I am trying to get communication working with a arduino nano clone and purr data with Pduino. I have just moved the Pd files from the mac where it worked fine (but I had to go through a process to get the nano port visible in the system).

Can anyone tell me how to do this on linux?

Edit: In Arduino IDE under ports it says ttyS0 and ttyS4, but NOT "ttyUSB..." as I see it should in instruction videos. Can I have been installing Arduino IDE the wrong way?

On Linux, the Arduino usually appears as /dev/ttyACMx where x is 1 or greater. Sometimes it does appear like /dev/ttySOx, so I guess it's the one to open. Your best bet is to launch the IDE, set the correct board and port and upload a sketch. If all goes fine, just check on the bottom right corner of the IDE window what the port is called.
When you say you have moved the files from the mac, what do you mean exactly? What kind of files? Is it just Pd patches or binary files as well?