load pdb1.xyz
Xt(:,1) = pdb1(:,2)
Xt(:,2) = pdb1(:,3)
Xt(:,3) = pdb1(:,4)



load alpha.txt

STAEND = zeros(size(alpha,1)*2,3);
leng(size(alpha,1)) = 0 ;
alpha

for i=1:size(alpha,1)

      % Load the Helix
      X = [0,0,0];
      for j=alpha(i,1):alpha(i,2)
     X(j-alpha(i,1)+1,:) = Xt(j,:);
      end

      [a,b,t,epsilon] = line_fit(X);
      STAEND(2*i-1,:) = a + b*t(1) ;  
      STAEND(2*i,:) = a + b*t(size(X,1));  
      leng(i) = epsilon;  
end

save low_p_alpha_pos.txt STAEND -ascii
save low_p_alpha_r.txt leng -ascii