Subsections


structure.get_pos

Image structure

Synopsis

Extract the atomic positions from the loaded structures for the given spins.

Defaults

structure.get_pos(spin_id=None, ave_pos=True)

Keyword arguments

spin_id: The spin identification string.

ave_pos: A flag specifying if the position of the atom is to be averaged across models.

Description

This allows the atomic positions of the spins to be extracted from the loaded structures. This is automatically performed by the structure.load_spins user function, but if the sequence information is generated in other ways, this user function allows the structural information to be obtained.

If averaging the atomic positions, then average position of all models will be loaded into the spin container. Otherwise the positions from all models will be loaded separately.

Prompt examples

For a model-free backbone amide nitrogen analysis whereby the N spins have already been created, to obtain the backbone N positions from the file `1F3Y.pdb' (which is a single protein), type the following two user functions:

[numbers=none]
relax> structure.read_pdb('1F3Y.pdb')

[numbers=none]
relax> structure.get_pos(spin_id='@N')


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