QTM

QTM (Quality Triangle/Tetrahedral Meshes) constructs quality meshes for implicit solvation models of biomolecular structures starting from atomic resolution data in the Protein Data Bank (PDB). A smooth volumetric electron density map is constructed from atomic data using weighted Gaussian isotropic kernel functions and a two-level clustering technique. A modified dual contouring method is used to extract triangular meshes for the surface, and tetrahedral meshes for the volume inside or outside the molecule within a bounding sphere/box of influence. Geometric flow techniques are used to improve the surface and volume mesh quality.