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On selecting from the menus File -> Save Coordinates... you are first presented with a list of molecules which have coordinates. As well as the molecule number, there is the molecule name - very frequently the name of the file that was read in to generate the coordinates in coot initially. However, this is only a molecule name and should not be confused with the filename to which the coordinates are saved. The coordinates filename can be selected using the Select Filename... button.
If your filename ends in .cif, .mmcif or
.mmCIF then an mmCIF file will be written (not a “PDB”
file).