I have recently added the function

coot.set_colour_by_ncs_chain(imol, goodsell_mode)

  • where imol is the molecule index
  • goodsell_mode is either 0 or 1

The function works as you would expect, given its name - i.e. chains that are related by NCS (or molecular symmetry) have the same colour.

Here, for example, is the 5iv5 assembly (from T4 bacteriophage)

5iv5 assembly top

5iv5 assembly bottom

(I also turned on the outline mode):

I think that there’s a bug in the assembly that I got from the RCSB (for whatever that’s worth) - you might be able to tell from the occassional overlapping chain colours.