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Active bass, recording, and tone ideas

Bass I'm using is an Ibanez sr506 running into an set Silverado special. On the guitar I have the bass boosted slightly, tremble is at center, and pick ups blended 60-40 to the front.

From the amp it sounds really nice, smooth and full tone. I am running a direct out to the my sound board for PA and recording, using cubase for software. When we record as group sounds good on playback but when the bass is soloed out it sounds nothing like it does through the amp. Sounds choppy, thin and flat with a slight popping sound coming from the plucks. The direct signal from amp should be post eq on the amp and the gate on the board is turned off it 25% compression. The popping sound I think is coming from to much gain, but sure why the tone sounds like that or why its choppy.

Any tips?
 
The clipping was really bad when I was blending the pick ups 90-10 on the front, but again it wasn't coming out of the amp. So I adjusted my equipment to sound somewhat equivalent using more of the bridge pick up and it definitely helped but still in there occasionally. That's why I'm thinking its from to much gain if the direct out is post eq. Still looking into that. Won't know that until tuesday.

Is it common practice that you record using a direct line as well as a mic'd amp and over lap them?
 
The first time a bass player hear his bass recorded alone it always make him feels surprised.
The DI sounds it's always the best HiFi tone you can get from your bass and usually in Studio is the preferred one because let the engineer edit it.
Anyway there are several factors that made our bass tone:
- bass electronics and wood
- strings kind and action
- your touch dynamics
- recording ways
Nowdays recording yourself is the best way to find out what kind of tone your actually produce and how you can work to reach the tone you have in mind.
Strictly talking to recording the first thing any bassist have to understand is, how handle your touch, when you record in ensemble using amp as monitor usually the touch is always heavier, this will produce more noise if you will hear the bass alone BUT sometime alone tone are horrible but in the mix works perfectly.
Bass woods always influence the tone in my opinion fingerboard woods more than anything else, rosewood middle warm tone with some highs, maple bright punchy, ebony like maple but less bright.
Electronics, more you will mess with bass onboard preamps, more the engineer will work, average on-preamps are boomy, not very clean and precise, for this reason studio musicians always have a good roster of passive fenders or active basses with great onpreamp or bass that sounds great with passive mode selected.
Strings, when you record are probably the best resources for your tone, always preferable have new ones, you can always get a great warm dark tone from a bright tone, you can't do the inversion from dead strings.
Action is very important too, what kind of tone you like, warm and dark or bright and growly? Depending of that the first will produced by high action the second from low action.
And finally the recording "device" usually the DI is the best method because give the most precise tone you can get from your bass and your playing. Any particular is detailed.
It's also popular to dub the DI with mic to give a bit of warm and cab color to the DI tone. Some times I also recorded using a mic on my fretboard, like acoustic player, any scenario is different but the DI is the most common.
I hope I gave you some helpful infos, if you like more please check my YouTube channel, you will find several additional informations.
Cheers.