PROFILER_3D reads the output file of the program ENVIRONMENTS and a
 3D-1D scoring table and creates a profile.

 It will ask for the following:

 1) The ENVIRONMENTS output file
 
 2) A file containing the 3D-1D scoring table
 
 3) A gap penalty multiplier for the coil regions.  This number is placed
     in the last two columns of the profile in the non-secondary structure
     regions.  The secondary structure regions get a value of 100.  What
     does this mean?  In PROFILESEARCH, you will enter a gap opening and
     a gap extension penalty.  These will be modified for each position
     according to the penalty multiplier for that position. So the
     actually gap penalty for position i = GapPen x M(i)/100, where M(i)
     is the gap penalty multiplier from the profile at position i and   
     GapPen is the gap penalty entered in PROFILESEARCH.  So, if the value
     of the multiplier is 100 (the usual situation) then the gap penalty
     at the position will be the gap penalty you enter in PROFILESEARCH.
     If the multiplier is 10, the the gap penalty for the position will
     be 1/10 the value entered in PROFILESEARCH. Since gaps appear to
     occur more frequently in coil regions, you might want to lower the
     multiplier for those areas.  I would try keeping it at 100 for
     starters.  Like gap penalties, its an empirical thing.  Play games.
 
 4) A file name for the output profile.