Water refinement module
Module contents
Explicit solvent MD refinement with CNS.
The [mdref] module (also known as itw in HADDOCK2.X series), is a small
molecular dynamics simulation, in cartesian space, using explicit solvent.
A layer of solvent (8A for water, 12.5A for DMSO) is generated around surface residues.
The mdref protocol is composed of 4 sequential steps: - Short energy minimization - 3 stages of molecular dynamics to reach 300K (at 100, 200 and 300K) - Molecular dynamics at 300K. - 3 stages of molecular dynamics, to reach 100K (at 300, 200 and 100K)
Using this protocol, with default parameters, no spectacular changes are expected, however, the scoring of the various structures might be improved.
Number of MD steps can be modified using the waterheatsteps, watersteps
and watercoolsteps.
- class haddock.modules.refinement.mdref.HaddockModule(order: int, path: Path, initial_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/haddock/modules/refinement/mdref/defaults.yaml'))[source]
Bases:
BaseCNSModuleHADDOCK3 module for water refinement.
Default Parameters
Easy
ambig_fname
default: ‘’
type: file
title: Ambiguous distance restraints filename
short description: Filename of the ambiguous distance restraints file
long description: Filename of the ambiguous distance restraints file. By default 50% of those restraints will be randomly discared. This can be changed/turned off and is controlled by the randremoval and npart parameters. Note that this file can contain both ambiguous and unambiguous restraints.
group: distance restraints
explevel: easy
dihe_fname
default: ‘’
type: file
title: Dihedral angle restraints filename
short description: Filename of the Dihedral angle restraints file
long description: Filename of the Dihedral angle restraints file.
group: dihedral restraints
explevel: easy
dihedrals_on
default: False
type: boolean
title: Use dihedral angle restraints
short description: Turns on dihedral angle restraints.
long description: Turns on dihedral angle restraints. Those should be defined in the dihe_fname file.
group: dihedral restraints
explevel: easy
dihedrals_scale
default: 200
type: integer
title: Force constant for dihedral angle restraints
min: 0
max: 9999
short description: Force constant applied to the dihedral angle restraints read from dihe_fname.
long description: Force constant applied to the dihedral angle restraints read from dihe_fname.
group: dihedral restraints
explevel: easy
dnarest_on
default: False
type: boolean
title: Restrain the DNA conformation
short description: Automatically creates restraints to maintain the conformation of DNA/RNA
long description: This option allows to restraint the conformation of nucleic acids based on the values from the input structures. The following restraints will be automatically defined: - single base planarity - sugar pucker - phosphate backbone diherdral angle restraints - Watson-Crick base pairing
group: other restraints
explevel: easy
elecflag
default: True
type: boolean
title: Include electrostatics energy
short description: Include electrostatics energy during the calculations.
long description: Include electrostatics energy during the calculations. If set to false electrostatics will not be considered.
group: force field
explevel: easy
error_dih
default: 10
type: integer
title: Force constant for backbone dihedral angle restraints
min: 0
max: 180
short description: Force constant for backbone dihedral angle restraints (ssdihed option)
long description: Force constant for backbone dihedral angle restraints (ssdihed option)
group: dihedral restraints
explevel: easy
hbond_fname
default: ‘’
type: file
title: H-bond restraints filename
short description: Filename of the hydrogen bond distance restraints file
long description: Filename of the hydrogen bond distance restraints file. Note that this file can contain any type of distance restraints.
group: distance restraints
explevel: easy
ligand_param_fname
default: ‘’
type: file
title: Custom ligand parameter file
short description: Ligand parameter file in CNS format
long description: Ligand parameter file in CNS format containing all force field parameters (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK
group: force field
explevel: easy
ligand_top_fname
default: ‘’
type: file
title: Custom ligand topology file
short description: Ligand topology file in CNS format
long description: Ligand topology file in CNS format containing the ligand topologies (atoms, masses, charges, bond definitions…) for any ligand not supported by default by HADDOCK
group: force field
explevel: easy
mol_shape_1
default: False
type: boolean
title: Is the molecule a shape?
short description: Defines a molecule as a shape.
long description: Defines a molecule as a shape, which is a collection of beads.
