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xray.ModelvsData(1) Manual Page


xray.ModelvsData - Compare the PDB model to the diffraction data.


xray.ModelvsData [-AhpStUVw] [--rmo] [--sf] [--aRadBuffer=0.75] [-B=1.0] [--FSigFCutoff=-1.0] [-G=0.6] [-m=coordinates] [--nBins=10] [--nResidueBFactor=0] [-R=-1] [--sigmaATol=0.05] [--sol=POLYNOMIAL] [--wA=1.0] [--xrayScaleTol=1.0e-4] [-X=<data> <data> <data>]…​ files…​


Compare the PDB model to the diffraction data.


-h, --help

Print command help and exit.

-p, --maps

Output sigmaA weighted 2Fo-Fc and Fo-Fc electron density maps.

-t, --timings

Perform FFT timings.

-V, --version

Print the Force Field X version and exit.

-w, --mtz

write out MTZ containing structure factor coefficients.

--wA, --dataWeight=1.0

The weight of the experimental data (wA).

X-ray Refinement Options

-m, --mode=coordinates

Refinement mode: coordinates, bfactors and/or occupancies.

--rmo, --refineMolOcc

Refine on molecules.

X-ray Reflection Data Options


F / SigF cutoff (-1.0 is no cutoff).


The number of refection bins.

-R, --rFreeFlag=-1

R-Free Flag value (-1 attempts to auto-determine from the data).

-X, --data=<data> <data> <data>

Specify input data filename, its weight (wA) and if its from a neutron experiment (e.g. -X filename 1.0 false).

X-ray B-Factor Options

-B, --bSimWeight=1.0

B-Factor similarity weight.


Number of residues per B-factor. 0 uses atomic B-factors (default).

-U, --addAnisoU

Add Anisotropic B-Factors to refinement.

X-ray Target Options

-A, --allGaussians

Use all defined Gaussians for atomic scattering density (the default is to use the top 3).


Set the distance beyond the atomic radius to evaluate scattering (A).

-G, --sampling=0.6

The number of grid spaces per Angstrom for the scattering FFT grid.

--sf, --splineFit

Use a resolution dependent spline scale.


Sigma A optimization tolerance.


X-ray scale optimization tolerance.

X-ray Bulk Solvent Options

-S, --solventGridSearch

Perform a grid search for optimal bulk solvent parameters.

--sol, --solvent=POLYNOMIAL

Bulk solvent scattering model [Polynomial/Gaussian/Binary/None]



PDB and Diffraction input files.