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I just recently bought a new Mobo (MSI H97 PC Mate) because my old one went dead. So I installed it and was confronted with kind of a strange problem. When trying to install the backplate of the cooler, it would not only touch some metal pins (the things that stand out at the back from the mainboard) but be right on top of one (or at least I think so).

I never heard of that kind of a problem, and it seems strange, that MSI would design a Mainboard where you can't install a backplate from a CPU-Cooler, because it would damage the mainboard (or would it?!). 
I am confused on what to do right now, because atm I am using the Intel Stock-Cooler, but it feels strange to have a pretty decent cooler (Scythe Mugen 4) laying around but not beeing able to use it.

 

I am not quite certain, whether it would really touch it, but I was so scarred when trying to install it, so I didn't even bother trying.

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https://linustechtips.com/topic/788799-problem-with-cooler-backplate/
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You should try installing the backplate to see if the metal pins really touch it. If they do, you could just wrap the backplate in electrical tape. Just make sure that the backplate wouldn't introduce too much force on those pins, since that could damage the tape.

 

I also managed to find a post on an MSI forum that has listed this board and cooler combo, so it looks like someone is using it without problems.

My heart belongs to AMD but that doesn't mean I furiously hate Intel or NVIDIA :)

 

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