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I don't think it will look bad if you don't have her write you a letter, especially since you already have 3 research PIs. Unless you're going for MD/PhD, 3 is more than enough research letters. Unless your biggest accomplishments by far were under this person, then maybe you should try and get a letter. But even then, your professor would be the more appropriate person to vouch for your experience.

In short, I think you are worrying over nothing. 3 strong research letters is more than enough. If you want to be a clinician, I suggest getting more letters from non-research oriented endeavors such as medical/clinical volunteering.
 
You don't need it. You have more than enough letters.
 
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