X-ray Timer
Time calculation of the X-ray target.
Usage: ffxc xray.Timer [-AghSUv] [--rmo] [--sf] [--aRadBuffer=0.75] [--FSigFCutoff=-1.0] [--nBins=10] [--nResidueBFactor=0] [--nt=0] [--sigmaATol=0.05] [--sol=POLYNOMIAL] [--wA=1.0] [--xrayScaleTol=1.0e-4] [-B=1.0] [-G=0.6] [-m=coordinates] [-n=5] [-R=-1] [-X=<data> <data> <data>]... files...
Time calculation of the X-ray target.
files... PDB and Diffraction input files.
--aRadBuffer=0.75 Set the distance beyond the atomic radius to evaluate scattering (A).
--FSigFCutoff=-1.0 F / SigF cutoff (-1.0 is no cutoff).
--nBins=10 The number of refection bins.
--nResidueBFactor=0 Number of residues per B-factor. 0 uses atomic B-factors (default).
--nt, --threads=0 Number of SMP threads (0 specifies use of all CPU cores).
--rmo, --refineMolOcc Refine on molecules.
--sf, --splineFit Use a resolution dependent spline scale.
--sigmaATol=0.05 Sigma A optimization tolerance.
--sol, --solvent=POLYNOMIAL Bulk solvent scattering model [Polynomial/Gaussian/Binary/None]
--wA, --dataWeight=1.0 The weight of the real space data (wA).
--xrayScaleTol=1.0e-4 X-ray scale optimization tolerance.
-A, --allGaussians Use all defined Gaussiansfor atomic scattering density (the default is to use the top 3).
-B, --bSimWeight=1.0 B-Factor similarity weight.
-g, --noGradient Ignore computation of the atomic coordinates noGradient.
-G, --sampling=0.6 The number of grid spaces per Angstrom for the scattering FFT grid.
-h, --help Print this help message.
-m, --mode=coordinates Refinement mode: coordinates, bfactors and/or occupancies.
-n, --iterations=5 Number of iterations.
-R, --rFreeFlag=-1 R-Free Flag value (-1 attempts to auto-determine from the data).
-S, --solventGridSearch Perform a grid search for optimal bulk solvent parameters.
-U, --addAnisoU Add Anisotropic B-Factors to refinement.
-v, --verbose Print the energy for each iteration.
-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).