[phenixbb] how to easily find old subjects

Pavel Afonine PAfonine at lbl.gov
Wed Sep 9 12:39:16 PDT 2009


Hi Maia,

1) You can use phenix.refine for this:

phenix.refine model.pdb data.mtz strategy=none 
main.number_of_macro_cycles=1 output.prefix=maps_only

Remarks:

- you need to use strategy=none to tell phenix.refine to not refine 
atomic parameters (such as B-factors, coordinates, etc.);

- you need to use "main.number_of_macro_cycles=1" (or its shortcut 
"main.number_of_mac=1"), so phenix.refine does bulk-solvent correction 
and anisotropic scaling, which is critical to get good maps.

- of course, in twin-refinement, you also need to append a twin law to 
the above command, for example:

phenix.refine model.pdb data.mtz strategy=none 
main.number_of_macro_cycles=1 output.prefix=maps_only twin_law="k,-k,-l"

2) You can use new PHENIX GUI for this, just type:

phenix.create_maps

3) Recent version of phenix.model_vs_data has "--map" keyword:

phenix.model_vs_data model.pdb data.mtz --map="2mFo-DFc"

Pavel.


> I remember, there was a question how to generate maps without 
> refinement. I finished the refinement, but I need a map (in explor 
> format) to show the 2fo-fc density in the publication.
>   



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