group: molecule
explevel: easy
solvent
default: ‘water’
type: string
title: Solvent
choices: [‘water’, ‘dmso’]
short description: Solvent to use during the short MD refinement
long description: Solvent to use during the short MD refinement. Water and DMSO are supported. A solvent shelll is generated by shifting pre-equilibrated boxes around the complex. For water an 8A water shell is generated and for DMSO a 12.5A shell. For DMSO,
group:
explevel: easy
ssdihed
default: ‘none’
type: string
title: Define automatically backbone dihedral angle restraints
choices: [‘none’, ‘all’, ‘alpha’, ‘alphabeta’]
short description: If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.
long description: This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.
group: dihedral restraints
explevel: easy
unambig_fname
default: ‘’
type: file
title: Unambiguous restraints filename
short description: Filename of the unambiguous distance restraints file
long description: Filename of the unambiguous distance restraints file. All restraints in that file will be used. Note that this file can contain both ambiguous and unambiguous restraints.
group: distance restraints
explevel: easy
Expert
ambig_scale
default: 50
type: integer
title: Force constant for ambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in ambig_fname.
long description: Force constant applied to the distance restraints defined in ambig_fname.
group: distance restraints
explevel: expert
c2sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first C2 symmetry segment
long description: Residue number of last residue in the first C2 symmetry segment
group: symmetry
explevel: expert
c2sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second C2 symmetry segment
long description: Residue number of last residue in the second C2 symmetry segment
group: symmetry
explevel: expert
c2sym_seg1_1
default: ‘’
type: string
title: Segment ID of first C2 segment
short description: Segment ID of first C2 segment
long description: Segment ID of first C2 segment
group: symmetry
explevel: expert
c2sym_seg2_1
default: ‘’
type: string
title: Segment ID of second C2 segment
short description: Segment ID of second C2 segment
long description: Segment ID of second C2 segment
group: symmetry
explevel: expert
c2sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first C2 symmetry segment
long description: Residue number of first residue in the first C2 symmetry segment
group: symmetry
explevel: expert
c2sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second C2 symmetry segment
long description: Residue number of first residue in the second C2 symmetry segment
group: symmetry
explevel: expert
c3sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first C3 symmetry segment
long description: Residue number of last residue in the first C3 symmetry segment
group: symmetry
explevel: expert
c3sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second C3 symmetry segment
long description: Residue number of last residue in the second C3 symmetry segment
group: symmetry
explevel: expert
c3sym_end3_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the third C3 symmetry segment
long description: Residue number of last residue in the third C3 symmetry segment
group: symmetry
explevel: expert
c3sym_seg1_1
default: ‘’
type: string
title: Segment ID of first C3 segment
short description: Segment ID of first C3 segment
long description: Segment ID of first C3 segment
group: symmetry
explevel: expert
c3sym_seg2_1
default: ‘’
type: string
title: Segment ID of second C3 segment
short description: Segment ID of second C3 segment
long description: Segment ID of second C3 segment
group: symmetry
explevel: expert
c3sym_seg3_1
default: ‘’
type: string
title: Segment ID of third C3 segment
short description: Segment ID of third C3 segment
long description: Segment ID of third C3 segment
group: symmetry
explevel: expert
c3sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first C3 symmetry segment
long description: Residue number of first residue in the first C3 symmetry segment
group: symmetry
explevel: expert
c3sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second C3 symmetry segment
long description: Residue number of first residue in the second C3 symmetry segment
group: symmetry
explevel: expert
c3sym_sta3_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the third C3 symmetry segment
long description: Residue number of first residue in the third C3 symmetry segment
group: symmetry
explevel: expert
c4sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first C4 symmetry segment
long description: Residue number of last residue in the first C4 symmetry segment
group: symmetry
explevel: expert
c4sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second C4 symmetry segment
long description: Residue number of last residue in the second C4 symmetry segment
group: symmetry
explevel: expert
c4sym_end3_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the third C4 symmetry segment
long description: Residue number of last residue in the third C4 symmetry segment
group: symmetry
explevel: expert
c4sym_end4_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the fourth C4 symmetry segment
long description: Residue number of last residue in the fourth C4 symmetry segment
group: symmetry
explevel: expert
c4sym_seg1_1
default: ‘’
type: string
title: Segment ID of first C4 segment
short description: Segment ID of first C4 segment
long description: Segment ID of first C4 segment
