You can do it programatically by using Biojava (from version 4). See for instance the tutorial or the demo.

You will be able to do it with either PDB or mmCIF files as input. Thus it will work for even very large molecules. Note that since December 2014 the PDB has transitioned to mmCIF as the main format for data distribution. Legacy programs like NACCESS or AREAIMOL won't be able to read mmCIF files.