On the Kid A recording of Motion Picture Soundtrack, Thom played the band’s Putnam & Co. Harmonium (also known as a “pump organ). Oddly enough, the band used the exact same organ on Thinking About You:
"It’s a harmonium from West Virginia from like the 1850’s that is actually on our first album, Pablo Honey, on a track called ‘Thinking About You’, and the studio closed down, and the guy wanted to sell us the equipment, which is sort of like a passing on of this stuff, so I love the idea that it’s on our fourth and first record…” — Colin (KCRW; Oct 12, 2000).
In contrast to the portable harmoniums associated with Indian music, Radiohead’s harmonium is about the size of an upright piano and has foot pedals to operate the bellows. Those pedals and bellows are responsible for the mechanical noises on Motion Picture Soundtrack.
A photo of Jonny sitting at the Putnam & Co. Harmonium in around 2007, during the recording of In Rainbows.
For live performances in 2000 (Toronto) and 2001 (Canal+), Thom played the song on Jonny’s Hammond XB2 Digital Organ. The live sound is definitely grittier, and lacks the mechanical artifacts of the harmonium.