Thanks a lot Pavel! Hailiang

Hi Hailaing,

there is no functionality exposed to the end-user that does it, however, this is what many PHENIX tools do internally.

I can write a few lines Python script that will do just this. I will post it to phenixbb in a day or two (I am traveling to ACA today).

Pavel.

...

Hi,

If I only provide a mtz file with Fo, Fc and phase data, and do NOT have the pdb file, can any phenix utility calculate the sigmaA-weigted 2FoFc maps?

Thanks!

Hailaing

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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.

Hi Hailiang,

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

can't we just use a PDB file or it is not available for whatever reason in your context? Like I said before, anisotropic scaling can be done without model, so you don't have to do it. If you still want to, then everything is described in this paper: P.V. Afonine, R.W. Grosse-Kunstleve & P.D. Adams. Acta Cryst. (2005). D61, 850-855. "A robust bulk-solvent correction and anisotropic scaling procedure" Good luck! Pavel.