ENVIRONMENTS reads an input coordinate file in PDB format and
 a secondary structure file also in PDB format and writes out
 Area Buried, Fraction Polar, Secondary Structure and the
 Environment Class for each residue.

 It will ask for the following:

 1) A coordinate file in PDB format
 2) A secondary structure file in PDB format.  The secondary
     structure can be read from the PDB file directly if its
     present in the header.  Otherwise you have to create a
     secondary structure file.  All the program cares about is
     the type of secondary structure, i.e., whether its a HELIX
     or SHEET record and the residue numbers.  Other information
     in the lines are ignored.  IT IS IMPORTANT TO DESIGNATE THE
     SECONDARY STRUCTURE OR THE ENVIRONMENT CLASSES WILL BE
     ASSIGNED INCORRECTLY.
 3)  A name for the output file.
 4) Write out all the chains (A) or just the unique one (U).  If
    U is entered, the program will determine the lengths of each
    chain and only write out one chain of a particular length. 
    ALL CHAINS ARE WRITTEN TO THE SAME FILE. AT THIS POINT YOU 
    MUST EDIT THE OUTPUT FILE TO DELETE CHAINS YOU DON'T WANT TO 
    CALCULATE A PROFILE FOR.  If you edit the environment file, 
    leave two periods '..' anywhere in the header in the line just 
    before the data. This will signal PROFILER_3D that it should 
    start reading data on the next line.  Nothing else in the 
    header matters.