remarks file geomanal/distance_diff_plot.inp -- Makes a matrix of all
remarks residue centroid to residue centroid distance differences
remarks between the coordinates in the main set and in the comparison
remarks coordinate set.  The matrix can be interpreted by Mathematica. 

{===>}                                               {*Read structure file.*}
structure @../generate/generate.psf end 
 
{===>}                                                  {*Read coordinates.*}
coordinates @../xtalrefine/slowcool.pdb    
coordinates disp=comp @../generate/generate.pdb    

{===>} 
vector ident (store9) ( tag )              {*This selects all residues to  *}
                                           {*be analyzed.   Change it      *}
                                           {*to analyze portions,          *}
                                           {*e.g., ( tag and segid "A" ).  *}
                                           {*"tag" assigns one unique atom *}
                                           {*per residue (see <selection>).*}
                 
parameter
{===>}  
   @TOPPAR:parhcsdx.pro                 {*Read empirical energy parameters.*}
end

set message off echo off end                     {*This reduces the output.*}
set abort off end


{====>}
set display distance_diff_plot.matrix end         {*Filename of the matrix.*}

display  matrix={


evaluate ($count1=0)
for $id1 in id ( tag ) loop id1
   if ($count1=0) then
      display  {
   else
      display ,{
   end if
   evaluate ($count1=$count1+1)

   evaluate ($count2=0)
   for $id2 in id ( tag ) loop id2

  {*The following statement computes the distance between the mass-weighted*}
  {*centroids of the two residues.                                         *}
      pick bond 
        (byresidue ( id $id1)) (byresidue ( id $id2)) geometry
      evaluate ($distance1=$result) 
      coor swap end
      pick bond 
        (byresidue ( id $id1)) (byresidue ( id $id2)) geometry
      evaluate ($distance2=$result) 
      evaluate ($diff=$distance1-$distance2)
      coor swap end

      if ($count2=0) then
         display  $diff 
      else
         display , $diff
      end if
      evaluate ($count2=$count2+1)

   end loop id2
   display } 
end loop id1

display };


stop