[phenixbb] sigmaA-weigted 2FoFc maps by only mtz file

Pavel Afonine pafonine at lbl.gov
Fri May 27 16:21:19 PDT 2011

Hi Hailaing,

> By the way, if it is possible, prior to generating the 2mFo-DFc map
> coefficients, can you also include the solvent modeling

you can't do it sensibly without a atomic model. The total model 
structure factor used everywhere (in R-factor, maps, refinement, ... etc 
calculations) is:

Fmodel = scale * exp(-h*U_overall*ht) * (Fcalc + k_sol * exp(-B_sol*s^2) 
* Fmask)

where Fmask is computed from atoms.

Of course, assuming your input Fcalc are from atomic model, one can use 
Babinet based bulk-solvent model, but this is not implemented in PHENIX 
because of well known deficiencies of this model.

This is why most of tools that compute R-factors, maps, do refinement 
etc require PDB file with a model (and not just Fcalc) and a data file 
with Fobs.

> and anisotropic
> scaling based on the provide Fo/Fc data?

This can be done without atoms.

Let me know if you still want this. Also it would be encouraging for me 
to know why you want this - just in case I may be able to suggest an 
alternative way to do what you want.


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