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I have the STM32F302R8 MCU board.l Its user manual is here.

There are two crystal oscillators on the board. X3 is missing and X1 seems to be used for the small debugger microcontroller (circled in red below):

enter image description here

In STM32CubeMX I can set external high speed oscillator as the main clock, but it seems X1 is used only for the debugger. If so, how come I can set the clock as HSE? Does that mean this X1 can be used for the main microcontroller? Is there a way to figure out this from the manual?

Clock configuration I can either select:

enter image description here

or:

enter image description here

In the above cases is LSE connected to X3 which is missing? In the second case is HSE the main system clock and connected to X1?

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The answer is in the manual on p.24.

Excerpt from the respective page:

There are two possible default configurations of the HSE pins, depending on the version of the STM32 Nucleo board hardware.

The board version MB1136 C-01 or MB1136 C-02 is mentioned on the sticker, placed on the bottom side of the PCB.

The board marking MB1136 C-01 corresponds to a board, configured as HSE not used.

The board marking MB1136 C-02 (or higher) corresponds to a board, configured to use ST-LINK MCO as the clock input.

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