Can I conjugate the copula です、だ instead of the adjective when I want to describe something?
ex: Conjugate “this pen is long” to “this pen is not long”
copula conjugation: このペンは長いです。to このペンは長いではない。
adjective conjugation: このペンは長いです。to このペンは長くないです。
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With i-adjectives you HAVE to conjugate the adjective, so your second example is the right way.
Na-adjectives you treat as nouns most of the time, and conjugate the です.
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To say what OP wants to say (“not long”), the answer is of course the second one as you said. But there are also tag questions. 
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Interesting! Thanks, Sean!
I do feel like if your early enough in your studies, sometimes extra info like that might only confuse you.
The adjective conjugation rule is very solid, and I would advice the OP to treat the じゃん/しゃない mentioned in the article as a sentence ender particle, so as not get them mixed up in your conjugations. If you look closely at the example sentences, you can see that the adjectives get conjugated in all different ways, before the tag question.
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I completely agree. It’s definitely a good idea to treat them as different things.
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Also, don’t forget that you don’t use だ with い-adjectives.
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Right, you make it colloquial by just omitting the copula altogether.
Mind you, when you’re talking pre-nominal adjectives, that’s different. There’s a slight change in meaning when you conjugate a pre-nominal adjective.
これは長かったペンです = This was a long pen (but it’s not long any more… because someone broke it?)
これは長いペンでした = This was a long pen (but it’s not a pen any more… because it’s turned into stone?)
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In my opinion, I find it weird that い adjectives just get tagged with です for the polite form. In Japanese, い adjectives, like verbs, are complete predicates, while nouns (and な adjectives, which are kind of like nouns) require the copula to form a predicate.
From a linguistic point of view it is weird to attach two predicates one after another, and it is something that works only for adjectives. It’s an exception, the です here is not really the copula and can’t be conjugated, it’s just added to make the adjective sound polite.
It’s also a pretty modern addition to the language. In older Japanese the polite form was formed by conjugating the adjective to an adverb and then adding ございます, which is the polite version of ある. You can still see this conjugation in set phrases that have remained fixed since a long time ago.
Example:
早い becomes お早うございます (御 is a honorific prefix)
めでたい becomes おめでとうございます
ありがたい becomes ありがとうございます
Your example, 長い would conjugate as 長うございます
This way of conjugating the adjective into an adverb is not a feature of the Edo dialect that later became what we now know as standard Japanese, but rather of the Kyoto dialect that was the prestige dialect when the capital was in Kyoto (and other western Japan dialects have this feature).
In modern standard Japanese, this same conjugation would look like 長くあります, but you’ll very probably never see or hear it like this. In the negative it is more common though, and when speaking formally you can often hear 長くありません instead of 長くないです.
TLDR: Using です to make adjectives polite is an exception, and it’s not the copula です, which means you don’t conjugate the です itself, but rather the adjective,
If you want to learn more about the honorifics part I rambled about before, you can find some info here. OMG this turned into a wall of text. Sorry, I tend to ramble on topics I find interesting.
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I kinda always thought of です as just a pure politeness marker and not as being the copula at all, and it’s just that だ gets omitted when using it.
It’s the only thing that made things like the below make any sense to me:
ええとですね、
これはですね、
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Yeah, those situations give the same vibes, it sounds more polite so it’s just tagged on there ¯\(ツ)/¯
です is a copula. But it also has the non-copula role of just being polite in some circumstances.
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I’ve just stumbled across an article on imabi that deals with exactly this topic, if anyone wants to read more about it: https://www.imabi.net/adjectivedesu.htm
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