Restraints.make_distance() -- make distance restraints

make_distance(atmsel1, atmsel2, aln, spline_on_site, restraint_group, maximal_distance, residue_span_range=(0, 99999), residue_span_sign=True, distance_rsr_model=1, basis_pdf_weight='LOCAL', basis_relative_weight=0.05, spline_dx=0.5, spline_min_points=5, spline_range=4.0, accessibility_type=8, restraint_stdev=(0.1, 1.0), restraint_stdev2=(0.0, 0.0, 0.0), surftyp=1, distngh=6.0, edat=None, io=None, exclude_distance=0.0)

Requirements:

topology & parameters

This command calculates and selects new distance restraints. See Restraints.make() for full details.

Distance restraints are generated for all pairs of atoms $i,j$ where atom $i$ is from selection atmsel1 and atom $j$ is from selection atmsel2. Moreover, for a restraint to be created, at least one distance in the template structures must be less than maximal_distance (in Å). 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.

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()).

If the restrained distance for a given atom pair is less than exclude_distance, that pair is also excluded from the nonbonded list. This is useful if you are building short distance restraints to approximate bonds.