Great advice on the witness point.
My first bass was a 5 string and I've played them almost exclusively for years. I went through several different types of strings and several basses before I finally figured out what was causing that "woofiness" of the B string.
It's not the bass. It's not the scale length. In most cases it's not the string (but some B strings sound better than others). It was my installation technique.
When you put on a string and you seat the ball end in the bridge and start cranking the tuner to get the two to three wraps around the post like we've all been taught...you end up twisting the string. Think about it like wringing out a wash cloth. If you hold that cloth by the corners and pull it tight, it still flops around a good bit....just like you want your string to do. But twist it up and it becomes rock hard...almost feels solid. Doesn't move very well. Same applies for your strings.
The smaller strings aren't effected as much (although they are effected), but take a big .130 or .135 guage string and twist it, and that sucker will vibrate in some funny ways. That is what is producing the "woof" tone. That muffled, dark, dim sound.
So how do you fix it? EASY!
After you seat the ball end in the bridge, measure, and cut your string....Put the cut end of the string into the tuner and give it one wrap around by hand. Then pull the ball end back out as far as you can. Start winding your string. You will see the ball end turning as the string wraps around the tuning post. This force would be twisting your string if the ball end wasn't free to move. Once you get close to the end, you can seat the ball end and tune the string to pitch.
Next...the witness point. You need to rough in the intonation before you set your witness point as you don't want multiple witness points. Get the intonation spot on, then press the string down at the bridge to set the witness point. Don't get goofy with it. Just make sure there is a nice break over and the string isn't "humped up" going over the bridge.
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Check your intonation...guess what...it's way out now huh? Intonate again.
Lastly, check your pickup height. Due to the way our ears work with our brain, we perceive louder sounds to be "better". This leads people to raise their pickups higher than optimal and the magnets can effect the vibration of the string. The larger the string, the more metal for the magnet to pull on. Larger strings also vibrate in a bigger arc than smaller ones making them pass closer to the magnet. So lowering your pickup under the B string will give me better tone and you can adjust for the volume change with EQ. Keep in mind that really low notes (under 40hz or so) are difficult for speaker cabinets and rooms to reproduce. So you may be producing the note, but the speaker and room can't...which means you think the note is weaker. You can find out if this is the case by simply watching your speaker or laying your hand on it. If you can see the cone moving when you play that open B string and you feel the cabinet vibrate...but you don't hear it as loud as other notes...then it's a matter of acoustics...not your bass.
Hope this helps someone.