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I have two transceivers, one for CAN and one for RS485, and both are isolated. Both standards require 3 wires (two differential pairs and one common GND). I am trying to use one termination connector and depending on which standard I am going to use (CAN or RS485) only one bus is going to be connected to termination connector pins, and question is: - Is it good to use jumpers for choosing which differential pair is going to connector and if not, what is solution for that?

EDIT: Could I use ferrit beads (that are anyhow included on lines) and make assembly variant for placing beads on line I would like to use?

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If I had to design a product that needed to be able to connect to either CAN or RS-485, I'd probably start by considering separate connectors or separate pins on the same connector for the two busses. The ground pin can be common if on the same connector.

Jumpers can be made to work, but users don't always set them right, especially if multiple jumpers need to be set a particular way, which is probably the case between RS-485 and CAN. Jumpers will also likely be more expensive and take more space than a connector with two extra pins.

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How hard are you "pushing" the bus? For a relatively short, lowish speed bus, you could probably connect them in parallel and use PHY chips with an output enable function and disable the device you are not using in software...

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If using assembly variants is an option, why not de populate the entire transceiver circuitry? Different connectors are a good idea to provide a quick visual check and potentially the inability to connect to the wrong bus, but you can get visually different connectors with the same footprint so you only need one position. You can use a pull down on the cpu side which is populated or not depending on the transceiver so software knows which protocol to use.

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