Image frame_order Image document-save


Structural representation of the individual frame order motional components.


frame_order.decompose(root=`decomposed', dir=None, atom_id=None, model=1, total=None, reverse=False, mirror=False, force=False)

Keyword arguments

root: The file root for the PDB files created. Each motional component will be represented by a different PDB file appended with `_mode1.pdb', `_mode2.pdb', `_mode3.pdb', etc.

dir: The directory where the files are to be saved.

atom_id: The atom identification string to allow the representation to be applied to a subset of all atoms.

model: Only one model from an analysed ensemble of structures can be used for the representation, as the decomposition PDB files consist of one model per state.

total: The total number of structures to distribute along the motional modes. This overrides the fixed angle value.

reverse: Set this to reverse the ordering of the models distributed along the motional mode.

mirror: Set this to have the models distributed along the motional mode shift from the negative angle to positive angle, and then return to the negative angle.

force: A flag which, if set to True, will overwrite the any pre-existing file.


An alternative way to visualise the frame order motions is to decompose the motions and visualise each mode separately. This user function will create a uniform distribution of structures shifted from the original position and rotated around the eigenvector for that motional mode. Each distribution will be output to a PDB file appended with `_modeX.pdb', where X are the discrete motional modes ordered from largest to smallest. The curved line of positions will extend over the full distribution of structures.

The relax user manual (PDF), created 2020-08-26.