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Here was the query.
What is the easiest way, these days, to calculate the buried surface area
between two subunits of a protein?
Here are the software and links received (thank you all):
1. 4+ votes for PISA  - This following website is great and does a very nice job
of analyzing protein interfaces (including, but not
limited to, buried surface area calculations):
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
FYI. the next website can also yield useful info
to figure out if an interface is physiologically
relevant or not (less detailed output though):
http://www.ebi.ac.uk/thornton-srv/databases/pita/
2. surface ( http://www.ccp4.ac.uk/dist/html/surface.html ). 
 
3. Two or three votes for areaimol in CCP4 works well - but beware that for cases we have worked on the default value for point density needs to be increased to get accurate values.
With the subunits A and B and their surfaces surf(A) and surf(B) the equation should hold:
surf(A) + surf(B) = surf(A+B) +2x
where x is the surface between them. So if you calculate the surfaces of each subunit separately and of the complex that yields x.
4. NACCESS  http://wolf.bms.umist.ac.uk/naccess/
 
5.  CCP4mg will do this - and show you graphically..
http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/analysis.html#sas

6.  see the discussion and references in:
http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=84
7.  Chimera.
http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-December/001131.html

Thanks again.
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Gloria Borgstahl                                            
Eppley Institute for Cancer Research and Allied Diseases
987696 Nebraska Medical Center   
10732A Lied Transplant Center               
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Associate Professor                
Interests:  Cancer, Biochemistry, DNA Metabolism,  Protein Crystallography, 
Modulated Crystals,  Crystal Perfection, X-ray Topography,
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