Hi Wei The explanation from looking at your FFT log file would appear to be that what you have calculated is not a Patterson at all but an anomalous difference Fourier, which would of course explain the lack of peaks! The evidence for this is that the FFT run 1) has the phase & FOM assigned, 2) is calculated in P1 (not P-1), and 3) doesn't have an origin peak (and it's not origin-subtracted).
With that information I think we can explain the peaks you observed: Peak 'X 2' is due to the disulphide A20-B19. 'X 4' is from A6-A11 (with symmetry operator x, 1-y, 1/2-z). 'X 7' is from A7-B7 (same symop). As I said, each peak appears 3 times in the list because of the 3-fold and all the other peaks are noise. Cheers -- Ian On 25 January 2013 14:58, <ccp4...@hotmail.com> wrote: > Dear Ian, > Thank you for your detail reply. > There are something should be clear: > 1.The SAD Patterson vectors are calculated by I(+), Isig(+),I(-), Isig(-). > 2. In order to submit more complete data, some information have to be > renewed and some useful files can be found in the attachment. > (1)The unit cell > CRYST1 77.904 77.904 77.904 90.00 90.00 90.00 I 21 3 > (2)S-S coordinate: > ATOM 43 SG CYS A 6 20.158 40.510 32.477 1.00 16.55 > S > ATOM 49 SG CYS A 7 24.211 47.917 30.445 1.00 22.23 > S > ATOM 76 SG CYS A 11 21.536 39.121 32.557 1.00 17.77 > S > ATOM 167 SG CYS A 20 16.485 32.136 26.247 1.00 15.38 > S > ATOM 240 SG CYS B 7 26.123 46.933 30.643 1.00 18.58 > S > ATOM 336 SG CYS B 19 17.904 33.034 25.125 1.00 15.26 > S > (3)fft.pdb > ATOM 10 OW WAT X 1 32.611 25.754 17.013 8.54 8.54 > O > ATOM 10 OW WAT X 2 17.013 32.611 25.754 8.54 8.54 > O > ATOM 10 OW WAT X 3 25.755 17.013 32.611 8.54 8.54 > O > ATOM 5 OW WAT X 4 21.257 38.213 6.305 7.17 7.17 > O > ATOM 5 OW WAT X 5 6.305 21.257 38.213 7.17 7.17 > O > ATOM 5 OW WAT X 6 38.213 6.305 21.257 7.17 7.17 > O > ATOM 6 OW WAT X 7 25.414 29.923 8.402 5.30 5.30 > O > ATOM 6 OW WAT X 8 29.923 8.402 25.414 5.30 5.30 > O > ATOM 6 OW WAT X 9 8.402 25.414 29.923 5.30 5.30 > O > ATOM 1 OW WAT X 10 26.150 11.364 2.260 3.89 3.89 > O > ATOM 1 OW WAT X 11 11.364 2.260 26.150 3.89 3.89 > O > ATOM 1 OW WAT X 12 2.260 26.150 11.364 3.89 3.89 > O > ATOM 7 OW WAT X 13 29.944 37.250 7.974 3.72 3.72 > O > ATOM 7 OW WAT X 14 7.975 29.944 37.250 3.72 3.72 > O > ATOM 7 OW WAT X 15 37.250 7.974 29.944 3.72 3.72 > O > ATOM 12 OW WAT X 16 22.628 20.215 27.834 3.50 3.50 > O > ATOM 12 OW WAT X 17 27.834 22.628 20.215 3.50 3.50 > O > ATOM 12 OW WAT X 18 20.215 27.834 22.628 3.50 3.50 > O > ATOM 11 OW WAT X 19 23.336 23.420 18.588 3.39 3.39 > O > ATOM 11 OW WAT X 20 23.420 18.588 23.336 3.39 3.39 > O > ATOM 11 OW WAT X 21 18.588 23.336 23.420 3.39 3.39 > O > ATOM 3 OW WAT X 22 9.104 17.214 5.101 3.19 3.19 > O > ATOM 3 OW WAT X 23 5.101 9.104 17.214 3.19 3.19 > O > ATOM 3 OW WAT X 24 17.214 5.101 9.103 3.19 3.19 > O > ATOM 8 OW WAT X 25 20.507 38.952 12.372 3.19 3.19 > O > ATOM 9 OW WAT X 26 22.099 14.351 35.000 3.15 3.15 > O > ATOM 9 OW WAT X 27 14.351 35.000 22.099 3.15 3.15 > O > ATOM 9 OW WAT X 28 35.000 22.099 14.351 3.15 3.15 > O > ATOM 2 OW WAT X 29 5.038 28.656 5.496 3.12 3.12 > O > ATOM 2 OW WAT X 30 28.656 5.496 5.038 3.12 3.12 > O > ATOM 2 OW WAT X 31 5.496 5.038 28.656 3.12 3.12 > O > ATOM 13 OW WAT X 32 33.307 37.596 24.016 3.05 3.05 > O > ATOM 13 OW WAT X 33 37.596 24.016 33.307 3.05 3.05 > O > ATOM 13 OW WAT X 34 24.016 33.307 37.596 3.05 3.05 > O > ATOM 4 OW WAT X 35 5.606 8.131 35.777 3.04 3.04 > O > ATOM 4 OW WAT X 36 35.777 5.606 8.130 3.04 3.04 > O > ATOM 4 OW WAT X 37 8.131 35.777 5.606 3.04 3.04 > O > > Thanks a lot! > Wei > > > > > > > > > > At 2013-01-25 21:10:04,"Ian Tickle" <ianj...@gmail.com> wrote: > > Hi Wei > > Are you saying that the highest 9 peaks in your list that you highlighted > correspond to disulphide-disulphide vectors and the rest don't? Actually > of the 9 only 3 are independent, the other 6 are related by the 3-fold so > you need to take that into account in your calculation of the no of peaks > expected. AFAICS on a superficial check none of the intra-asymmetric unit > vectors appear in the complete list (all the ones in the list seem to be > too far from the origin) & since you didn't specify your unit cell > dimension it's impossible to verify whether any of the inter- vectors > appear in the list. > > Just to be clear: this is a SAD Patterson you're talking about, not a > native Patterson, right? If the latter it wouldn't surprise me at all that > you don't see any S-S <=> S-S peaks. Could you give more details of your > data processing protocol & data quality indicators? - likely that's the > source of your problem. > > Cheers > > -- Ian > > > 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 >> >> >> > > >
