  Advances in imaging methods such as electron microscopy, tomography and other
modalities are enabling high-resolution reconstructions of cellular and
organelle geometries. Such advances pave the way for using these geometries for
biophysical and mathematical modeling once these data can be represented as a
geometric mesh, which, when carefully conditioned, enables the discretization
and solution of partial differential equations. In this study, we outline the
steps for a na\"ive user to approach GAMer 2, a mesh generation code written in
C++ designed to convert structural datasets to realistic geometric meshes,
while preserving the underlying shapes. We present two example cases, 1) mesh
generation at the subcellular scale as informed by electron tomography, and 2)
meshing a protein with structure from x-ray crystallography. We further
demonstrate that the meshes generated by GAMer are suitable for use with
numerical methods. Together, this collection of libraries and tools simplifies
the process of constructing realistic geometric meshes from structural biology
data.

Computational Physics;Quantitative Methods