Refine an X-ray/Neutron target.
xray.Minimize(1) Manual Page
Name
xray.Minimize - Refine an X-ray/Neutron target.
Synopsis
xray.Minimize [-AhStUV] [--nsf] [--rmo] [--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…
Description
Options
- -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.
- --nbfgs=7
-
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 molecular occupancy.
X-ray Reflection Data Options
- --FSigFCutoff=-1.0
-
F / SigF cutoff (-1.0 is no cutoff).
- --nBins=10
-
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.
- --nResidueBFactor=0
-
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).
- --aRadBuffer=0.75
-
Scattering is evaluated within the atomic radius plus this buffer (Å).
- -G, --sampling=0.6
-
The number of grid spaces per Angstrom for the scattering FFT grid.
- --nsf, --noSplineFit
-
Use a resolution dependent spline scale factor.
- --sigmaATol=0.05
-
Sigma A optimization tolerance.
- --xrayScaleTol=1.0e-4
-
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]
Arguments
- files…
-
PDB and Diffraction input files.