chemdiff: command not found

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On Debian possible default full paths are:

/usr/bin/chemdiff - from package: indigo-utils

You may install the required package with command apt-get install {package}

Error in other languages:
chemdiff: bevel nie gevind nie
chemdiff: comandă negăsită
chemdiff: comando não encontrado
chemdiff: commande introuvable
chemdiff: command not found
chemdiff: käsku ei ole
chemdiff: không tìm thấy lệnh
chemdiff: komanda nerasta
chemdiff: Kommando nicht gefunden.
chemdiff: kommandot finns inte
chemdiff: komut yok
chemdiff: nie znaleziono polecenia
chemdiff: níor aimsíodh an t-ordú
chemdiff: no se encontró la orden
chemdiff: no s'ha trobat l'ordre
chemdiff: opdracht niet gevonden
chemdiff: parancs nem található
chemdiff: perintah tidak ditemukan
chemdiff: príkaz nenájdený
chemdiff: příkaz nenalezen
chemdiff: команда не найдена
chemdiff: командата не е открита
chemdiff: 命令找不到
chemdiff: コマンドが見つかりません