group: symmetry
explevel: expert
c4sym_seg2_1
default: ‘’
type: string
title: Segment ID of second C4 segment
short description: Segment ID of second C4 segment
long description: Segment ID of second C4 segment
group: symmetry
explevel: expert
c4sym_seg3_1
default: ‘’
type: string
title: Segment ID of third C4 segment
short description: Segment ID of third C4 segment
long description: Segment ID of third C4 segment
group: symmetry
explevel: expert
c4sym_seg4_1
default: ‘’
type: string
title: Segment ID of fourth C4 segment
short description: Segment ID of fourth C4 segment
long description: Segment ID of fourth C4 segment
group: symmetry
explevel: expert
c4sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first C4 symmetry segment
long description: Residue number of first residue in the first C4 symmetry segment
group: symmetry
explevel: expert
c4sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second C4 symmetry segment
long description: Residue number of first residue in the second C4 symmetry segment
group: symmetry
explevel: expert
c4sym_sta3_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the third C4 symmetry segment
long description: Residue number of first residue in the third C4 symmetry segment
group: symmetry
explevel: expert
c4sym_sta4_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the fourth C4 symmetry segment
long description: Residue number of first residue in the fourth C4 symmetry segment
group: symmetry
explevel: expert
c5sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first C5 symmetry segment
long description: Residue number of last residue in the first C5 symmetry segment
group: symmetry
explevel: expert
c5sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second C5 symmetry segment
long description: Residue number of last residue in the second C5 symmetry segment
group: symmetry
explevel: expert
c5sym_end3_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the third C5 symmetry segment
long description: Residue number of last residue in the third C5 symmetry segment
group: symmetry
explevel: expert
c5sym_end4_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the fourth C5 symmetry segment
long description: Residue number of last residue in the fourth C5 symmetry segment
group: symmetry
explevel: expert
c5sym_end5_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the fifth C5 symmetry segment
long description: Residue number of last residue in the fifth C5 symmetry segment
group: symmetry
explevel: expert
c5sym_seg1_1
default: ‘’
type: string
title: Segment ID of first C5 segment
short description: Segment ID of first C5 segment
long description: Segment ID of first C5 segment
group: symmetry
explevel: expert
c5sym_seg2_1
default: ‘’
type: string
title: Segment ID of second C5 segment
short description: Segment ID of second C5 segment
long description: Segment ID of second C5 segment
group: symmetry
explevel: expert
c5sym_seg3_1
default: ‘’
type: string
title: Segment ID of third C5 segment
short description: Segment ID of third C5 segment
long description: Segment ID of third C5 segment
group: symmetry
explevel: expert
c5sym_seg4_1
default: ‘’
type: string
title: Segment ID of fourth C5 segment
short description: Segment ID of fourth C5 segment
long description: Segment ID of fourth C5 segment
group: symmetry
explevel: expert
c5sym_seg5_1
default: ‘’
type: string
title: Segment ID of fifth C5 segment
short description: Segment ID of fifth C5 segment
long description: Segment ID of fifth C5 segment
group: symmetry
explevel: expert
c5sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first C5 symmetry segment
long description: Residue number of first residue in the first C5 symmetry segment
group: symmetry
explevel: expert
c5sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second C5 symmetry segment
long description: Residue number of first residue in the second C5 symmetry segment
group: symmetry
explevel: expert
c5sym_sta3_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the third C5 symmetry segment
long description: Residue number of first residue in the third C5 symmetry segment
group: symmetry
explevel: expert
c5sym_sta4_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the fourth C5 symmetry segment
long description: Residue number of first residue in the fourth C5 symmetry segment
group: symmetry
explevel: expert
c5sym_sta5_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the fifth C5 symmetry segment
long description: Residue number of first residue in the fifth C5 symmetry segment
group: symmetry
explevel: expert
c6sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first C6 symmetry segment
long description: Residue number of last residue in the first C6 symmetry segment
group: symmetry
explevel: expert
c6sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second C6 symmetry segment
long description: Residue number of last residue in the second C6 symmetry segment
group: symmetry
explevel: expert
c6sym_end3_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the third C6 symmetry segment
long description: Residue number of last residue in the third C6 symmetry segment
group: symmetry
explevel: expert
c6sym_end4_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the fourth C6 symmetry segment
long description: Residue number of last residue in the fourth C6 symmetry segment
group: symmetry
explevel: expert
c6sym_end5_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the fifth C6 symmetry segment
