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

Smith Liu smith_liu123 at 163.com
Fri Jul 10 16:58:47 PDT 2015

Dear Terwilliger,
Is any software convert mtz file into mrc file (for viewing in chimera)?
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?
Best regards.

At 2015-07-11 01:31:00, "Terwilliger, Thomas Charles" <terwilliger at lanl.gov> wrote:
Hi Reza,

Just use:

    phenix.map_to_structure_factors map.ccp4 d_min=2.5

or something like that,
All the best,
Tom T

On Jul 10, 2015, at 11:27 AM, Reza Khayat wrote:


Is it possible to convert a map to structure factors using Phenix? Thanks.

Best wishes,

Reza Khayat, PhD
Assistant Professor 
City College of New York
Department of Chemistry
New York, NY 10031
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