Subsections


frame_order.distribute

Image frame_order Image document-save

Synopsis

Structural distribution of the frame order motions.

Defaults

frame_order.distribute(file=`distribution.pdb.gz', dir=None, atom_id=None, total=1000, max_rotations=100000, model=1, force=False)

Keyword arguments

file: The PDB file for storing the frame order motional distribution. The compression is determined automatically by the file extensions `*.pdb', `*.pdb.gz', and `*.pdb.bz2'.

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

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

total: The total number of structures to include in the uniform distribution.

max_rotations: The maximum number of rotations to generate the distribution from. This prevents the user function from executing for an infinite amount of time. This occurs whenever a frame order amplitude parameter (cone opening angle or torsion angle) is zero so that the subset of all rotations within the motional distribution is also zero.

model: Only one model from an analysed ensemble of structures can be used for the distribution, as the distribution PDB file consists of one model per state.

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

Description

To visualise the frame order motions, this user function generates a distribution of structures randomly within the bounds of the uniform distribution of the frame order model. The original structure is rotated randomly and only accepted for the distribution if it is within the bounds. This is a more faithful representation of the dynamics than the pseudo-Brownian simulation user function.

Note that the RDC and PCS data does not contain information about all parts of the real distribution of structures. Therefore the structures in this distribution only represent the components of the distribution present in the data, as modelled by the frame order models.

As the distribution consists of one model per state, if an ensemble of structures has been analysed, only one model from the ensemble can be used for the representation.


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