Subsections


structure.web_of_motion

Image structure

Synopsis

Create a PDB representation of motion between structures using a web of interconnecting lines.

Defaults

structure.web_of_motion(pipes=None, models=None, molecules=None, atom_id=None, file=None, dir=None, force=False)

Keyword arguments

pipes: The data pipes to generate the web between.

models: The list of models for each data pipe to generate the web between. The number of elements must match the pipes argument. If no models are given, then all will be used.

molecules: The list of molecules for each data pipe to generate the web between. This allows differently named molecules in the same or different data pipes to be superimposed. The number of elements must match the pipes argument. If no molecules are given, then all will be used.

atom_id: The atom identification string of the coordinates of interest.

file: The name of the PDB file.

dir: The directory to save the file to.

force: A flag which if set to True will cause any pre-existing files to be overwritten.

Description

This will create a PDB representation of the motion between the atoms of a given set of structures. Identical atoms of the structures are concatenated into one model, within a temporary internal structural object, linked together using PDB CONECT records, and then written to the PDB file.

Support for multiple structures is provided by the data pipes, model numbers and molecule names arguments. Each data pipe, model and molecule combination will be treated as a separate structure. As only atomic coordinates with the same residue name and number and atom name will be assembled, structures with slightly different atomic structures can be compared. If the list of models is not supplied, then all models of all data pipes will be used. If the optional molecules list is supplied, each molecule in the list will be considered as a separate structure for comparison between each other.

The atom ID string, which uses the same notation as the spin ID, can be used to restrict the coordinates compared to a subset of molecules, residues, or atoms. For example to only use backbone heavy atoms in a protein, set the atom ID to `@N,C,CA,O', assuming those are the names of the atoms in the 3D structural file.

Prompt examples

To create a web of motion for the models 1, 3, and 5, type:

[numbers=none]
relax> structure.web_of_motion(models=[[1, 3, 5]], file='web.pdb')

To create a web of motion for the molecules `A', `B', `C', and `D', type:

[numbers=none]
relax> structure.web_of_motion(molecules=[['A', 'B', 'C', 'D']], file='web.pdb')


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