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xray.ManyBody(1) Manual Page


xray.ManyBody - Discrete optimization using a many-body expansion and elimination expressions.


xray.ManyBody [-AEhOSTUVz] [--dee] [--rmo] [--sf] [-a=0] [--aRadBuffer=0.75] [-B=1.0] [--bB=0.0] [--bC=1] [--bL=20.0] [--ch=<A>] [--clashThreshold=25.0] [--eR=none] [--fB=<finalBox>] [--fR=<final>] [--FSigFCutoff=-1.0] [-G=0.6] [--iB=<initialBox>] [--increment=3] [-L=2] [--lR=<list>] [-m=coordinates] [--mC=-1] [--nB=3,3,3] [--nBins=10] [--nResidueBFactor=0] [--pairClashThreshold=25.0] [--pH=0] [--pr=1] [-R=-1] [--radius=2. _ 0_] [--sigmaATol=0.05] [--sol=POLYNOMIAL] [--sR=<start>] [--tC=3. _ 0_] [--thC=3.0] [--wA=1.0] [--window=7] [--xrayScaleTol=1.0e-4] [-X=<data> <data> <data>]…​ files…​


Discrete optimization using a many-body expansion and elimination expressions.


-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).

X-ray Refinement Options

-m, --mode=coordinates

Refinement mode: coordinates, bfactors and/or occupancies.

--rmo, --refineMolOcc

Refine on molecules.

X-ray Reflection Data Options


F / SigF cutoff (-1.0 is no cutoff).


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.


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).


Set the distance beyond the atomic radius to evaluate scattering (A).

-G, --sampling=0.6

The number of grid spaces per Angstrom for the scattering FFT grid.

--sf, --splineFit

Use a resolution dependent spline scale.


Sigma A optimization tolerance.


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]

Many-Body Optimization Options

-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)

--dee, --deadEnd

Use dead-end elimination criteria instead of Goldstein criteria.

-E, --decompose

Print energy decomposition for the input structure (no optimization!).

--eR, --energyRestart=none

Load energy restart file from a previous run (requires that all parameters are the same).

-L, --library=2

Ponder and Richards (1) or Richardson (2) rotamer library.

--mC, --monteCarlo=-1

Follow elimination criteria with (n) Monte Carlo steps, or enumerate all remaining conformations, whichever is smaller.

-O, --noOriginal

Do not include starting coordinates as their own rotamer.

--pH, --titrationPH=0

Optimize the titration state of ASP, GLU, HIS and LYS residues at the given pH (pH = 0 turns off titration

-z, --revert

Revert unfavorable changes.

Many-Body Box Optimization Options

--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).

--fB, --finalBox=<finalBox>

Final box to optimize.

--iB, --initialBox=<initialBox>

Initial box to optimize.

--nB, --numBoxes=3,3,3

Specify number of boxes along X, Y, and Z (default: 3,3,3)

Many-Body Window Optimization Options


Sliding window increment.


Size of the sliding window with respect to adjacent residues.

Many-Body Energy Expansion and Cut-off Options


The threshold for pruning clashes.


The threshold for pruning pair clashes.

--pr, --prune=1

Prune no clashes (0), only single clashes (1), or all clashes (2)


The sliding box and window cutoff radius (Angstroms).

-T, --threeBody

Include 3-Body interactions in the elimination criteria.

--tC, --twoBodyCutoff=3.0

Cutoff distance for two body interactions.

--thC, --threeBodyCutoff=3.0

Cutoff distance for three-body interactions.

Many-Body Residue Selection Options

--ch, --chain=<A>

Include only specified chain ID (default: all chains).

--fR, --final=<final>

Final residue to optimize (default: all residues).

--lR, --listResidues=<list>

Select a list of residues to optimize (eg. A11,A24,B40).

--sR, --start=<start>

Starting residue to optimize (default: all residues).



PDB and Real Space input files.