X-ray Target Simulated Annealing
Simulated annealing on a X-ray refinement target.
Usage: ffxc xray.Anneal [-AhoSU] [--rmo] [--sf] [--aRadBuffer=0.75] [--FSigFCutoff=-1.0] [--nBins=10] [--nResidueBFactor=0] [--sigmaATol=0.05] [--sol=POLYNOMIAL] [--tl=10.0] [--tu=1000.0] [--wA=1.0] [--xrayScaleTol=1.0e-4] [-b=Bussi] [-B=1.0] [-d=1.0] [-G=0.6] [-i=Verlet] [-k=1.0] [-m=coordinates] [-n=1000000] [-r=0.25] [-R=-1] [-t=298.15] [-w=10.0] [-W=10] [-X=<data> <data> <data>]... files...
Simulated annealing on an 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).
--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]
--tl, --temperatureLow=10.0 Low temperature limit (Kelvin).
--tu, --temperatureUpper=1000.0 High temperature limit (Kelvin).
--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, --thermostat=Bussi Thermostat: [Adiabatic / Berendsen / Bussi].
-B, --bSimWeight=1.0 B-Factor similarity weight.
-d, --dt=1.0 Time discretization step in femtoseconds.
-G, --sampling=0.6 The number of grid spaces per Angstrom for the scattering FFT grid.
-h, --help Print this help message.
-i, --integrator=Verlet Integrator: [Beeman / Respa / Stochastic / Verlet].
-k, --checkpoint=1.0 Interval to write out restart files (.dyn, .his, etc).
-m, --mode=coordinates Refinement mode: coordinates, bfactors and/or occupancies.
-n, --numberOfSteps=1000000 Number of molecular dynamics steps.
-o, --optimize Optimize and save low-energy snapshots.
-r, --report=0.25 Interval to report thermodynamics (psec).
-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.
-t, --temperature=298.15 Temperature (Kelvin).
-U, --addAnisoU Add Anisotropic B-Factors to refinement.
-w, --write=10.0 Interval to write out coordinates (psec).
-W, --windows=10 Number of annealing windows.
-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).