You need to check the "custom" button on your 3D screen and you will then have access to the AA and AF slider bars, as well as some other custom settings at the bottom of that page. SH3 uses D3D, but you also need to set your Open GL setting for other games too after you configure your D3D settings.
AA is what eliminates the "jags" when you look at a diaginal line. The higher the AA setting, the smother the diagional line, but the heavier the load on the graphics card.
AF is what allows your to see things clearer the further they are away from you. An example are the "lines" in a sidewalk. The higher the AF, the clearer the lines will be as they get further away from you. Again the higher the AF, the heavier the load on your graphics card.
I have a ATI X800XT PE card and my settings are 1280x1024x32, 4AA & 4AF. This gives me a fantastic quality picture and I only drop below 24 FPS (the "magic" visual number) using the 16km visibility and Harbor Traffic 1.47 mods while looking back at the subpens (both of these mods are a heavy load on the graphics card), otherwise I am between 35 and 50 FPS on the open ocean.
You need to try differrent settings to see what you like best and are willing to live with in each game.
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