I accidentally connected the wrong pin (GPIO21) as RTS to uart to MAX3485 IC on my PCB. Is it possible to control this pin via software for half duplex data flow for RS485? It only needs to read modbus registers at a low baud rate(9600).

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I don't see any reason why not, e.g. this hat can be configured to use GPIO4, as shown in the schematic.

My primary concern would be that your MAX3485 is powered from the 3.3V rail, as per that schematic, so it is interoperable with the Pi's 3.3V logic.

And I am curious what pin you intended to use - what is the correct pin?.

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