[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.
>
More information about the phenixbb
mailing list