How to do HOLE analysis

HOLE is a program written in 1996 and has been widely used for characterizing ion channels.

In short, a channel radius profile along z-axis can be computed by

$ hole <hole.inp> out.txt
$ cat hole.inp
coord input.pdb
radius /path/to/hole2/rad/amberuni.rad
cvect 0.0 0.0 1.0
sphpdb out.sph
endrad 15

To format the output texts

egrep "mid-|sampled" out.txt | awk '{print $1" "$2}' > formatted.dat

Here is how HOLE integrates with VMD.