long description: Residue number of last residue in the fifth C6 symmetry segment
group: symmetry
explevel: expert
c6sym_end6_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the sixth C6 symmetry segment
long description: Residue number of last residue in the sixth C6 symmetry segment
group: symmetry
explevel: expert
c6sym_seg1_1
default: ‘’
type: string
title: Segment ID of first C6 segment
short description: Segment ID of first C6 segment
long description: Segment ID of first C6 segment
group: symmetry
explevel: expert
c6sym_seg2_1
default: ‘’
type: string
title: Segment ID of second C6 segment
short description: Segment ID of second C6 segment
long description: Segment ID of second C6 segment
group: symmetry
explevel: expert
c6sym_seg3_1
default: ‘’
type: string
title: Segment ID of third C6 segment
short description: Segment ID of third C6 segment
long description: Segment ID of third C6 segment
group: symmetry
explevel: expert
c6sym_seg4_1
default: ‘’
type: string
title: Segment ID of fourth C6 segment
short description: Segment ID of fourth C6 segment
long description: Segment ID of fourth C6 segment
group: symmetry
explevel: expert
c6sym_seg5_1
default: ‘’
type: string
title: Segment ID of fifth C6 segment
short description: Segment ID of fifth C6 segment
long description: Segment ID of fifth C6 segment
group: symmetry
explevel: expert
c6sym_seg6_1
default: ‘’
type: string
title: Segment ID of sixth C6 segment
short description: Segment ID of sixth C6 segment
long description: Segment ID of sixth C6 segment
group: symmetry
explevel: expert
c6sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first C6 symmetry segment
long description: Residue number of first residue in the first C6 symmetry segment
group: symmetry
explevel: expert
c6sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second C6 symmetry segment
long description: Residue number of first residue in the second C6 symmetry segment
group: symmetry
explevel: expert
c6sym_sta3_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the third C6 symmetry segment
long description: Residue number of first residue in the third C6 symmetry segment
group: symmetry
explevel: expert
c6sym_sta4_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the fourth C6 symmetry segment
long description: Residue number of first residue in the fourth C6 symmetry segment
group: symmetry
explevel: expert
c6sym_sta5_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the fifth C6 symmetry segment
long description: Residue number of first residue in the fifth C6 symmetry segment
group: symmetry
explevel: expert
c6sym_sta6_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the sixth C6 symmetry segment
long description: Residue number of first residue in the sixth C6 symmetry segment
group: symmetry
explevel: expert
cmrest
default: False
type: boolean
title: Center of mass restraints
short description: Automatically defines distance restraints between the geometric center of the various molecules.
long description: When turned on, this option will automatically define center of mass restraints between the various molecules. This allows HADDOCK to operate in ab-initio mode in the absence of any other restraints. But those restraints can also be combined with other restraints to ensure more compact solutions. The distance restraints are defined between the geometrical centers of the various molecules (calculated on CA atoms for proteins (BB in case of Martini coarse-grained molecules) and N1 atoms for nucleic acids. For small ligands, all atoms will be used to define the geometric center. The upper limit distance is automatically calculated based on the dimension of the molecules (see cmtight description).
group: distance restraints
explevel: expert
cmtight
default: True
type: boolean
title: Center of mass restraint tightness
short description: Defines the upper distance limit based on the sum of the average dimension of the two molecule, if cmtight=false all three dimensions are used, if set to true the shortest two only are used, resulting in tighter distance restraints.
long description: This parameter controls how the upper limit distance is defined for the center of mass restraints between molecules. Each molecule is oriented along its principle components and the x,y and z dimensions are calculated. If cmtight=true, the molecule distance (size) is set to the average of its smallest two half dimensions. If cmtight=false, the molecule distance (size) is set to the average of its three half dimensions.. In case of DNA or small ligands the molecule distance (size) is set to 0. The effective upper distance limit for the center or mass distance restraint is the sum of the two molecule distances.
group: distance restraints
explevel: expert
contactairs
default: False
type: boolean
title: Contact restraints
short description: Contact restraints between molecules
long description: Contact restraints between molecules. These are defined as ambiguous distance restraint between each residue of a molecule and all residues of the other molecules with 5A from that residue. This can be used to restraint the contacts between the interfaces. Note that this can generate a large number of ambiguous restraints and slow down the computations
group: distance restraints
explevel: expert
dielec
default: ‘cdie’
type: string
title: Constant (cdie) or distance-dependent dielectric (rdie) constant.
choices: [‘cdie’, ‘rdie’]
short description: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential.
