Distance is defined by points and :

(A.38) |

where

(A.39) |

The first derivatives of
with respect to Cartesian coordinates are:

(A.40) | |||

(A.41) |

Angle is defined by points , , and , and spanned by vectors and :

(A.42) |

It lies in the interval from 0 to 180°. Internal MODELLER units are radians.

The first derivatives of α
with respect to Cartesian coordinates are:

(A.43) | |||

(A.44) | |||

(A.45) |

These equations for the derivatives have a numerical instability when the angle goes to 0 or to 180°. Presently, the problem is ‘solved’ by testing for the size of the angle; if it is too small, the derivatives are set to 0 in the hope that other restraints will eventually pull the angle towards well behaved regions. Thus, angle restraints of 0 or 180° should not be used in the conjugate gradients or molecular dynamics optimizations.

Dihedral angle is defined by points , , , and ( ):

sign | (A.46) |

where

sign sign | (A.47) |

The first derivatives of χ with respect to Cartesian coordinates are:

(A.48) |

where

(A.49) |

and

(A.50) | |||

(A.51) | |||

(A.52) | |||

(A.53) | |||

(A.54) | |||

(A.55) |

These equations for the derivatives have a numerical instability when
the angle goes to 0. Thus, the following set of equations is used
instead [van Schaik *et al.*, 1993]:

(A.56) | |||

(A.57) | |||

(A.58) | |||

(A.59) | |||

(A.60) | |||

(A.61) |

The only possible instability in these equations is when the length of the central bond of the dihedral, , goes to 0. In such a case, which should not happen, the derivatives are set to 0. The expressions for an improper dihedral angle, as opposed to a dihedral or dihedral angle, are the same, except that indices are permuted to . In both cases, covalent bonds , , and are defining the angle.

This is the accessibility value calculated by the PSA algorithm
(see **model.write_data()**). This is usually set by the last call to
**Restraints.make()** or **Restraints.make_distance()**.
First derivatives are not calculated, and are always returned as 0.

Atomic density

Atomic density for a given atom is simply calculated as the number of atoms
within a distance *energy_data.contact_shell* of that atom. First
derivatives are not calculated, and are always returned as 0.

The absolute atomic coordinates , and are available for every point , primarily for use in anchoring points to planes, lines or points. Their first derivatives with respect to Cartesian coordinates are of course simply 0 or 1.

Automatic builds 2018-05-30