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Why does it seem so many players use 5th fret vs Open string?

In my opinion, it's just a matter of personal taste and fingering habit. But Is also true that there is a difference between in terms of frequency and tone when you play an A as open string compared to the fifth fret of the E strings.
Depending on which type of strings you use and how your action was set, usually, the A open string is a bit less punchy compared the to the one on the E. The second is warmer, is complete on low frequencies. The open A has more mids and off course a longer sustain.
So the use just depends on which kind of bass line you're playing and what kind of tone you wanna reach.
 
The tonal differences of open vs. fretted notes are IMO not that obvious when playing flats (like many said, the overtones are what makes open strings sound different than fretted notes, and on flats, there overtones are less obvious). I play flats and use open strings whenever the situation calls for it; however, very rarely do I use them as a bare replacement for the 5th fret- when I stay in the lower register I might as well choose the fretted note. But I use open strings on position changes all the time when changing register or playing arpeggios, something I adapted from upright when playing lines over two octaves- in 9 out of the 12 keys, you can use one of the open strings to shift to what would be the 7th fret with either index or middle finger, and you're saving one or two shifts as opposed to playing everything fingered (oh, and in the remaining keys like esp. Db, the open strings make for excellent chromatic approach notes when playing bop-style melodies :-) ).
Very music dependent, but quite a few of Jamerson's lines use open strings in the same way (like, the Eb-chord in the beginning of "Bernadette", it's the first example coming to mind: Eb fretted on G-string, G open, rake down to Bb on D-string and Eb on G-string). Of course, with all the foam dampening on Jamerson's bass, and the crusty dead strings, there's even less overtones.

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Sidecar
 
Generally it depends on what music I'm playing. For reggae I tend to play mostly fretted notes and use occasional open strings where I want that sound. For when I'm playing with acoustic guitarists find I tend to use more open strings, funky stuff where I slap the open strings are used quite useful to have going on.
It's not something I think too consciously about i just tend to do what works best for the sound of the band.
 
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fretless guy here: sometimes i'll use open strings to get my 'pitch bearings' during a tune/riff, and then i'm back to 'fretted' notes.

but mostly: whatever works or sounds better to me at that moment. if i had a rule: choose the easy way, and then move on.

also: i play a lot in flat keys (horn bands), so not a lot of open string riffs. when i play in 'guitar keys' (e.g., E,A,D ...) i (might) use open strings more.
 
I want to add, that in my opinion the "different tone" argument is bad. I know it's real, but, I consider that a flaw in the instrument, strings, pickups, amp, cabs, EQ, etc.

That's extremely vague...

As you said, it's real. And that's the beauty of having the same note in more than one location on the fretboard...we have options.

My B-string is enormous, and my E-string is pretty standard. I chose to have it that way because they have slightly different tones.

The bass guitar is all about flaws, that's what gives it character, right down to the random finger noise
 
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What am I missing as a beginner to the instrument?

It's situational.

If there is a specific lick that has to use an open string, then fine, I'll use an open string. But only if there is absolutely no way around it. Like a pedaling lick.

For everything else I use closed positions. I play in a lot of cover bands, Soul, Motown, Classic Rock, Blues, Pop, Etc., and singers constantly change keys on me. If I learn a song in A and use lots of open strings, then get to the gig and they want to do the song in G, well that's a problem. But it's not a problem to change keys if I learned the song without any open licks. I can do it on the fly. :)

In my world of old farts there are two types of bands: Guitar bands, and horn bands. Song keys are all over the place based on the genre of music and the keys that a singer is comfortable with. If a horn song in F is being covered by a guitar driven band, there's a 99.9% chance the guitarist is gonna want to play it in E. And the singer will nod, happily. :)

So my reasons are more for efficiency. And for the record, I much prefer the sound of open bass strings. :) Fretted strings are easier to control. Muting, damping, whatever you want to call it, is really important for me, so being able to control the beast that is the bass, and change keys on the fly are really the main reason I play almost every note fretted.
 
There is a difference between open and fretted notes - Duh - say the laws of physics -

Another choice for tone - choice is good

Roundabout by Yes is a great example - plenty of dudes posting covers of it being played up the neck - Chris plays it with open strings 1st position in plenty of live clips - sounds different -

Certainly professionalism has nothing at all to do with it
 
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I always feel the fretted note have a better tighter tone. Some tunes we do in "E" like Play that Funky Music " The E note on the A string is to thin. Always use the open E. If I'm pumping 1/8 notes. I always fret them. I will use an open here and there in a more complex run to stay in position.
 
One of the reasons I use fretted notes when an open string would work is to be able to move patterns around up and down the neck. As someone who often subs and does sit-in gigs, it's easier to transpose on the fly when I'm not relying on open strings. Another reason is for muting the note, which can be done easily with the left hand on a fretted note.
 
I use open strings mostly if I want them to ring out more. My band has a punky song and for that I ride the open A and D a lot. Clangy and bright, good for rockin' out.

Generally I avoid open strings otherwise. Fretted notes higher up the neck sound sweeter and bassist and that's usually what I go for.
 
Phil Lesh said if you're using an open string, you better mean it. I tend to go with this philosophy

Exactly right.

Same goes for whatever fretted note you're playing.

The characteristics (timbre, attack, bloom, sustain) of the notes change when played on different strings at different positions on the neck. The thickness of the string as well as its speaking length produce an audible difference such that an E played on the second fret of the D string is a different animal than "the same E" played in the seventh fret of the A string. Or the twelfth fret on the E.

There's really no such thing as "the same note" anywhere on the bass neck. Each is subtly different even though they're notated identically on the music staff.

You can use those differences to your advantage.
 
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If I go higher (notewise, say, C to D), I'll use the open string. If I go down (like D to C) I'll be using the 5th. Usually. I dunno whatever feels better, regardless of whether it's "right".

Sometimes Jazz elitists annoy me :P
 
One think I *think* nobody's mentioned: really repetitive basslines, even when they're not that hard, can be an endurance test. If I'm not thinking about it, I tend to get a lot of tension and eventually cramping and pain. I find it helps me relax if practice them in a variety of positions, and then shift between them a bit while I'm playing. Maybe that's just me.

As others say, muting can be a problem. And for some reason I don't always notice the problem when I'm playing, even if it sounds pretty ugly. So, watch that you aren't letting open strings ring longer than you meant to--maybe record yourself just to make sure.