long description: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential. A distance dependent dielectric constant will effectively scale down the electrostatic energy by having a 1/r**2 dependency instead of 1/r
group: force field
explevel: expert
dihedflag
default: True
type: boolean
title: Use torsion angle dihedral energy term
short description: Turns on the torsion angle dihedral energy terms of the force field.
long description: Turns on the torsion angle dihedral energy terms of the force field.
group: force field
explevel: expert
epsilon
default: 1.0
type: float
title: Dielectric constant
min: 1
max: 78
short description: Dielectric constant for the electrostatic Coulomb energy term.
long description: Dielectric constant for the electrostatic Coulomb energy term.
group: force field
explevel: expert
fle_end_1
default: nan
type: integer
title: End residue number
min: -9999
max: 9999
short description: Residue number defining the end of the fully flexible segment.
long description: Residue number defining the end of this (1st) fully flexible segment.
group: flexibility
explevel: expert
fle_seg_1
default: ‘none’
type: string
title: Segment ID (segid)
short description: Segment ID of the molecule for which this flexible segment is defined.
long description: Segment ID of the molecule for which this (1st) flexible segment is defined.
group: flexibility
explevel: expert
fle_sta_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the fully flexible segment.
long description: Residue number defining the start of this (1st) fully flexible segment.
group: flexibility
explevel: expert
hbond_scale
default: 50
type: integer
title: Force constant for hbonds distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in hbond_fname.
long description: Force constant applied to the distance restraints defined in hbond_fname.
group: distance restraints
explevel: expert
kcm
default: 1.0
type: float
title: Center of mass restraints force constant
min: 0
max: 1000
short description: Force constant applied to the center of mass restraints
long description: Force constant applied to the center of mass restraints
group: distance restraints
explevel: expert
kcont
default: 1.0
type: float
title: Contact restraints force constant
min: 0
max: 1000
short description: Force constant applied to the contact restraints.
long description: Force constant applied to the contact restraints.
group: distance restraints
explevel: expert
kncs
default: 1.0
type: float
title: Force constant for non-crystallographic restraints
min: 0
max: 1000
short description: Force constant for non-crystallographic restraints
long description: Force constant for non-crystallographic restraints
group: symmetry
explevel: expert
ksym
default: 10.0
type: float
title: Force constant for symmetry restraints
min: 0
max: 1000
short description: Force constant for symmetry restraints
long description: Force constant for symmetry restraints
group: symmetry
explevel: expert
max_nmodels
default: 50000
type: integer
title: Maximum number of models to refine
min: 1
max: 100000
short description: This parameter controls the maximum number of models to refine.
long description: This parameter controls the maximum number of models to refine.
group: sampling
explevel: expert
mol_fix_origin_1
default: False
type: boolean
title: Fix molecule
short description: Fixes the molecule in its original position.
long description: Fixes the molecule in its original position.
group: molecule
explevel: expert
ncs_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first NCS segment
long description: Residue number of last residue in the first NCS segment
group: symmetry
explevel: expert
ncs_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second NCS segment
long description: Residue number of last residue in the second NCS segment
group: symmetry
explevel: expert
ncs_on
default: False
type: boolean
title: Non-crystallographic symmetry restraints
short description: Non-crystallographic symmetry restraints to ensure two molecules will have the same conformation.
long description: Non-crystallographic symmetry restraints to ensure two molecules will have the same conformation. This does not apply any symmetry between the two molecules but rather defines restraints such as the RMSD between those is 0.
group: symmetry
explevel: expert
ncs_seg1_1
default: ‘’
type: string
title: Segment ID of first NCS segment
short description: Segment ID of first NCS segment
long description: Segment ID of first NCS segment
group: symmetry
explevel: expert
ncs_seg2_1
default: ‘’
type: string
title: Segment ID of second NCS segment
short description: Segment ID of second NCS segment
long description: Segment ID of second NCS segment
group: symmetry
explevel: expert
ncs_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first NCS segment
long description: Residue number of first residue in the first NCS segment
group: symmetry
explevel: expert
ncs_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second NCS segment
long description: Residue number of first residue in the second NCS segment
group: symmetry
explevel: expert
nemsteps
default: 200
type: integer
title: Number of EM steps
min: 1
max: 10000
short description: Number of energy minimisation steps to perform.
long description: Number of energy minimisation steps to perform in the various EM stages of this refinement protocol. Note that the effective number might be smaller if the minimisation converges earlier.
