Discrete optimization using a many-body expansion and elimination expressions.
xray.ManyBody(1) Manual Page
Name
xray.ManyBody - Discrete optimization using a many-body expansion and elimination expressions.
Synopsis
xray.ManyBody [-AEhOSTUVz] [--dee] [--nsf] [--oP] [--oT] [--rmo] [--tR] [-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>] [--iC=<inclusionCutoff>] [--increment=3] [--iR=<interestedResidue>] [--kPH=0.0] [-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…
Description
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).
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]
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
- --tR, --titration
-
Turn on titration state optimization
- -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
- --increment=3
-
Sliding window increment.
- --window=7
-
Size of the sliding window with respect to adjacent residues.
Many-Body Energy Expansion and Cut-off Options
- --clashThreshold=25.0
-
The threshold for pruning clashes.
- --kPH, --pHRestraint=0.0
-
Only allow titration state to change fromstandard state is self energy exceeds the restraint.
- --pairClashThreshold=25.0
-
The threshold for pruning pair clashes.
- --pr, --prune=1
-
Prune no clashes (0), only single clashes (1), or all clashes (2)
- --radius=2.0
-
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).
- --iC, --inclusionCutoff=<inclusionCutoff>
-
Distance which rotamers will be included when using only protons, titratable residues, or interested residue.
- --iR, --interestedResidue=<interestedResidue>
-
Optimize rotamers within some distance of a specific residue.
- --lR, --listResidues=<list>
-
Select a list of residues to optimize (eg. A11,A24,B40).
- --oP, --onlyProtons
-
Rotamer optimize only proton movement.
- --oT, --onlyTitration
-
Rotamer optimize only titratable residues.
- --sR, --start=<start>
-
Starting residue to optimize (default: all residues).
Arguments
- files…
-
PDB and Real Space input files.