Hi Michael, phenix.reciprocal_space_arrays outputs a number of arrays that are popular in various crystallographic calculations (I can add more if needed): http://phenix-online.org/documentation/reciprocal_space_arrays.htm For example: 1) 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) where: - 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 phenix.reciprocal_space_arrays. 2) To compute a map, like 2mFobs-DFmodel, you also need m (=FOM, figure or merit) and D (=ALPHA, in this notations). etc.. Hope this answers your questions. Pavel 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.