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I came across the following sentence in an exercise, with the following propositions:

森さんが飼っている魚は、とてもきれいな色_____している。

A. に

B. を

C. で

D. が

I learnt that する is used with が when talking about something that has an effect on senses, like "大変な音がする" or "いい匂いがする". So I picked D, but the solution was B.

What did I understand wrong? In what respective cases are "~をする" and "~がする" appropriate and correct?

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To answer your question, only をしている is correct and がしている is wrong in this example.

Actually, those two are confusingly similar but unrelated. What the verb する means in the two idioms are different things.

  • する → to strike the (i.e. your) sensation
  • する → to wear some (persistent) traits

がする is to describe an ephemeral sense (stimulus) that can appear and disappear. For example, there is no sound when you hear nothing, and no odor when you smell nothing, because those sensations are direct interaction between your organ and the medium. Usually you can understand Xがする as "I sense X".

誰もいない部屋から物音がした I heard something from an empty room
とてつもなく悪い予感がする I have (= get) an extraordinarily bad feeling

However, we don't perceive colors likewise. Although today we know that everything is quantum, most people still take it for granted that a red apple never ceases to be red if you look aside. In other words, we believe that the redness belongs to the apple, not to the light (unless it's a laser ray) in the usual sense. That makes がする unusable in that sentence. But if you had some eye disease and saw a red color for no reason, 赤い色がする would make sense.

Some previous answers tell that をする is for visual stimuli, but this is somewhat superficial. We do say:

優しい性格をした人 a person who has a gentle personality
彼女は高い声をしている she has a high voice
どんな育ち方をしたらこんな絵が描けるのか what kind of life makes (= experiencing what life history) him/her create such a drawing

Of course, 彼女は高い声をしている doesn't mean she emits a high frequency wave 24 hours, but that she does when she speaks. 高い声がしている means that you hear a voice persisting as long as it may.

One grammar point is that, since をする depicts a sort of state rather than action, the dictionary form is virtually unusable. You should always say をしている and をしていた as the main verb of the sentence.


PS
By the way I don't think the original quiz is very well thought out. You can easily find a context where A is valid, and if you stretch your imagination, D actually might be.

A: ~とてもきれいな色している
→ Mori-san makes their fish have a beautiful color (painted?)

D: ~とてもきれいな色している
→ maybe some alien fish that shines (emits light) like a mirror ball?

  • That definitely helps in "feeling" the difference between がする and をする. So, to sum it up, をする describes a trait, that is inherent (or at least persistent) to the subject, while がする describes a temporary phenomenon that impacts the sense, correct? To take it even further, could we say something like 彼女はいつも素晴しい匂いをしている to describe a girl's natural fragrance? – Right leg Jul 22 at 14:03
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    @Rightleg When I hear that, I feel nothing wrong but I'm not sure what your Japanese teacher thinks. I'd just wonder whether you're talking about her perfume or the natural one. We don't deem the body odor an identifying property of people in our culture, but it may sound more natural in some, say... Medieval Europe context or so. – broccoli forest Jul 22 at 14:21
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    @Rightleg By "identifying property" I wanted to say that we don't usually use the smell like wolves that "I smell strangers dropped by here recently". Of course if you like the girl you'll remember her specific fragrance, but not for everyone, unlike how you remember them if someone has blue eyes or red hair. The naturalness will get discounted for that reason IMO. – broccoli forest Jul 22 at 14:36

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