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Magical dmg is when? When it's used with imbue?
So, the total damage when using imbue is weapon's magic dmg + imbue lvl dmg?
That is correct.
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How about when you are just using nukes like thunderbolt or flamewave skills that doesn't use weapons? Is damage purely dependent on lvl of the particular skill; or weapon's magic damage still come in to the equation?
The damage of the nuke is dependent on the level of the skill, the weapon's magic damage and attack rating, and (in PvP) any other factors such as an opponent's buffs, shield, etc. You can also add imbue when nuking, giving a boost in damage. The factors that determing damage are the same.