It didn't help that you didn't define what a "PDB file" is. A little Googling led me to RCSB PDB Protein Data Bank. There are actually tools on that site, including a structure comparison tool. Perhaps there is information on this seemingly rich site to help? I also looked at the BioPerl site, but the only hit was a link to Wikipedia's reference for Protein Data Bank, which has a further link back to the RCSB site listing many tools to use.

You'll find help here for your specific problem, but it's not clear what your asking. Are you literally wanting the 1st three lines of the file and the last three lines of the file removed and then have a resulting file that's 6 lines shorter? If so, then you can use the head and tail utilities to remove the lines. I think you're actually asking for some processing of the data fields, though, and thus think that the RCSB site would be the best place to look