X-ray Target Rotamer Optimization
Discrete optimization using a many-body expansion of an X-ray target function and elimination expressions.
Usage: ffxc xray.ManyBody [-AEhOSTUz] [--dee] [--out] [--rmo] [--sf] [--aRadBuffer=0.75] [--bB=0.0] [--bC=1] [--bL=20.0] [--ch=-1] [--eR=none] [--fi=-1] [--fR=-1,-1] [--FSigFCutoff=-1.0] [--increment=3] [--Ln=Richardson] [--lR=none] [--mC=-1] [--nB=3,3,3] [--nBins=10] [--nResidueBFactor=0] [--pr=1] [--radius=2.0] [--sigmaATol=0.05] [--sol=POLYNOMIAL] [--tC=3.0] [--thC=3.0] [--wA=1.0] [--window=7] [--xrayScaleTol=1.0e-4] [-a=0] [-B=1.0] [-G=0.6] [-L=2] [-m=coordinates] [-R=-1] [-s=-1] [-x=-1] [-X=<data> <data> <data>]... files...
Discrete optimization using a many-body expansion and elimination expressions.
files... PDB and Real Space input files.
--aRadBuffer=0.75 Set the distance beyond the atomic radius to evaluate scattering (A).
--bB, --boxBorderSize=0.0 Extent of overlap between optimization boxes in Angstroms.
--bC, --boxInclusionCriterion=1 Criterion to use for adding a residue to a box: (1) uses C alpha only (N1/9 for nucleic acids), (2) uses any atom, and (3) uses any rotamer
--bL, --approxBoxLength=20.0 Approximate side lengths of boxes to be constructed (over-rides numXYZBoxes).
--ch, --chain=-1 Single character chain ID of the residues to optimize.
--dee, --deadEnd Use dead-end elimination criteria instead of Goldstein criteria.
--eR, --energyRestart=none Load energy restart file from a previous run (requires that all parameters are the same).
--fi, --final=-1 Final residue to perform the optimization on (-1 exits). For box optimization, final box to optimize.
--fR, --forceResidues=-1,-1 Force residues in this range to be considered for sliding window radii, regardless of whether they lack rotamers.
--FSigFCutoff=-1.0 F / SigF cutoff (-1.0 is no cutoff).
--increment=3 Sliding window increment.
--Ln, --libraryNucleic=Richardson Nucleic acid library to select: [Richardson]
--lR, --listResidues=none Choose a list of individual residues to optimize (eg. A11,A24,B40).
--mC, --monteCarlo=-1 Follow elimination criteria with (n) Monte Carlo steps, or enumerate all remaining conformations, whichever is smaller.
--nB, --numBoxes=3,3,3 Specify number of boxes along X, Y, and Z (default: 3,3,3)
--nBins=10 The number of refection bins.
--nResidueBFactor=0 Number of residues per B-factor. 0 uses atomic B-factors (default).
--out, --output Save eliminated singles and eliminated pairs to a text file.
--pr, --prune=1 Prune no clashes (0), only single clashes (1), or all clashes (2)
--radius=2.0 The sliding window cutoff radius (Angstroms).
--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]
--tC, --twoBodyCutoff=3.0 Cutoff distance for two body interactions.
--thC, --threeBodyCutoff=3.0 Cutoff distance for three-body interactions.
--wA, --dataWeight=1.0 The weight of the real space data (wA).
--window=7 Size of the sliding window with respect to adjacent residues.
--xrayScaleTol=1.0e-4 X-ray scale optimization tolerance.
-a, --algorithm=0 Algorithm: default automatic settings (0), independent residues (1), all with rotamer elimination (2), all brute force (3), sliding window (4), or box optimization (5)
-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.
-E, --decompose Print energy decomposition for the input structure (no optimization!).
-G, --sampling=0.6 The number of grid spaces per Angstrom for the scattering FFT grid.
-h, --help Print this help message.
-L, --library=2 Ponder and Richards (1) or Richardson (2) rotamer library.
-m, --mode=coordinates Refinement mode: coordinates, bfactors and/or occupancies.
-O, --noOriginal Do not include starting coordinates as their own rotamer.
-R, --rFreeFlag=-1 R-Free Flag value (-1 attempts to auto-determine from the data).
-s, --start=-1 Starting residue to perform the optimization on (-1 exits). For box optimization, first box to optimize.
-S, --solventGridSearch Perform a grid search for optimal bulk solvent parameters.
-T, --threeBody Include 3-Body interactions in the elimination criteria.
-U, --addAnisoU Add Anisotropic B-Factors to refinement.
-x, --all=-1 Optimize all residues beginning from the passed value (overrides other options); for box optimization, optimizes all boxes beginning from the passed index.
-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).
-z, --revert Revert unfavorable changes.