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You know those orange diamonds in front of some affixes on items? Do you know what they mean? If not, hop on!
A little off-tour for an important clarification before we proceed: the explanation below is true not only for elemental affixes, but skill-related ones as well (for example "Increases Arcane orb damage by 13% (Wizard only)"). Also many, many others, but the elemental damage is among the most convenient ones for our "demonstration".
The Usual Item
Let's say we've looted a pretty common item and comparing it to our currently equipped one, the damage allegedly drops by 6.9%. What you see on the image below is exactly the thing we're exploring - the orange diamond in front of one of the affixes has a key role:
If it's orange, this means its effect is not included in the calculations you see at the bottom of the tooltip: It basically can't be automatically considered as changing the base Damage (because it's conditional - works for lightning skills only), nor does it affect the Toughness or Healing.
So here is an example of a lightning skill that we'd be using: Electrocute. As seen on the tooltip, this skill is based on Lightning damage and it deals 138% weapon damage as Lightning. This, of course, is important to keep in mind!
With our currently equipped item, our hero has 1,000,369 Damage. Through basic calculations we can see that Electrocute will be dealing 1,380,509 lightning damage (as previously mentioned, it's 138% of the weapon damage).
After the switch this is what happens to the sheet damage if we switch our currently equipped item with the newly found one: Just as expected, the base damage drops quite a lot - to 931,521. Sad, right? You guessed it - it isn't sad at all!
Electrocute does 138% weapon damage. So now it should be dealing 1,285,499 damage, but this is WITHOUT the help of our precious affix. What happens is the affix adds 12 more percent to that number and increases Electrocute's damage to 1,439,759! About 60k more than the damage this skill dealt with the previous ("stronger") item!
If you use the newly found ("worse") item for fire based skills for example, it really will be worse for your damage. This means, of course, such items are good bases for builds - if you have several Lightning enhancing items, you can do tons of damage by using one or - even better - more than one Lightning skills! And at that point you shouldn't care the tooltip shows this when compared to your old Lightning-affixless item:
So don't be rash selling, salvaging or throwing away your "worse" item - it may be way more precious than the sheet gives away!