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New shortscale player, wondering about unfocused E string

I just picked up a used CIJ Fender mustang. Overall I'm pretty impressed with the sound and pickups (much to my surprise, they are higher output and fuller range than my P bass with an EMG GZR pup). I'm just finding that it's difficult getting a focused and clear sound on the E string, especially above the 5th fret. I did make sure to lower the pickups to Fender specs, so I don't think it's that magnetic interference issue.

Could it be an issue with the individual E string? I had a fretless 34 scale with a similar issue and found that it was a problem with the specific string. Right now there are flats on the bass with a blue winding. Chromes maybe? I'd been looking at La Bella mustang flats, but at 50 dollars per set, I'm looking for advice before making a change.
 
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I wouldn't call it a problem or issue. I have found that this is just the way short-scale basses are. Search this forum for "overtones + short scale" or something like that and you will find more detail.

My understanding is, before you ever get to the strings, pickups, etc., the basic physics of an unplugged short-scale bass will produce a boomier sound with much less overtones than a 34" scale bass, and this is especially noticeable on the E string.
 
If you don't want to drop the money on a new set of strings without first doing some troubleshooting, I would suggest the following: if you have a spare set of lightly used roundwound strings kicking around, I would try the E from that set. Even if it's technically a long scale set, this typically is not a problem with rounds, as long as they fit through the tuning machine peg. My guess is, if these are old Daddario Chromes, they may have just gone fully broken-in dark thump mode. Though shortscales in general may indeed be prone to a little less definition on the low E, due to a lack of the overtones inherent on a longer scale... I have a house full of shortscales (mostly wearing flats) and none of them have an inherent lack of definition on the E. Just have to find the right string set for each bass, regardless of scale length generalizations.
 
Also, as someone who wrestled with short scales and overtones - try a set neck or neck-thru short scale. I have the Italia Maranello Cava with a set neck, and the low E is much more tightly defined and carries the overtones I want more than my experience with bolt-on short scales.
 
I went the the other way and scored a couple of 35" scale 4 strings a few years back (Peavey Grind and a Dean something-or-other) that left me wishing all my other 34" basses sounded as good on the E string. The crazy thing is that they're both cheapish basses - the Peavey is a BXP and the Dean is some economy line bass, too - and they both sound punchier on the low E than the more expensive basses that I own.
 
If the bass hasn't been played, it's possible the witness points haven't been set yet. I preach this wherever I can, because when I learned about it myself, it vastly improved the tone of the thicker strings for me. Make sure there's a hard bend in each string at both the bridge and the nut, and you will get the best that string has to offer.
 
Check the break angle past the nut. If the string is loosely sitting in the nut slot without much downward tension, then it could sound a little less resonant or focused. This can be fixed with more wraps around the tuning machine post very easily.

It might also be worth it to try another set of new strings.

My short scale low E is more bloomy than my Precision basses which are more boingy or bingy on the open low E.
 
If the bass hasn't been played, it's possible the witness points haven't been set yet. I preach this wherever I can, because when I learned about it myself, it vastly improved the tone of the thicker strings for me. Make sure there's a hard bend in each string at both the bridge and the nut, and you will get the best that string has to offer.

Check the break angle past the nut. If the string is loosely sitting in the nut slot without much downward tension, then it could sound a little less resonant or focused. This can be fixed with more wraps around the tuning machine post very easily.

It might also be worth it to try another set of new strings.

My short scale low E is more bloomy than my Precision basses which are more boingy or bingy on the open low E.

Did you bend the string over the saddle when you strung it up, or is it just floating over the top of the saddle? A bit of pressure on the neck-side of the saddle downwards on the string will bend that string over the saddle and improve contact dramatically. I find it makes a big difference.

Great minds certainly think alike.
 
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