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Scales: do you practice the lowest position with the most open strings?

Good question. The use of open strings is invaluable. In my early days (which was the early 70s for me) of learning, my instructor had me using strict OFPF over the 1st four frets and open strings, playing all of the available notes of the arpeggios following the Circle of 4ths. Granted, I concentrated more or arpeggios than scales, but the desired learning objective was the same; the ability to incorporate open strings in my playing without getting lost. The use of open strings allows you to efficiently change positions and are really great to use as passing notes. I've been doing it a long time and even today, when I'm just sitting around noodling, I'll run thru that exercise. I'd like to see more open string exercises by those who teach on YT.
 
Closed positions (no open strings) seem easier because the same shapes work for any key.

But which position you play in should be a conscious choice based on the sound and feel you want.
If you can't play open positions, you do not have that choice.
So practice open positions enough that you get to choose.

Personally I love paying the open strings, every key has its own unique feel under my hands. Plus the challenge of getting the open notes to dynamically match the fretted ones refines my technique.

"knowing something is better than not knowing something" - Anthony Wellington

If you need an example of a top level player using open positions, look to James Jamerson.
 
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The only open string you ever have to play is the E (or the B on a fiver). Nowadays I usually play the other notes at the fifth fret, though sometimes I will play them open to accommodate a pattern that's much more easily played that way.

However, when I first learned to play, the instrument I owned wasn't very good and I played a lot of things in the first position because I didn't really know any better and, with very high action toward the bridge, it was easier to play there. I developed what some would call bad habits, but learned to play all sorts of patterns using the open strings. There's a time and a place for both ways and it doesn't hurt you to know how to use them, but as mambo4 said it should, ideally, be a choice based on the situation at hand, not just because you have a crappy bass, like I did :)
 
Jamerson was big on open strings - it helps you move around a lot - you can shift positions easily when you've got an open string holding things down for half a second. One advantage that he had that we don't - in his day, the instrument was so new that people hadn't decided the "rules" for things - he did what worked. I suggest you follow that approach.

I sometimes play open strings. Obviously, if I want to play a low B, I kinda have to. But mostly I play where it sounds best for the music I'm playing. When I want big and round sounding, playing higher up facilitates that. When I want the harmonics to be more prevalent, playing low on the neck works better for that. I typically set my instruments up with a bit less relief than most, so it's easier to get clank and grind on the lower part of the neck, but easy to play cleanly further up - that helps me have more range of sounds from the instrument.

Where to play isn't a rule you need to follow - playing in different places give you opportunities that you can, if you know the neck well, use to your advantage.
 
Take the key of C for example:
  • I can play in open position and take advantage of the open D and G
  • I can start on the third fret of the A string
  • I can start on the eighth fret of the E string
But they each sound a little different. Open strings don’t allow for the normal muting you get when you fret. Third fret sounds the most natural to me. Eighth fret has an unnaturally high sound – – not very bass like at all.
 
Open strings have been used on string instruments, and fretted string instruments, for hundreds of years. It's extremely unlikely that an instrument that is 70 odd years young is going to come along and buck that tend.

Having the knowledge of both open strings and fretted strings will only ever benefit your bass playing. Open strings facilitate so many shifts in position easier than fretted notes will. Whereas a fretted note may allow you to execute a passage easier. Context is everything. Yes there is a slight difference in sound but the more you use open strings the more control you'll get over them. When you are playing in a band or hearing the bass in the mix of a studio recording most people can't tell it's an open string and only bass players can generally tell that it is or isn't when they really focus in on it.

Learn as many ways as possible because they are all of value to you.
 
I was wondering something about practicing scales: how important is it to practice scales in the very lowest position, the one where you'll be playing multiple notes on open strings? It seems like I rarely see pros playing in this position, but I may be mistaken. Thoughts?

It is very important to know how to play all scales in EVERY position. Once you've mastered that, play every scale ON ONE STRING (each string).
 
My dumb opinion. There are 4 or 5 or 6 opens (or 2 if you are Stig Pedersen). They do sound slightly different so in some circumstances I avoid them but usually it's not something a non-bassist would notice. A bone nut sounds different than a fret (or fingerboard). But honestly I don't avoid them. There are times in transition where it's simply more efficient to land open. So I'd play them in a scale, sure.
 
Do you "have to" know how to use open strings as part of the patterns on the bass? Of course; it's fundamental understanding of your instrument. But that said, in practice, almost the only open note I ever play is E.

Certain drone/octave parts might utilize an open string sometimes, and you can sometimes use an open string passing note to allow for a big left hand shift. But other than those reasons, or hitting the low E that is so often needed, I don't find it advantageous to use open strings on a bass guitar.

You have easier control over the character of your notes if you are fingering them, rather than playing them open. I usually play right on the frets (or just slightly behind them), use a lot of barring, and do a ton of subtle tonal and note control using my left hand (usually without even realizing it), based on small variations in where exactly I finger in relation to the fret, how hard I press, how I roll or lift or tap my fingertips to control the decay of notes, etc. Take that away by incorporating lots of open strings, and I realize how much I am doing with my left hand, without even realizing I'm doing it. The instrument starts to feel a bit clumsy to me. When I do use open strings, I find myself fingering them at the nut anyhow, to give me the same tonal and muting control I have in any other position.
 
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Good question. The use of open strings is invaluable. In my early days (which was the early 70s for me) of learning, my instructor had me using strict OFPF over the 1st four frets and open strings, playing all of the available notes of the arpeggios following the Circle of 4ths. Granted, I concentrated more or arpeggios than scales, but the desired learning objective was the same; the ability to incorporate open strings in my playing without getting lost. The use of open strings allows you to efficiently change positions and are really great to use as passing notes. I've been doing it a long time and even today, when I'm just sitting around noodling, I'll run thru that exercise. I'd like to see more open string exercises by those who teach on YT.
I use that open string trick to change positions faster too, but I don't let the note ring. I mute the string. I have a million muting techniques. I play with a pick and learned guitar first. I transferred a bunch of guitar muting to the Bass.