[phenixbb] on b factor refine for phenix.real_space_refine

Pavel Afonine pafonine at lbl.gov
Thu Aug 13 23:14:53 PDT 2015


B-factor refinement does refine B-factors (change B-factors) and 
coordinate refinement does refine coordinates (change coordinates). In 
turn, B-factor refinement does not change coordinates, and coordinate 
refinement does not change B-factors. And if you do both, then 
coordinates and B-factors will be changed, obviously.

Pavel

On 8/12/15 19:18, Smith Lee wrote:
> 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)
>
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>
> 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.
>
> Smith

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