The FFT software tries to limit the volume to the asymmetric unit for the spacegroup. This has to be a 3-D box, so cubic spacegroups give more peaks than expected, but not a full list of 1260 .. However there may not be a complete list - these S are in di-sulphide bonds, and at limited resoluton you would not expect all the patterson peaks to be discrete.
You could use the program vectors to generate a list of Patterson peaks from your S coordinates, then display those in coot on the Patterson map to see how well it predicts the sites. Eleanor On 25 January 2013 07:07, Wei Feng <ccp4...@hotmail.com> wrote: > Dear all, > I have a Zn-free insulin crystal and there are 3 *disulfide bonds* in > one asymmetry unit.* > * > ATOM 43 SG CYS A 6 20.112 40.351 32.363 1.00 > 16.55 S > ATOM 49 SG CYS A 7 24.024 47.785 30.285 1.00 > 22.23 S > ATOM 76 SG CYS A 11 21.504 38.985 32.424 1.00 > 17.77 S > ATOM 167 SG CYS A 20 16.482 31.957 26.203 1.00 > 15.38 S > ATOM 240 SG CYS B 7 25.993 46.755 30.463 1.00 > 18.58 S > ATOM 336 SG CYS B 19 17.764 32.878 25.093 1.00 > 15.26 S* > > *The space group of the crystal is < I213>. > As we konw, there are 12 symmetry operations of the space group I213, so > there will be > 3*12=36 disulfide bond in the unit cell. > And the number of the patterson peaks of these disulfide bond should be > 36*(36-1)=1260 > But when we use FFT to calculate the patterson peaks of it, only 9 peaks > （Peak height >6.0）are found. > > *ATOM 6 OW WAT X 1 37.672 6.512 20.437 9.13 > 9.13 O > ATOM 6 OW WAT X 2 20.437 37.672 6.512 9.13 > 9.13 O > ATOM 6 OW WAT X 3 6.512 20.437 37.672 9.13 > 9.13 O > ATOM 13 OW WAT X 4 31.906 26.078 16.823 7.99 > 7.99 O > ATOM 13 OW WAT X 5 16.823 31.906 26.078 7.99 > 7.99 O > ATOM 13 OW WAT X 6 26.078 16.823 31.906 7.99 > 7.99 O > ATOM 7 OW WAT X 7 24.775 30.019 8.741 6.74 > 6.74 O > ATOM 7 OW WAT X 8 30.019 8.741 24.775 6.74 > 6.74 O > ATOM 7 OW WAT X 9 8.742 24.775 30.019 6.74 > 6.74 O > *ATOM 8 OW WAT X 10 25.060 34.755 10.969 4.24 > 4.24 O > ATOM 8 OW WAT X 11 34.755 10.969 25.060 4.24 > 4.24 O > ATOM 8 OW WAT X 12 10.969 25.060 34.755 4.24 > 4.24 O > ATOM 10 OW WAT X 13 38.803 11.242 19.278 4.04 > 4.04 O > ATOM 10 OW WAT X 14 11.243 19.278 38.803 4.04 > 4.04 O > ATOM 10 OW WAT X 15 27.561 19.278 38.803 4.04 > 4.04 O > ATOM 10 OW WAT X 16 38.803 27.561 19.278 4.04 > 4.04 O > ATOM 19 OW WAT X 17 31.656 29.083 22.684 3.83 > 3.83 O > ATOM 19 OW WAT X 18 22.684 31.656 29.083 3.83 > 3.83 O > ATOM 19 OW WAT X 19 29.083 22.684 31.656 3.83 > 3.83 O > ATOM 17 OW WAT X 20 29.945 29.101 21.650 3.59 > 3.59 O > ATOM 17 OW WAT X 21 21.650 29.945 29.101 3.59 > 3.59 O > ATOM 17 OW WAT X 22 29.101 21.650 29.945 3.59 > 3.59 O > ATOM 1 OW WAT X 23 19.402 13.112 0.000 3.53 > 3.53 O > ATOM 24 OW WAT X 24 34.640 34.640 34.640 3.50 > 3.50 O > ATOM 21 OW WAT X 25 31.626 23.245 37.418 3.37 > 3.37 O > ATOM 21 OW WAT X 26 37.418 31.626 23.245 3.37 > 3.37 O > ATOM 21 OW WAT X 27 23.245 37.418 31.626 3.37 > 3.37 O > ATOM 20 OW WAT X 28 23.826 29.990 26.590 3.35 > 3.35 O > ATOM 20 OW WAT X 29 26.590 23.826 29.990 3.35 > 3.35 O > ATOM 20 OW WAT X 30 29.990 26.590 23.826 3.35 > 3.35 O > ATOM 9 OW WAT X 31 11.321 28.206 36.494 3.33 > 3.33 O > ATOM 9 OW WAT X 32 28.206 36.494 11.321 3.33 > 3.33 O > ATOM 9 OW WAT X 33 36.494 11.321 28.206 3.33 > 3.33 O > ATOM 23 OW WAT X 34 33.090 30.414 36.290 3.22 > 3.22 O > ATOM 23 OW WAT X 35 30.414 36.290 33.090 3.22 > 3.22 O > ATOM 23 OW WAT X 36 36.290 33.090 30.414 3.22 > 3.22 O > ATOM 11 OW WAT X 37 11.962 19.803 33.965 3.21 > 3.21 O > ATOM 11 OW WAT X 38 33.965 11.962 19.802 3.21 > 3.21 O > ATOM 11 OW WAT X 39 19.803 33.965 11.962 3.21 > 3.21 O > ATOM 14 OW WAT X 40 37.964 18.211 35.654 3.20 > 3.20 O > ATOM 14 OW WAT X 41 18.211 35.654 37.964 3.20 > 3.20 O > ATOM 14 OW WAT X 42 35.654 37.964 18.211 3.20 > 3.20 O > ATOM 5 OW WAT X 43 13.907 5.734 5.035 3.19 > 3.19 O > ATOM 5 OW WAT X 44 5.734 5.035 13.907 3.19 > 3.19 O > ATOM 5 OW WAT X 45 5.035 13.907 5.734 3.19 > 3.19 O > ATOM 15 OW WAT X 46 27.533 22.090 19.525 3.19 > 3.19 O > ATOM 15 OW WAT X 47 19.525 27.533 22.090 3.19 > 3.19 O > ATOM 15 OW WAT X 48 22.090 19.525 27.533 3.19 > 3.19 O > ATOM 12 OW WAT X 49 20.446 14.674 21.092 3.17 > 3.17 O > ATOM 12 OW WAT X 50 21.092 20.446 14.674 3.17 > 3.17 O* > * > Can you tell me why? Thank a lot! > Wei > > >
