Well I'm still getting used to doing max damage in trait, at least in the corner, but usually mid screen your objective once you've gotten a hit is to corner carry and get out of trait safely. You can switch sides mid combo by doing a 1 in midair while juggling in order to make corner carry easier. If you watch Grr at Winter Brawl you'll see him do this a far few times as Atom, I think it also might increase the damage a wee bit.
I think Raptor's video on Atom trait combo's is still the highest damage in the corner IIRC but it was confusing af for me and I was lazy to learn it. I think it involved using 1 as a hit since 12 hits faster than 22, so you can get more hits I think? Idk he had a video on it if you were set to learn it. Also try and leave trait while the opponent is still in the air so they can't punish you with a wakeup.
Just wanted to add a bit more. Atom’s trait hits in different directions depending on the distance the Atom is from the opponent. If he is at a long distance away (ie at starting screen distance) then trait is a great tool for corner carry in which he consistently travels in one direction. However, if you begin your trait combo right next to your opponent, you will go through the opponent and the second hit will return you to your original position assuming you’re doing the 22 combo.
On hit, I find it helpful to count in pairs of hits starting from his first grounded 2. I usually only use the 22 combo and don’t care too much about the side-switching since I suck at execution. For example, if I start a trait combo at the starting screen (ie trait on the GROUND and into 22...) I will count the reps of 22s that I can do. Usually it’s 6 reps, so 12 hits (hence my button presses will be 22, 22, 22, 22, 22, 22~4) Of course, doing all 6 reps is not good for Atom. However, the general plan is to count your hits. It’s good to just experiment in training mode to see how the starting distance of your combos affect the gravity, usually I end it at 4-5 reps so I know I can cancel out of trait somewhat safely. Even if Atom get his first hit in the air, I still like to count my reps from the first GROUNDED 2 I do, just for consistency, though you’ll have to adjust according to the gravity how many reps you are doing. Balance between damage output and safety and ease of execution.
Now for how to end his trait combos. Midscreen usually I just end in grounded 2, you’re safe but you can’t recover fast enough to do anything for oki, especially if your opponent has a wake up that is fast and covers a long distance. However, if you see that your opponent is in the corner, always trade the last rep of 22 into 13, this gives more damage and a HKD in which you can actually do MBf3 to destroy some wakeups, which of course leads to your setups in the corner. Alternatively, you can do 1223 as a corner ender for the same effect. However, if you happen to move into the corner early in your trait combo, it is good to change the 22 reps into 11 reps. However, be careful since the timing is different and you can do less reps for 11 than you can for 22. The most you can do is (assuming you’re right next to the opponent in the corner) 11, 11, 11, 11, 13~4. The payoff is greatly increased damage. Trait combos are a valuable source of damage especially in the corner. Raptor posted a video with Atom doing up to 600 damage using chemicals and trait. Even with a simplified version, off a MBf3 I can hit past 400 on Superman (MBf3, 3~4, 11, 11, 13~4). His trait is also his main source of damage anywhere on the screen, so it is up to the player to decide how he/she should invest trait in different aspects of gameplay (punishing pressure, damage, anti-zoning, etc)
Hope this helps
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