I don't know what exactly you have done and how, so I can't offer meaningful comments. Why don't yo just refine against the map directly?

Also, it sounds like you juts try things out to learn.. It may be a good idea to attend a Phenix workshop that we have occasionally in different places. From you email "163.com" I figure you are in China. Chances are that we may be doing a Phenix workshop in Shanghai beginning of next year, so if you are nearby or keen to attend regardless the travel distance - you are welcome.

Pavel



On 7/10/15 19:20, Smith Liu wrote:
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?

Smith






At 2015-07-11 09:41:48, "Pavel Afonine" <[email protected]> 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.

Pavel