group: sampling
explevel: expert
npart
default: 2
type: integer
title: Number partitions for ambiguous restraints
min: 1
max: 20
short description: Number of sets into which to randomly partition the ambiguous restraints.
long description: Number of sets into which to randomly partition the ambiguous restraints. The fraction of restraints randomly removed depends on the npart parameter which defines in how many sets the restraints should be randomly split. The first set will be removed. The fraction of randomly removed ambiguous restraints is thus 1/npart.
group: distance restraints
explevel: expert
nseg1
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg10
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg11
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg12
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg13
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg14
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg15
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg16
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg17
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg18
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg19
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg2
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg20
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg3
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg4
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg5
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg6
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg7
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg8
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg9
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
previous_ambig
default: False
type: boolean
title: Boolean condition on the previous ambiguous distance restraints file
short description: Boolean condition on the previous ambiguous distance restraints file. If true, use the the restraint information coming from the previous CNS module. If false, don’t use previous information.
long description: Boolean condition on the ambiguous distance restraints file. If true, use the restraint information coming from the previous CNS module, as long as an ambig_fname is not defined for the current module. If false, don’t use previous information.
group: distance restraints
explevel: expert
randremoval
default: True
type: boolean
title: Random removal of ambiguous restraints
short description: If set to true (default) this will cause the random removal of ambiguous restraints for each model generated.
long description: If set to true (default) this will cause the random removal of ambiguous restraints for each model generated. The fraction of restraints randomly removed depends on the npart parameter which defines in how many sets the restraints should be randomly split. The first set will be removed. The fraction of randomly removed ambiguous restraints is thus 1/npart.
group: distance restraints
explevel: expert
s3sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first S3 symmetry segment
long description: Residue number of last residue in the first S3 symmetry segment
group: symmetry
explevel: expert
s3sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second S3 symmetry segment
long description: Residue number of last residue in the second S3 symmetry segment
group: symmetry
explevel: expert
s3sym_end3_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the third S3 symmetry segment
long description: Residue number of last residue in the third S3 symmetry segment
group: symmetry
explevel: expert
s3sym_seg1_1
default: ‘’
type: string
title: Segment ID of first S3 segment
short description: Segment ID of first S3 segment
long description: Segment ID of first S3 segment
group: symmetry
explevel: expert
s3sym_seg2_1
default: ‘’
type: string
title: Segment ID of second S3 segment
short description: Segment ID of second S3 segment
long description: Segment ID of second S3 segment
group: symmetry
explevel: expert
s3sym_seg3_1
default: ‘’
type: string
title: Segment ID of third S3 segment
short description: Segment ID of third S3 segment
long description: Segment ID of third S3 segment
group: symmetry
explevel: expert
s3sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first S3 symmetry segment
long description: Residue number of first residue in the first S3 symmetry segment
group: symmetry
explevel: expert
s3sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second S3 symmetry segment
long description: Residue number of first residue in the second S3 symmetry segment
group: symmetry
explevel: expert
s3sym_sta3_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the third S3 symmetry segment
long description: Residue number of first residue in the third S3 symmetry segment
group: symmetry
explevel: expert
sampling_factor
default: 1
type: integer
title: Sampling factor for each starting model
min: 1
max: 500
short description: This parameter control how many times a model will be refined.
long description: This parameter control how many times a model will be refined.
group: sampling
explevel: expert
seg_end_10_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_11_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_12_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_13_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_14_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_15_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_16_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_17_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_18_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_19_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_1_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_20_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_2_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_3_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_4_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_5_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_6_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_7_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_8_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_9_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_10_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_11_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_12_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_13_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_14_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_15_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_16_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_17_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_18_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_19_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_1_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_20_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_2_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_3_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_4_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_5_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_6_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_7_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_8_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_9_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
sym_on
default: False
type: boolean
title: Symmetry restraints
short description: Enables symmetry restraints
long description: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 supported) and the segments to which those apply must be defined. In addition a custom symmetry restraint file can be supplied (symrest_fname).
group: symmetry
explevel: expert
symtbl_fname
default: ‘’
type: file
title: Custom symmetry restraints filename
short description: Filename of the custom symmetry restraints file
long description: Filename of the custom symmetry restraints file.
group: symmetry
explevel: expert
tolerance
default: 5
type: integer
title: Failure tolerance percentage
min: 0
max: 99
short description: Percentage of allowed failures for a module to successfully complete
long description: Percentage of allowed failures for a module to successfully complete
group: module
explevel: expert
unambig_scale
default: 50
type: integer
title: Force constant for unambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in unambig_fname.
