Subsections


structure.find_pivot

Image structure

Synopsis

Find the pivot point of the motion of a set of structures.

Defaults

structure.find_pivot(pipes=None, models=None, molecules=None, atom_id=None, init_pos=None, func_tol=1e-05, box_limit=200)

Keyword arguments

pipes: The data pipes to use in the motional pivot algorithm.

models: The list of models for each data pipe to use in the motional pivot algorithm. The number of elements must match the pipes argument. If no models are given, then all will be used.

molecules: The list of molecules for each data pipe to use in the motional pivot algorithm. This allows differently named molecules in the same or different data pipes to be used. The number of elements must match the pipes argument. If no molecules are given, then all will be used.

atom_id: The atom identification string of the coordinates of interest.

init_pos: The initial position of the pivot.

func_tol: The function tolerance. This is used to terminate minimisation once the function value between iterations is less than the tolerance. The default value is 1e-5.

box_limit: The pivot point is constrained withing a box of +/- x Ă…the using the logarithmic barrier function together with simplex optimisation. This argument is the value of x.

Description

This is used to find pivot point of motion between a set of structural models. If the list of models is not supplied, then all models will be used.

Support for multiple structures is provided by the data pipes, model numbers and molecule names arguments. Each data pipe, model and molecule combination will be treated as a separate structure. As only atomic coordinates with the same residue name and number and atom name will be assembled, structures with slightly different atomic structures can be compared. If the list of models is not supplied, then all models of all data pipes will be used. If the optional molecules list is supplied, each molecule in the list will be considered as a separate structure for comparison between each other.

The atom ID string, which uses the same notation as the spin ID, can be used to restrict the coordinates compared to a subset of molecules, residues, or atoms. For example to only use backbone heavy atoms in a protein, set the atom ID to `@N,C,CA,O', assuming those are the names of the atoms in the 3D structural file.

By supplying the position of the centroid, an alternative position than the standard rigid body centre is used as the focal point of the superimposition. The allows, for example, the superimposition about a pivot point.


The relax user manual (PDF), created 2016-10-28.