[phenixbb] phenix.reciprocal_space_arrays question

Pavel Afonine pafonine at lbl.gov
Thu Mar 1 13:40:10 PST 2012

Hi Michael,

phenix.reciprocal_space_arrays outputs a number of arrays that are 
popular in various crystallographic calculations (I can add more if needed):


For example:

Fmodel - is the total model structure factor, that is used almost 
everywhere: R-factor, maps, refinement targets calculations, etc. Fmodel 
includes all scales and bulk-solvent, and it is defined as:

   Fmodel = scale * exp(AnisoScale) * (Fcalc + k_sol * exp(-b_sol*s^2/4) 
* Fmask)


   - Fmodel - total model structure factor (complex value)
   - AnisoScale = -ht*A(-1)*b_cart*A(-1)th/4
   - h - column vector with Miller indices
   - A - orthogonalization matrix
   - b_cart - anisotropic scale matrix
   - t and (-1) denotes transposition and inversion operations
   - scale - overall scale factor
   - Fcalc - structure factors calculated from atomic model
   - k_sol and b_sol - Flat Bulk solvent model parameters
   - Fmask - structure factors calculated from bulk solvent mask

You will notice that Fmask, Fbulk and Fcalc are also output by 

2) To compute a map, like 2mFobs-DFmodel, you also need m (=FOM, figure 
or merit) and D (=ALPHA, in this notations).


Hope this answers your questions.


On 3/1/12 1:30 PM, Michael Thompson wrote:
> Hi All,
> I have a very simple question about phenix.reciprocal_space_arrays. I apologize if this is obvious, but I could not find any info in the documentation or the bb archives. I just want to make sure that I am actually doing what I think I am doing. If I provide phenix.reciprocal_space_arrays with an .mtz file containing Fobs and a .pdb file for which I would like to calculate Fmodel and PHImodel, will the resulting Fmodel (and Fcalc, Fmask, Fbulk, etc.) be scaled to the Fobs from the input .mtz?
> Thanks for the help!
> Mike T.

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