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Whats the best custom screen size to use to get best quality?

Is is better to use 2x native than custom size?

Custom sizes usually result in more problems. Using things like 2x../3x/4x etc tend to work better. Custom rez could be for INSANE machines, if you wanted to do 8192x8192, but I don't think that's possible by today's standards, and you wouldn't be able to tell a difference from 5x/6x anyway. Custom is usually used for slower machines to use a "worse than native" rez. Just try different settings out, you'll find what works best. There is no one setting for all games, each is different.