Force Field Xxray.Timer(1)
Synopsis
xray.Timer [-AghSUvV] [--nsf] [--rmo] [--aa=<selection>] [--aRadBuffer=0.75] [-B=1.0] [--FSigFCutoff=-1.0] [-G=0.6] [--ia=<selection>] [-m=coordinates] [-n=5] [--nBins=10] [--nResidueBFactor=0] [--nt=0] [-R=-1] [--sigmaATol=0.05] [--sol=POLYNOMIAL] [--wA=1.0] [--xrayScaleTol=1.0e-4] [-X=<data> <data> <data>]… files…
Options
- -h, --help
- Print command help and exit.
- -V, --version
- Print the Force Field X version and exit.
- --wA, --dataWeight=1.0
- The weight of the experimental data (wA).
Timing Options
- -g, --noGradient
- Ignore computation of the atomic coordinates gradient.
- -n, --iterations=5
- Number of iterations.
- --nt, --threads=0
- Number of SMP threads (0 specifies use of all CPU cores).
- -v, --verbose
- Print the energy for each iteration.
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]