[phenixbb] on b factor refine for phenix.real_space_refine

Smith Lee smith_lee123 at yahoo.com
Wed Aug 12 19:18:50 PDT 2015

 Dear All,
I first run a default phenix.real_space_refine with the map and initial model, with the model got, I run phenix.real_space_refine  with run=adp, I find for the second phenix.real_space_refine step with run=adp, it can gives a reasonable value of b-factors for each residues in the model, and it cannot modify the coordinates of any atoms in the model (in comparison with the model got by the default phenix.real_space_refine in the first step).
I just read a Nature paper from David Baker group "Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement", it says "Because cryo-EM maps are frequently better in resolution in some regions than others, atomic B factors are fit against cryo-EM density data to maximize the real-space correlation between model and map".

For Real-space B-factor refinement, the math functions used by that Nature paper include,

( f is a scattering factor fit to each element)


My question is, does b-factor refine only give a reasonable b-factor to each atom or residue  in the model (so that we know the displacement of each atom or residue), or besides giving reasonable b-factor, it can also change and optimize the x y z coordinates of each atom in the model, and the  phenomenon I observed in phenix.real_space_refine on that it only gives reasonable b-factor without modification of the x y z coordinates was only limited to the case I see in phenix.real_space_refine? 
Best regards.
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