[phenixbb] [ccp4bb] Phenix; converting a map to structure factors

Smith Liu smith_liu123 at 163.com
Fri Jul 10 19:20:24 PDT 2015

Dear Pavel,

The other question is, if we convert mrc file to mtz file by phenix.map_to_structure_factors and then run the GUI phenix refine, in the refilne output, it indicates the FOFCWT map is much much stronger than then 2FOFCWT map, as shown by Coot, for this reason I doubt the correctness of  the GUI phenix refine for this purpose. Can you explain why?


At 2015-07-11 09:41:48, "Pavel Afonine" <pafonine at lbl.gov> wrote:

  Is any software convert mtz file into mrc file (for viewing in chimera)?

phenix.mtz2map .

 In addition, by mrc file I can run phenix,real_space_refine very nicely. But for knowledge gaining purpose, I convert a mrc file to a mtz file by phenix.map_to_structure_factors, and then run the GUI phenix refine with the phenix.map_to_structure_factors converted mtz file (from mrc) file and a model PDB (from mrc), first the GUI phenix refine will give very high Rwork and Rfree, secondly the mtz output density by GUI phenix looks does not fit the initial mrc density at all, thus the pdb models given by phenix,real_space_refine and GUI phenix refine seem strongly different.
Is any way to get similar pdb models by phenix,real_space_refine and GUI phenix refine?

Results should be similar, in general without doing anything special.

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