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

11 Jul 2015

      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"  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