Gag self assembly model

This section describes how to set up a model for Gag self-assembly.

Reshape Gag

reshape_gag(PathName)

Description: Constructs a model of the Gag monomer. Experimentally measured Gag lattice structures must be regularized to eliminate thermal fluctuations and other experimental errors. This function reshapes and regularizes these structures.

Parameters:

• PathName (string): The path of the .pdb file.

Returns:

• finalPositionsVec (list of shape 144 x 3): The coordinates of the center of mass (COM) and 5 interfaces for each of the 18 Gag monomers.

Example:

import ionerdss as ion
finalPositionsVec = ion.reshape_gag('path/to/file.pdb')