Subsections


paramag.centre

Image align_tensor

Synopsis

Specify which atom is the paramagnetic centre.

Defaults

paramag.centre(pos=None, atom_id=None, pipe=None, verbosity=1, fix=True, ave_pos=True, force=False)

Keyword arguments

pos: The atomic position of the paramagnetic centre.

atom_id: The atom ID string.

pipe: The data pipe containing the structures to extract the centre from.

verbosity: The amount of information to print out.

fix: A flag specifying if the paramagnetic centre should be fixed during optimisation.

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

force: A flag which if True will cause the current paramagnetic centre to be overwritten.

Description

This is required for specifying where the paramagnetic centre is located in the loaded structure file. If no structure number is given, then the average atom position will be calculated if multiple structures are loaded.

A different set of structures than those loaded into the current data pipe can also be used to determine the position, or its average. This can be achieved by loading the alternative structures into another data pipe, and then specifying that pipe.

If the average position flag is set to True, the average position from all models will be used as the position of the paramagnetic centre. If False, then the positions from all structures will be used. If multiple positions are used, then a fast paramagnetic centre motion will be assumed so that PCSs for a single tensor will be calculated for each position, and the PCS values linearly averaged.

Prompt examples

If the paramagnetic centre is the lanthanide Dysprosium which is labelled as $ \mathfrak{D}_y$ in a loaded PDB file, then type one of:

[numbers=none]
relax> paramag.centre('Dy')

[numbers=none]
relax> paramag.centre(atom_id='Dy')

If the carbon atom `C1' of residue `4' in the PDB file is to be used as the paramagnetic centre, then type:

[numbers=none]
relax> paramag.centre(':4@C1')

To state that the Dy3+ atomic position is [0.136, 12.543, 4.356], type one of:

[numbers=none]
relax> paramag.centre([0.136, 12.543, 4.356])

[numbers=none]
relax> paramag.centre(pos=[0.136, 12.543, 4.356])

To find an unknown paramagnetic centre, type:

[numbers=none]
relax> paramag.centre(fix=False)


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