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Is it ok that our chickens roost on the rafter of their coop instead of inside on the roost bars?

What you're calling the roosting box is the coop. Then you have a small run attached to that, and what looks like a bigger run enclosing the whole thing.

The coop layout is the issue, that's why they're not roosting in there. Looks like you modeled this after many prefab style coops that are seen online? The problem is, you modeled it after pretty bad coops.

Roosts should be well higher than nests, not 1" off the floor. Coop also has almost no natural light and no ventilation (those tiny holes are woefully insufficient, you want to aim for at least 1 sq ft per bird of vents).

If you're fine with them sleeping in the mini run, then really don't have to change anything. Do they ever go inside the coop at all? Since the coop is dead space if they're not using it, I'd really be tempted to tear out the inside walls completely and just open it up for them to use the full space inside the mini run as their coop. Nests can be reused, probably moved down a bit on that wall.
 
Not sure what the area where the chickens are intended to roost is called?
The small enclosed portion above it called the 'coop', were roosts and nests are located and predator proof for safety at night.
The lower portion with all the mesh is called the 'run', where they usually spend most the day.

Your coop looks small with no ventilation, probably why they don't want to sleep there.

ETA: oops didn't see @rosemarythyme's post before I replied.
 
What you're calling the roosting box is the coop. Then you have a small run attached to that, and what looks like a bigger run enclosing the whole thing.

The coop layout is the issue, that's why they're not roosting in there. Looks like you modeled this after many prefab style coops that are seen online? The problem is, you modeled it after pretty bad coops.

Roosts should be well higher than nests, not 1" off the floor. Coop also has almost no natural light and no ventilation (those tiny holes are woefully insufficient, you want to aim for at least 1 sq ft per bird of vents).

If you're fine with them sleeping in the mini run, then really don't have to change anything. Do they ever go inside the coop at all? Since the coop is dead space if they're not using it, I'd really be tempted to tear out the inside walls completely and just open it up for them to use the full space inside the mini run as their coop. Nests can be reused, probably moved down a bit on that wall.
Hey thanks for the info! We bought the coop on Craigs list about 3-4 years ago for cheap. Guess we got what we paid for.

The coop (including the run, the whole thing was bolted all together, including the gopher cloth) sat in our yard for all that time. Finally due to Covid time, we moved it to a fenced in area that we actually call their run; and just close it up every night. Since the whole coop and small run are mesh enclosed, I think that's a great idea to tear out that wall and bottom. Not sure when I'll get a chance to do so, but could be a future project for sure. Thanks for the suggestion!
 
Since the whole coop and small run are mesh enclosed, I think that's a great idea to tear out that wall and bottom. Not sure when I'll get a chance to do so, but could be a future project for sure. Thanks for the suggestion!

Gotcha. Well the good news is converting this into a larger coop (where you use the whole unit) generally isn't too difficult. By taking out/cutting out the interior walls, you open up a lot more space. You can run roosts across the newly open area so everyone has plenty of space to roost. If you're in a fairly hot or moderate climate, to protect from wind/rain, board up the sides of wire that are facing predominant wind directions. If you get colder spells, you can partially cover up the sides during winter weather, then uncover again when it warms back up.
 

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