Unless you are in a warm climate, I don't think those bees are going to make it. I assume the tree was cut/fell down and that would have disrupted and killed some of the bees. I think you will have to leave it until early spring and hope the bees reorganize and get their hie working again.
To capture some of the bees: You want the field force of the bees to get from the tree to your hive. You will have to have a frame of brood. Put it in a hive body close to the entrance to the bees in the tree. Before this, locate all the entrances and use screen wire to fasten up all places the bees can go in and out, except one. Over that entrance, place a funnel you have made from screen wire. The hole in small end of the funnel should be 3/8 inch in diameter. This is the "bee space" the bees keep between their combs and the idea is that the bees can get out of the funnel but not find their way back in. Place the small end of the funnel in the entrance to the hive. The bees going out to work should come back to the frame with brood(and some bees in it), take care of the brood, and raise a new queen. I don't remember how long the process takes, probably a couple of weeks. Oh, when you get the frame of brood, be sure there are some freshly laid eggs for the bees to use to raise a new queen. It would be a good idea to have some drones(male bees) on the frame to mate with the new queen. after the process has had time to work, move your new hive at least 2 miles away. To move, go to the hive about dark, bring a narrow strip of screen wire, smoke any bees on the entrance to the hive to make them go in, fold the screen wire to fit in the entrance and keep the bees in, pick up the hive, move it to the new location, set it up on something decay proof, and open the entrance, go away and let the bees get adjusted. The rest of the bees are not going to make in in a log lying flat on the ground so you may as well kill them. If the bees earlier were getting along perhaps it would be best to saw the long in two and stand it upright, or saw it in two and put supports under it to get it off the ground. Over the winter, read up on beekeeping, possibly checking books out of the local library.