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Create a PDB file representation of the distribution of XH bond vectors.


structure.create_vector_dist(length=2e-09, file=`XH_dist.pdb', dir=None, symmetry=True, force=False)

Keyword arguments

length: The length of the vectors in the PDB representation (meters).

file: The name of the PDB file.

dir: The directory to place the file into.

symmetry: A flag which if True will create a second chain with reversed XH bond orientations.

force: A flag which if True will overwrite the file if it already exists.


This creates a PDB file containing an artificial vectors, the length of which default to 20 Å. A structure must have previously been read into relax. The origin of the vector distribution is located at the centre of mass (of the selected residues). This vector distribution PDB file can subsequently be read into any molecular viewer.

Because of the symmetry of the diffusion tensor reversing the orientation of the XH bond vector has no effect. Therefore by setting the symmetry flag two chains `A' and `B' will be added to the PDB file whereby chain `B' is chain `A' with the XH bonds reversed.

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