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