[ericshliao]

Based on my understanding, pdb format is open format with many sub-variations. So, many readers use pdb format with their own private-defined data field.
There is no open pdb encryption format. Although it's possible to encrypt pdb file, but, such pdb files are only readable by certain readers. Well, the reasoning must be reversed, you must choose a reader which is capable of reading encrypted pdb files, and you must create pdb files with the corresponding creator software. iSilo is a good example. Pdb files encrypted by iSilo creator can only be read by iSilo reader.
If you want to encrypt pdb file, you must make sure that the chosen reader is capable of decrypting the file. If the reader does not support reading encrypted pdb files, then of course you can't create encrypted pdb files which is readable on that reader.