your MTZ file, simply type:
phenix.mtz.dump file_name.mtz


On 7/1/09 5:29 PM, 丁玮 wrote:
> Hi Pavel,
> Thank you for responding to my question so eloquently.
> But there are still something confusing me.
> First of all, when I used coot to open the "_map_coeffs.mtz", only two
> mapswere displayed in the window,not four?
> Second, how to choose the mapscoefficients? In phenix documentation,
> we konw that any specified coefficients can be set, for example:
> 2mFo-DFc, 2.7mFo-1.3DFc, Fo-Fc, 3Fo-2Fc. but it do not tell us why we
> shouldchoose different coefficients.
> Thanks a lot.
> dream830106
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