[phenixbb] on phenix refine of the cryo-EM data

Smith Liu smith_liu123 at 163.com
Sat Aug 29 07:41:29 PDT 2015

Dear All,

Phenix.real_space_refine can give nice results, but I still want to refine it by phenix refine graphical interface so that the refined PDB by Phenix.real_space_refine  can have a much better resolution PDB from crystal structure as a reference PDB for further refine by phenix refine GUI, in case a fragment of the sequence may adopt a sheet structure as the reference structure, rather than a loop structure as obtained by Phenix.real_space_refine.

When I use the phenix refine GUI for further refine, do I need to use electron scattering table, or I continue to use n-Gaussian scattering table? For the phenix refine GUI for this purpose, there will ne no necessity to click Optimized X-ray/sterochemistry weight and Optimize X-ray/ADP weight, as for it has no relationship with X-ray, am I right?

The phenix.map_to_structure_factors converted mtz file, should correspond to the 2FoFcWT file. In the phenix GUI refine process, it will calculate the FoFcWT file. But each time I tried the refine by phenix GUI related to phenix.map_to_structure_factors converted mtz file, the signal of the FoFcWT file was almost as strong as or even much stronger than the  2FoFcWT file, which was in strong contrast with the phenix refine based on the crystal mtz file. Will you please explain why for  phenix.map_to_structure_factors converted mtz file, phenix GUI can give such high signal of FoFcWT file?

Best regards.

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