!Set the title for output
s tit;Fe(dmpp)\3\;q
gs tab no
!Set up an empty site - as the ligand is bidentate, this
!will be used for the pivotal atom
site e;c;0;=
!Read the Fe K-edge data
r ex;r41799.exb;1;32;Fe k;;;
!Set emergy limits to the range where background subtraction is adequate
c emin 19.8;c emax 590
!Read in crystallographic parameters
r par br;fedmpp1;1;1
!Remove the hydrogen atoms and sort in order of distance
sort del H
c atom6 0
!Draw the original structure
dr
!Remove furthest atoms
c ns 31
!Check the orientation of 'rotation axis' using the 3rd shell N atoms
!(the molecule has approximate C3 symmetry)
plane;23;24;25;0;0;1
!The axis is almost exactly parallel to z - no need to rotate it
!Divide the cluster into 3 units, + one odd atom
!(necessary because the .pdb file defined everything as one residue)
c un[1-ns] 0
c un[1,4,7,9,13,16,20,23,26,29] 1
c un[2,6,8,11,14,17,21,24,27,30] 2
c un[3,5,10,12,15,18,22,25,28,31] 3
!Put the single O atom on the z-axis
c th19 0
!Remove units 1 and 3, increase the occupation number for unit 2
c uoc[1,3] 0
c uoc2 3
!Remove empty shells
sort del
!Create the pivotal atom between atoms 1 and 2
c ns ns+1
c x[ns] .5*x1+.5*x2
c y[ns] .5*y1+.5*y2
c z[ns] .5*z1+.5*z2
!Ensure the occupation number and unit are the same as the other atoms
!The occupation number should be changed first
c n[ns] 3;c un[ns] 2
!Rename unit 2 as unit 1
c un[1-6,8-ns] 1
!Define the extra shell as the pivotal atom for unit 1
c piv1 ns
!Define the symmetry
sym c3
!Draw the symmetrised structure on top of the original
dr noc
!Define the atom type for the extra atom
c t[ns] e
!Calculate the potentials
ca pot;C;O;1;FE;C;;;
!Use the constant interstitial potential option
s con v
ca pot;C;O;1;FE;C;;;
!Calculate the phaseshifts
!The core-hole lifetime is adjusted, so the amplitude is correct
!For AFAC=1
c cw .5
ca ph;;;;;;;;;;;;;;;;;;;
!Set up rules for DW factors - makes refinements easier
rule a2;a1
rule a4;a3
rule a6;a5
rule a9;a8
rule a10;a8
rule a11;a8
!Set DW factor limits
c dwmin .003;c dwmax .025
!Set starting value for EF
c ef -2
!Refine EF and A values without MS
ref ef+a
c;c;=
!Set up MS parameters
c atmax 5;c omax 5;c plmax 12
s ms units
!Re-refine As (slow at first)
ref a;c;c;=
!Constrained refinement
s cor on
!Reduce MS using filter
!c ef ef
fit
c minmag .005
!Refine the pivotal atom distance (slow)
ref 150;r12;=;c;c;
!Refine the DW factors
ref a;c;c;=
!That made no difference at all !
!Turn off constrained refinement
s cor of
!Uncomment code below for demonstartion of restrained refinement
!( really slow and pointless and pointless in this case)
pause
!c wd .5;c wex .5
!c d:
!c w: -5
!1;1.5
!c w: -2
!1.5;2.3
!fit
!ref x+y+z
!c;c;
!ref a;c;c;=
!Remove filters and re-refine DW factors
c minmag 0
ref a;c;p;c;=
