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(+1)

I tried that and it didn't look good because the movement was too exagerated (And I pretty much don't know what I'm doing since I'm not good at animating). What I did is moving one of the frames 1 pixel down compared to the rest, which looks pretty decent and makes a illusion of breathing.

is it a 3d model that you convert to a 2D animation, or something else?

(+1)

Model with 5 frames of animation. Each frame is rendered into separate image. Last frame is duplicated five times so I have 10 images total. I aplied a filter to each image and saved it (Shaders are non existant in RMXP). In the game, first five frames show at the start and after that the last 5 frames keep repeating.