Some lathes have a set of aluminum chuck jaws. You can bore the jaws out to the size of your barrel. That way you don't mar the finish and your barrel will run true.
mooncoon, I think he wants to thread the muzzle not chamber the barrel, or I have misunderstood what you meant??
Use a four jaw chuck and a spider on the other end. You need to get the bore at the muzzle end indicated less than a thou out and the breech end as close as you can. Just grabbing it in a chuck is not the way to do it...
You can protect the barrel with pieces of brass rod as shown in this picture of chambering and threading a dialed in bore.
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Is it not a bad idea to put any type of centering tool in the muzzle?? You would be better off dialing in with a steady rest and precision ground pin in the bore. I'm just a machinist not a gunsmith so, .02 worth.. Guys with access to lathes with too long of headstocks have this same issue, so I am very interested to hear a solution also.
How in the hell do you get all that lined up in the chuck? You'd need about 4 hands to get all those little bits in the right place all at the same time. :O