long description: Force constant applied to the distance restraints defined in unambig_fname.
group: distance restraints
explevel: expert
w_air
default: 0.1
type: float
title: Weight of the distance restraint energy
min: 0
max: 9999
short description: Weight of the distance restraints energy in the scoring function
long description: Weight of the distance restraints energy in the scoring function. Note that this is different from the force constants used during the calculations.
group: scoring
explevel: expert
w_bsa
default: 0.0
type: float
title: Weight of the buried surface area term
min: -9999
max: 9999
short description: Weight of the buried surface area term in the scoring function
long description: Weight of the buried surface area (BSA) term in the scoring function. Note that the BSA is only used for scoring.
group: scoring
explevel: expert
w_cdih
default: 0.0
type: float
title: Weight of the dihedral angle restraint energy
min: 0
max: 9999
short description: Weight of the dihedral angle restraints energy in the scoring function
long description: Weight of the dihedral angle restraints energy in the scoring function. Note that this is different from the force constant used during the calculations.
group: scoring
explevel: expert
w_desolv
default: 1.0
type: float
title: Weight of the desolvation energy term
min: -9999
max: 9999
short description: Weight of the desolvation energy term in the scoring function
long description: Weight of the desolvation energy term in the scoring function. Note that the desolvation energy is only used for scoring.
group: scoring
explevel: expert
w_elec
default: 0.2
type: float
title: Weight of the intermolecular electrostatic energy
min: -9999
max: 9999
short description: Weight of the intermolecular electrostatic energy in the scoring function
long description: Weight of the intermolecular electrostatic energy in the scoring function. Note that this does not affect the electostatic energy during the MD refinement.
group: scoring
explevel: expert
w_sym
default: 0.1
type: float
title: Weight of the symmetry restraint energy
min: 0
max: 9999
short description: Weight of the symmetry restraints energy in the scoring function
long description: Weight of the symmetry restraints energy in the scoring function. Note that this is different from the force constant used during the calculations.
group: scoring
explevel: expert
w_vdw
default: 1.0
type: float
title: Weight of the intermolecular van der Waals energy
min: -9999
max: 9999
short description: Weight of the intermolecular van der Waals energy in the scoring function
long description: Weight of the intermolecular van der Waals energy in the scoring function. Note that this does not affect the van der Waals energy during the MD refinement.
group: scoring
explevel: expert
watercoolsteps
default: 500
type: integer
title: Number of MD steps for the cooling
min: 0
max: 10000
short description: Number of MD steps for the cooling phase.
long description: Number of MD steps for the cooling phase. The cooling consists of three successive short molecular dynamics simluations at 300, 200 and 100 Kelvin.
group: sampling
explevel: expert
waterheatsteps
default: 100
type: integer
title: Number of MD steps for the heating
min: 0
max: 10000
short description: Number of MD steps for the heating phase.
long description: Number of MD steps for the heating phase. The heating consists of three successive short molecular dynamics simluations at 100, 200 and 300 Kelvin.
group: sampling
explevel: expert
watersteps
default: 1250
type: integer
title: Number of MD steps at 300K.
min: 0
max: 100000
short description: Number of MD steps for 300K simulation.
long description: Number of MD steps for 300K simulation. This is the sampling state of the refinement.
group: sampling
explevel: expert
Guru
iniseed
default: 917
type: integer
title: Random seed
min: 0
max: 9999999999999999
short description: Random seed used in CNS to initialize the random seed function
long description: Random seed used in CNS to initialize the random seed function
group: sampling
explevel: guru
keepwater
default: False
type: boolean
title: Write water molecules to output file
short description: Write water molecules if present to the output file.
long description: Write water molecules if present to the output file.
group: sampling
explevel: guru
log_level
default: ‘quiet’
type: string
title: Log level verbosity for CNS
choices: [‘verbose’, ‘normal’, ‘quiet’]
short description: Set the log level verbosity for CNS
long description: CNS, the computational engine used by HADDOCK can generate a lot of output messages. This parameter controls the verbosity of CNS (verbose, normal or quiet).
group: module
explevel: guru
timestep
default: 0.002
type: float
title: MD integrating time step
min: 0.0005
max: 0.004
short description: Integration time step for the molecular dynamics.
long description: Integration time step for the molecular dynamics.
group: sampling
explevel: guru