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?
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.
Pavel