restraints.make_distance() -- make distance restraints

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

Requirements:

topology & parameters

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:

• 'USER_DISTANCE'. This makes distance restraints between pairs of atoms from the atom selections atmsel1 and atmsel2 (inter-set only), using the value of restraint_parameters. Only distances satisfying the residue_span_range criterion are restrained. This command is useful for making non-specific ``compactization'' restraints.

• 'DISTANCE'. This makes distance restraints that are generated for all pairs of atoms $i,j$ where atom $i$ is from selection atmsel1 and atom $j$ is from selection atmsel2. The atoms also have to be within the residue spanning range specified by residue_span_range = r1 r2, such that the residue index difference $r1 \le \vert ir2 - ir1\vert \le r2$ when residue_span_sign = False and $r1 \le (ir2 - ir1) \le r2$ when residue_span_sign = True. Moreover, for a restraint to be created, at least one distance in the template structures must be less than maximal_distance (in ). The mean of this basis pdf is equal to the template distance and its standard deviation $\sigma$ is calculated from an analytic model specified by distance_rsr_model. Use model 5 for ${C}_\alpha$ - ${C}_\alpha$ distances and model 6 for N-O distances. For models 1 through 6, this standard deviation is transformed by $\sigma' = a + b*(\sigma+W_{g})$ where $a$ and $b$ are given by restraint_stdev and $W_{g}$ is a gap weighting function of the form $W_{g} = 0.6 * \max(0, 4-g_{av})$ . $g_{av}$ is the average distance of the two residues involved in the restraint from a gap. For models 3 through 6, this is additionally transformed by $\sigma'' = \sigma' + \sum_{i}[d+e*\max(0,f-g_{i})]$ where the sum is over each of the atoms $i$ involved in the distance, $d$ $e$ and $f$ are given by restraint_stdev2, and $g_{i}$ is the distance of each residue from a gap. The first six models are polynomials and depend on several structural features of the template and its similarity to the target. The polynomial coefficients are specified in library file '$PARAMS_LIB'. When ``polynomial model'' 7 is selected, the standard deviation of restraints is set to constant $a$ . Each basis pdf in the distance pdf corresponds to one template structure with an equivalent distance. The weights of basis pdf's depend on local sequence similarity between the target and the templates when basis_pdf_weight = 'LOCAL' and on global sequence identity when basis_pdf_weight = 'GLOBAL'. In addition, the atom pairs restrained by homology-derived restraints must by default not be in a chemical bond, chemical angle, dihedral angle, or on an excluded pairs list. This behavior can be changed by resetting energy_data.excl_local (see conjugate_gradients()).