When most saxophonists tune up they use a middle G or F-Sharp. The main problem with this is that the middle G or F-Sharp is traditionally very sharp notes... usually 30 cent plus if the embouchure is not adjusted. The young saxophonist will generally not know where these notes are just by playing them alone. When the student pulls the mouthpiece out far enough to make the unaltered F-Sharp or G play in tune then the lower register of the instrument sill most certainly be flat.
How to fix this problem:
The second option is to have the alto saxophonist play a first finger B natural, hold it for a while and then play the middle G or F-Sharp. This will allow the saxophonist to make the necessary adjustments to the embouchure when they hear the interval from the first finger B to the middle note.
*It is important to remember that the saxophone is generally an out of tune instrument. It is by the nature of the design that the instrument is always a challenge to play in tune. When you change a reed... when the room is to hot or cold.... a pad leaks... All of these things change the intonation of the instrument.
*The best way to play any instrument in tune is of course to...... hear it in tune! Practice with your tuner... now they do not need to get crazy with the tuner and bring it with them everywhere... When I see a guy get a tuner out before anyone has played I am pretty sure he cannot trust his ears.... use the tuner at home or just to get the first note where you need it.... then put it away.....
You must first hear in tune to play in tune.....
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