Our ears do not hear all notes equally, for instance we often hear the first and last notes of fast runs more than the notes in between. The harmonic structure of a passage also influences which notes are most noticed.
When working to improve intonation it is important to uncover the patterns in a passage. Here this passage is based on a diminished 7th with passing notes.
The intonation of the passing notes is heard primarily in relation to that of the main notes. Practise the 'core pattern' of the passage on its own and when you add the passing notes make sure that their pitch is heard in relation to these main notes.
This is the second subject of the Saint-Saens Violin Concerto No.3, 1st movement.
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