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If it's possible, you should shoot under the ship's chimneys or at the hull on water level. Usually, citadel is located between the first and the last turret of the main artillery, more or less starting from the water level to the half altitude of the hull. Citadel is the part of the ship in which the vital rooms are located, such as machine room. If you have high penetration and enemy is positioned side towards you, you should try to hit the so-called citadel. If you use small caliber cannons, then aim similarly to as with HE ammunition, at the front and the back of enemy ship. When shooting with armor piercing ammunition, you should aim only at ship's hull, preferably at water level. You won't deal large damage, but there is a large change to damage some important module or set the ship on fire. A good idea in case of HE ammunition is also shooting at the cannons, quarterdecks and chimneys. The armor is rather thin in that spot, you should deal large damage. High explosive ammunition should be aimed at the bow and the stern of the ship, more or less up to the place where the first main artillery turret is located. Once you learn how to hit enemy ship, you should focus on its specific parts. Image source: Official website of the game. Successive hit at citadel will deal maximum damage.
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From my own experience I might add that you should aim high-explosive bullets slightly above enemy ship and at water line or slightly above it in case of armor piercing ammunition. There is no better shooting training than that. It allows you to send few dozens of bullets in one minute. Luis cruiser is a very good idea, it has large amount of fast reloading cannons. You must simply train a lot until you're able to instinctively approximate where you should send the bullets. Sadly, there is no universal rule for aiming at long distance. If yes, then you can unleash the whole salvo. It is wise to shoot first from one cannon and check if you have aimed properly. Your bullet may fly for even few seconds. After switching to sniper mode (shift key by default) you must aim some distance in front of the ship itself. In case of aiming, the most important thing you must consider is distance between you and your enemy and how fast the enemy is moving. You must consider the direction in which enemy ship is sailing, its speed, and even type, which will tell you a lot about probable enemy behavior. Such attempt will work on close distance, but if enemy ship is 15 km away from you and the bullet is flying for eight seconds, you must think greatly ahead. It might seem trivial, all one need to do is aim at enemy ship silhouette and pull the trigger.
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To deal some damage to your enemy, you must hit him.
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