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.