anchor.diff:        close(4)
   c^^^^^^^^^^^^^^^^^^^^^^^^ n_str_all done ^^^^^^^^^^^^^^^^^^^^^^^^
   
  -cjmht we can now allocate the arrays
  -      allocate(x(Lch,n_str_all))
  -      allocate(y(Lch,n_str_all))
  -      allocate(z(Lch,n_str_all))
  -      allocate(amat(n_str_all,n_str_all))
  -      
   cccccccccccc read native structure cccccccccccccccccccc
         i=0
    11   read(3,1239,end=5)tx,ii,tx,tx,ii,tx,a1,a2,a3
  
positive.code:       
  cjmht Calculate the amat with the all-by-all scores
        if (n_para.eq.-2) then
            call tm_score_all(ndim,n_str,Lch,x,y,z,amat,rmsd_delta,
       &                      rmsd_a)
        elseif (n_para.eq.-3) then
            call read_score_matrix(nst,n_str,amat,rmsd_delta, rmsd_a)
        else
            call rmsd_score_all(ndim,w,n_str,Lch,x,y,z,amat,
       &                        rmsd_delta,rmsd_a)
        endif
  
  
negative.code: c       -2: no result obtained because of negative weights w
  c           or all weights equal to zero.
  cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
        subroutine rmsd_score_all(ndim,nst,w,n_str,Lch,x,y,z,amat,
       &                          rmsd_delta,rmsd_a)
        implicit none
  c     Intent In
        integer ndim,nst ! dimenson of arrays
        integer n_str,Lch
        double precision w(ndim)
        real x(ndim,nst),y(ndim,nst),z(ndim,nst)
  c     Intent Out
        real amat(nst,nst)
        real rmsd_delta
        double precision rmsd_a
  c     Local variables
  