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.