anchor.diff:        return
         end
   
  -      subroutine tm_score_all(ndim,n_str,Lch,x,y,z,amat,rmsd_delta,
  +      subroutine tm_score_all(ndim,nst,n_str,Lch,x,y,z,amat,rmsd_delta,
        &                        rmsd_a)
  -c
         implicit none
  -
   c     Intent In
         integer ndim
         integer n_str ! Number of structures in use
  +      integer nst ! Max number of structures
         integer Lch ! Chain length of the structures (all same)
  -c      real x(ndim,nst),y(ndim,nst),z(ndim,nst)
  -      real, allocatable, intent(in) :: x(:,:),y(:,:), z(:,:)
  -      real, allocatable, intent(inout) :: amat(:,:)
  +      real x(ndim,nst),y(ndim,nst),z(ndim,nst)
   c     Intent Out
  -c      real amat(nst,nst)
  +      real amat(nst,nst)
         real rmsd_delta
         double precision rmsd_a
   
  
positive.code:          y1(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)
           z1(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)
        enddo
  cjmht
  cjmht Attempt to get rmsd of TM-score component
  ccc   RMSD (d<5.0)-------->
        LL=0
        do i=1,n_cut
           m=i_ali(i)             ![1,nseqA]
           r_1(1,i)=xa(iA(m))
           r_1(2,i)=ya(iA(m))
           r_1(3,i)=za(iA(m))
           r_2(1,i)=xb(iB(m))
           r_2(2,i)=yb(iB(m))
           r_2(3,i)=zb(iB(m))
           LL=LL+1
        enddo
        call u3b(w,r_1,r_2,LL,0,rms,u,t,ier)
        Rcomm=dsqrt(rms/LL)
        Lcomm=LL
  cjmht END
        TM=score_max
  
  c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  
negative.code: c        1         2         3         4         5         6         7 !
  c 345678901234567890123456789012345678901234567890123456789012345678901234567
        program cluster
        parameter(ndim=2000)      !Length
        parameter(nst=13000)      !number of used structure, maximum allowed
  c      parameter(nst=100)      !number of used structure, maximum allowed
  