For all the programs type -h to get syntax list. examples:
>./Volume.exe -h
./Volume.exe -i file -g gridspacing -p probe_rad -e EZD_outfile -o PDB_outfile
>./Solvent.exe -h
./Solvent.exe -i file -s sm_probe_rad -b big_probe_rad
-t trim_probe_rad -g grid spacing -e EZD outfile -o PDB outfile
>./Channel.exe -h
./Channel.exe -i file -b big_probe -s small_probe
-t trim probe -x x-coord -y y-coord -z z-coord
-e EZD outfile -o PDB outfile -g gridspace
Channel is like Solvent, but select a particular channel at point x,y,z
Tunnel.exe is "worthless" unless you are studying the ribosome
Eveything has a
default value, except the input file.
neil