The Pantone system is not really a proper colour system: it has no technical basis like the Munsell system but was designed to be a visual communication system (...). It is used in the graphics, plastics, software and textile industry.

The original matching system from 1963 consisted of 500 colours, where each colour does have a three-digit reference number. During the past decades more colours could be manufactured because of improved processes, more knowledge of the chemistry, and better analysis machines (IIRC a spectrophotometer).
When adding these new colours, the palettes were arranged chromatically, with the colours falling into basic colour groupings. The newer Pantone colours that were, and still are, inserted between the existing colours, are given four-digit numbers. Two examples of those new colours are the pastel tints and metallic colours.
"In keeping with the visual nature of the system, it was felt that it was more important to keep the palette chromatically logical than to have the colors fall in strict numerical sequence." says Pantone. Logical??
Last, there are additional letters to the three digits, like C, M and U, and standing for coated, uncoated and matte coated paper. This means that the ink used is the same, but the visual interpretation of the colour is different because of the differences in type of carrier material.

It seems to me that it’s more a pretending there is a real colour system, but that the people who created this didn’t really have a clue about (the science of) colours. Apparently there are a lot of people out there who prefer to learn all those numbers by heart, instead of understanding a system.

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