so the way the sequence colours work in the SequenceGraph is as follows:
Anything that is already assigned is green, unassigned is black.
When you then select a connected NmrChain from the drop-down menu, the program will try to match it to the sequence. The sequence will turn orange for an unassigned stretch (this would be a good match) or red for an assigned stretch (this is a match in terms of Chemical Shifts, but obviously won’t currently work, as it’s already assigned).
This means that as soon as you assign something, it will turn red - because the current chain is being matched to an assigned stretch. I have to say that I have always found this slightly unintuitive, but the above scheme does have a certain logic to it. As yet, I haven’t really thought of a better, more intuitive/logical system (though neither I nor others on the team have given it a huge amount of thought - the above colour scheme was inherited from others).
So if you would like to suggest a better system, then please do let us know and we might well change it!
(I’m also aware that the whole green/red thing is of no use to colour blind people - so this really does need an overhaul.)