atmsel1 = <selection> | Atom selection | |
atmsel2 = <selection> | Atom selection | |
edat = <energy_data> | objective function parameters | |
aln = <alignment> | Template-model alignment | |
io = <io_data> | Options for reading atom files | |
restraint_type = <str:1> | 'STEREO' | restraint type to be calculated: 'STEREO' | 'BOND' | 'ANGLE' | 'IMPROPER' | 'DIHEDRAL' | 'SPHERE' | 'SPHERE14' | 'LJ' | 'LJ14' | 'COULOMB' | 'COULOMB14' | 'DISTANCE' | 'USER_DISTANCE' | 'NONB_PAIR_SPLINE' | 'PHI-PSI_BINORMAL' | 'PHI_DIHEDRAL' | 'PSI_DIHEDRAL' | 'OMEGA_DIHEDRAL' | 'CHI1_DIHEDRAL' | 'CHI2_DIHEDRAL' | 'CHI3_DIHEDRAL' | 'CHI4_DIHEDRAL' |
maximal_distance = <float:1> | 999 | maximal distance for distance restraints |
residue_span_range = <int:2> | 0 99999 | range of residues spanning the allowed distances; for MAKE_RESTRAINTS, PICK_RESTRAINTS, non-bonded dynamic pairs |
residue_span_sign = <bool:1> | True | whether to do N*(N-1)/2 loop for atom pairs in MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance' |
accessibility_type = <int:1> | 8 | type of solvent accessibility: 1-10 |
distance_rsr_model = <int:1> | 1 | the model for calculating distance restraints: 1-7 |
restraint_group = physical_type | physical restraint group | |
restraint_stdev = <float:2> | 0.0 1.0 | transforming factors for standard deviations (y=a+bx) in models 1-6 or standard deviation for model 7 (a) |
restraint_stdev2 = <float:3> | 0 0 0 | transforming standard deviation in models 3-6: S' = S + [ a + b max(0, c-g) ] |
restraint_parameters = <float:0> | 3 1 3 3 4 2 0 0.0 0.087 | restraint parameters for 'USER_DISTANCE' |
basis_pdf_weight = <str:1> | 'LOCAL' | a method for calculation of basis pdf weights: 'LOCAL' | 'GLOBAL' |
basis_relative_weight = <float:1> | 0.05 | the cutoff weight of basis pdf's for their removal |
spline_on_site = <bool:1> | False | whether to convert restraints to splines |
spline_dx = <float:1> | 0.5 | interval size for splining restraints |
spline_min_points = <int:1> | 5 | have at least as many intervals in a spline |
spline_range = <float:1> | 4.0 | range of the splines |
distngh = <float:1> | 6.0 | Maximum distance to consider residues as neighbors |
This command calculates and selects new distance restraints. See restraints.make() for full details.
Only two values of restraint_type are allowed for this command: