Figure 4

The interior volume of myoglobin. (A) The voids (green) identified in myoglobin using a grid-spacing of 0.2 Å. (B) With the volume-filling spheres, it is easy to select the residues (stick display) that define the interior volume by proximity to the volume-filling spheres. The interior volume is shown as a semi-transparent surface. (C) At increasingly small spacing the finite-grid approximation approaches ideality as seen in the convergence of the volume (red) of the dummy atoms for the voids in myoglobin. The time required to generate the dummy atoms at different grid-spacing (blue) shows a significant jump in time from a grid-spacing of 0.2 Å to 0.1 Å. The calculations were performed on an iMac where the optional compilation module Psyco [13] was used to accelerate the calculation.