Though I like our program HOLLOW for visualization, I think the tool for this job is MOLE (http://mole.chemi.muni.cz). You can use the online version to quickly generate two trajectories out from the center of the channel. MOLE has some mathematical advantages over HOLE or Caver. You then merge the two pdb files and delete the overlapping points. The resulting file will have a radius of the sphere at each point along the trajectory in the Bfactor field. The radius is the maximum sphere size that would fit within channel along the trajectory which should be the center of the pore. This can then be plotted as done by Smart et al. Biophys J. 1993. Dec;65(6):2455-60.
