Note in scale, only not E (3)
I believe the answer is:
sol
'note' is the definition.
(I've seen this in another clue)
'scale only not e' is the wordplay.
'scale' becomes 's' (this could be a standard abbreviation which I don't know about).
'only' becomes 'sole' (synonyms).
'not' suggests deleting specific letters.
'e' becomes 'Es' (synonyms).
'sole' with 'es' removed is 'ol'.
's'+'ol'='SOL'
'in' is the link.
Can you help me to learn more?
(Other definitions for sol that I've seen before include "Roman counterpart of Helios" , "Note, old french coin" , "The sun in 12 Across" , "Personification of the sun" , "Note - colloid - the Sun" .)