To overlay two structures, and save the overlay as a single pdb file.

• start swiss pdb viewer
• open the two files to be overlain
• fit
  • iterative magic fit
  • ok
• window layer information
• window control panel
• in the layers information, click on one of the structures to activate it
• select
  • all
• pick the other structure
• select
  • all
• edit
  • create merged layer from selection
• activate the first pdb file (click on it in the layers info window)
• file
  • close layer
• activate the second pdb file
• file
  • close layer
• select the residues of the chains to then rename them using
  • edit
    • rename current layer
      place A or B or whatever in the 'rename chain of selected groups' box
• this way you can create says chains A and B, one for each structure
• after renaming
• select
  • all
• file
  • save
  • selected residues
    as your new pdb file

You will probably want to edit the pdb file from swiss pdb viewer. The program places a bunch of instructions to itself for the next time you open the file. These are not needed for the file to deliver the structure information it is designed to deliver to other programs. So, use the word pad editor (start accessories wordpad) to edit the file, and at the bottom you want to remove all the pdbviewer stuff, with each line starting with SPDBVx. Be sure to leave the 'END' line at the bottom of the file.

An example: remove the stuff in red, leaving that in black.

HETATM 979 O4 SO4 1 1 9.307 12.868 6.243 1.00 46.82
CONECT 975 976 977 978 979
SPDBVT 1.0000000000 0.0000000000 0.0000000000
SPDBVT 0.0000000000 1.0000000000 0.0000000000
...
SPDBVl 1.00 1.00 0.00 1.00 1.00 0.00 1.00 1.00 0.00 1.00 1.00 0.00
SPDBVl 1.00 1.00 0.00 1.00 1.00 0.00 1.00 1.00 0.00 1.00 1.00 0.00
SPDBVb 0.50 0.50 0.50
END

Finally, don't forget to gzip the pdb file to maximize transmission speed for your Chime page.