The doctor has nothing on the ship but waste material (5)
I believe the answer is:
dross
'waste material' is the definition.
(dross is a kind of waste material)
'the doctor has nothing on the ship' is the wordplay.
'the doctor' becomes 'Dr' (abbreviation).
'has' means one lot of letters go next to another.
'nothing on' becomes 'o' (I've seen this in other clues).
'the ship' becomes 'SS' (prefix in ship names eg SS Great Britain).
'dr'+'o'+'ss'='DROSS'
'but' is the link.
(Other definitions for dross that I've seen before include "Scum on molten metals" , "Scum - dregs" , "Worthless matter" , "Impurity" , "Worthless stuff" .)