Tire not sitting properly after changing spokes

Let out the air. Then unscrew the valve stem nut almost up to the top of the valve. You can leave it off as they have no other function as to keep the valve from 'disappearing' into the tyre while installing a tyre. It won't happen anyway with such a long valve!

Then pinch the tyre between thumb and index at the bead from both sides while pushing the valve into the tyre with your other hand. The bead should drop down into the rim. Without (!) tightening the nut on the valve-stem, attach your pump and refill your tyre to low pressure. Take off the chuck of the pump, bounce the wheel several times and check if the bead is properly seated. If not, repeat the operation. Pump to required pressure if it is OK.