!This version demonstrates linked clusters and requires a version of the program with 
!high dimension values such as exbig. If this is not being used, type = at the next prompt,
!right-click the excurve icon and alter the executable to exbig.exe
pause
s tit;CuZn superoxide dismutase;q
gs tab no
!Read the Cu K-edge data
r ex 1;r51991a.ex1;1;32;cu k;;;;
!Read the Zn K-edge data
r ex 2;r52042a.ex1;1;32;zn k;;;;
!Set up the atom types
c atom1 cu*;c atom2 c;c atom3 n;c atom4 o;c atom5 zn;c atom6 cu;c atom7 zn*
!Set the search radius for residues
c maxrad 8.5
!Read the .pdb files
r par br;sod.pdb;1;2168;;;;
!This is how to set up an indepenent cluster for Zn
!r par br;sod.pdb;2;2169;;;;
!Calculate potentials
ca pot;c;n;1;c;c;n;n;n;n;
!Calculate phaseshifts
ca ph;;;;;;;;;;;;;;;;;;;;
!Sort in order of radius
sort
!Generate a second cluster centred on the Zn at 6 angstroms
gen l 2;53
!Sort again
sort
!Remove the unwanted part of the Zn cluster
c un[284-ns] 0
c ns 283
!Set some initial values of EF
c ef[1-2] -2
c emax2 450
!Set up DW factors based on model compounds
c a[1-4] .010;c a[5-14] .009;c a[15-26] .016;c a[26-250] .025
!Zn cluster model compounds
c a[252-255] .010;c a[256-265] .009;c a[266-275] .016;c a[276-ns] .025
!Define the symmetry
sym;c1;c1
c bond 2.1
dr cl 1;pause;dr cl 2;pause
!Plot the result
cp;pause
!Refine the EFs and central atom positions
ref 50;ef1;ef2;x0;y0;z0;x53;y53;z53;=
c;p;c;=
ref res 100;c;p;c;=
ref res 150;c;p;c;=
ref res 200;c;p;c;=
!Switch on MS - (slow - type = to exit)
pause
s ms un 
ref res;c;p;c;=
!Adjust DW factors
c a[1-4] .005;c a[252-255] .005
dr cl 1;pause;dr cl 2;pause
!Plot the result
cp
pause
!Create a modified .pdb file
pr par rep;
sod.pdb
