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xray.Minimize(1) Manual Page


xray.Minimize - Refine an X-ray/Neutron target.


xray.Minimize [-AhStUV] [--rmo] [--sf] [--aRadBuffer=0.75] [-B=1.0] [-e=1.0] [--FSigFCutoff=-1.0] [-G=0.6] [-I=Unlimited] [-m=coordinates] [--nbfgs=7] [--nBins=10] [--nResidueBFactor=0] [-R=-1] [--sigmaATol=0.05] [--sol=POLYNOMIAL] [--wA=1.0] [--xrayScaleTol=1.0e-4] [-E=-1.0 -1.0 -1.0]…​ [-X=<data> <data> <data>]…​ files…​


Refine an X-ray/Neutron target.


-E, --eps3=-1.0 -1.0 -1.0

RMS gradient convergence criteria for three stage refinement (default of -1.0 automatically determines eps for each stage).

-h, --help

Print command help and exit.

-t, --threeStage

Perform refinement in 3 stages: coordinates, b-factors, and then occupancies (overrides mode setting if true)

-V, --version

Print the Force Field X version and exit.

--wA, --dataWeight=1.0

The weight of the experimental data (wA).

Minimization Options

-e, --eps=1.0

Convergence criteria.

-I, --iterations=Unlimited

Number of minimization steps.


The number of correction vectors used by the L-BFGS optimization routine (0 for steepest-decent).

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.