Image n_state_model


The defunct centre of mass (CoM) analysis.


n_state_model.CoM(pivot_point=[0.0, 0.0, 0.0], centre=None)

Keyword arguments

pivot_point: The pivot point of the motions between the two domains.

centre: Manually specify the CoM of the initial position prior to the N rotations to the positions of the N states. This is optional.


WARNING: This analysis is now defunct!

This is used for analysing the domain motion information content of the N states from the N-state model. The states do not correspond to physical states, hence nothing can be extracted from the individual states. This analysis involves the calculation of the pivot to centre of mass (pivot-CoM) order parameter and subsequent cone of motions.

For the analysis, both the pivot point and centre of mass must be specified. The supplied pivot point must be a vector of floating point numbers of length 3. If the centre of mass is supplied, it must also be a vector of floating point numbers (of length 3). If the centre of mass is not supplied, then the CoM will be calculated from the selected parts of a previously loaded structure.

Prompt examples

To perform an analysis where the pivot is at the origin and the CoM is set to the N-terminal domain of a previously loaded PDB file (the C-terminal domain has been deselected), type:

relax> n_state_model.CoM()

To perform an analysis where the pivot is at the origin (because the real pivot has been shifted to this position) and the CoM is at the position [0, 0, 1], type one of:

relax> n_state_model.CoM(centre=[0, 0, 1])

relax> n_state_model.CoM(centre=[0.0, 0.0, 1.0])

relax> n_state_model.CoM(pivot_point=[0.0, 0.0, 0.0], centre=[0.0, 0.0, 1.0])

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