One can think it a clever line in chaff (5)
I believe the answer is:
brain
'one can think it a clever' is the definition.
I can't tell whether this defines the answer.
'line in chaff' is the wordplay.
'line' becomes 'i' (I can't justify this - if you can you should believe this answer much more).
'in' means one lot of letters goes inside another.
'chaff' becomes 'bran' (bran is a kind of chaff).
'i' placed within 'bran' is 'BRAIN'.
Can you help me to learn more?
(Other definitions for brain that I've seen before include "Organ of the intellect" , "Control centre of nervous system" , "Clever person" , "Hit hard; intellect" , "Seat of the intellect" .)