Copy Protection Used on Atari ST Computers
The Atari ST floppy disk system is based on the off-the-shelf WD1772 floppy disk controller chip. This chip controls all communication between the disk drive and the computer, which limits what the ST is able to write to the floppy disk to the standards provided by this chip. These limitations are what is exploited for copy protection. The disk drives most commonly found on the ST are 3.5" single or double sided.
Missing, or Extra Sectors
Some track(s) have a different sector count than normal tracks. The software tests sector presence usually with XBIOS #8 TOS calls.
Special Sector Numbers
A special sector number is used - like $F5, $F6, or $F7, which is not possible to create on the ST, because it is instead a command to generate sync bytes or the CRC.
CopyLock - Rob Northen Computing
This protection was very prolific, used by many publishers on hundreds of titles. When the protection is called, a sector is read and the time it takes to do so is measured. This will be different on a copy vs. the original because the sector will be recorded at a different bit rate. It takes this and some other checksum information and generates a key. This "key" is returned and acted on in the protected program to varying degrees.
Earlier versions of the protection don't have the bit rate changes, but may instead contain a short or long track that is checked for length, as well as checks for exact gap length.
It is used on the Amiga, and Atari ST.
This protection revolves around having sectors on the disk that "contain" other sectors, as well as sectors that run over the index mark, which is not possible to write back with an Atari ST.
Data over the Index
The Atari reads a track from index signal to index signal. If any data is read across this boundary, it will be corrupted. Likewise, it's not possible to write data this way by normal means.