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

zhangh1 at umbc.edu zhangh1 at umbc.edu
Fri May 27 16:31:13 PDT 2011

Hi Pavel:

Sure! Maybe I can prepare Fc with solvent modeling and anisotropic scaling
first. However, I am not sure how to generate the U_overall matrix in your
formula. The U_overall given by the pdb header is acturally in Cartesian
coordinate, and a "diagonalization matrix" is needed to do a
transformation before applying to h/ht. Not sure how to generate the
"diagonalization matrix" (still doing research:-(, any help will be


> 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.
> Pavel.
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