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

Pavel Afonine pafonine at lbl.gov
Fri Jul 10 19:30:25 PDT 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.


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" <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.
>     Pavel

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