A database can be set read-only or write protected. This is possible only for Scidb databases (.sci) and PGN archives (.pgn, .pgn.gz). Scid databases (.si3, .si4), ChessBase databases (.cbh, .cbf), and Zip archives (.zip) are always write protected.
The write protection has no effects on the file permissions, it is an application specific feature. The application is remembering the last setting, as long as the database is still existing in the history.
There are the following restrictions:
Database/PGN files without writing permission cannot be set writable, without a change of the file permissions.
If the loading process of a PGN archive has been interrupted, it is not allowed to set it writable due to technical reasons.
It is not possible to set the Clipbase read-only.
PGN archives (.pgn, .pgn.gz) will always be opened read-only, unless another setting is existing in the history. These databases must be set writable explicitly, if a modification of the archive is required.
Note that a modified PGN archive has to be saved explicitly, this can take a longer time if the archive is big. Whether a PGN archive is modified can be realized because of a reddish coloring of the database icon.