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Hi Wei Don't forget that a Patterson has space-group symmetry too so there will be symmetry-related peaks that may not be listed by the peak-search program. The Patterson space group is this case is Cmmm, so a peak at (0,2y,2z) will also occur at (1/2,1/2+2y,1-2z) (as well as 6 other positions in the unit cell). Bearing this in mind I think you'll find that the peak ATOM2 is your missing Harker vector. There are a number of programs that will do this analysis completely automatically for you (I wrote one 'VECSUM' for CCP4 many years ago, but there are probably better ones around now). However for the novice I would recommend doing it 'by hand' as you are doing it - it's very instructive! Cheers -- Ian On 26 January 2013 03:43, <[log in to unmask]> wrote: > Dear Ian, > Thank you very much for your patient reply! It have solved the trouble > comfusing me quite a while. > I try to use the method you taught me to analyse another crystal but there > are still some problems. > > Some information of the new crystal: (more detail can found in the > attachment) > > 1. Cell 79.342 89.343 74.719 90.000 90.000 90.000 c2221 > 2. One heavy atom (SE) in one asymmetry unit. > 3. Patterson-peaks are calculated by anomalous different data > (F,SIGF,DANO, SIGDANO,) > 4. The list of the Patterson-peaks. > GRID 80 88 72 > CELL 79.3420 89.3430 74.7190 90.0000 90.0000 90.0000 > ATOM1 Ano 0.0000 0.0000 0.0000 61.40 0.0 BFAC 20.0 > ATOM2 Ano 0.5000 0.1902 0.3218 8.84 0.0 BFAC 20.0 > ATOM3 Ano 0.3713 0.1908 0.5000 8.53 0.0 BFAC 20.0 > ATOM4 Ano 0.1282 0.0000 0.1784 7.14 0.0 BFAC 20.0 > ATOM5 Ano 0.0510 0.0680 0.0000 3.64 0.0 BFAC 20.0 > ATOM6 Ano 0.2985 0.0000 0.3644 3.23 0.0 BFAC 20.0 > > As we can see, 3 peak are found (exclude the origin peak) from the > patterson map. > As we know, the symmetry operations of the space group C2221 are > (x,y,z) (x,-y,-z) (-x,y,1/2-z) (1/2-x,1/2-y,1/2+z) > so harker positions can be > (1) (0,2y,2z) > (2) (2x,0,-1/2+2z) > (3) (1/2-2x,-1/2+2y,1/2) > using (2) and the coordinate of "ATOM4 Ano 0.1282 0.0000 0.1784", we > know that > x=0.0641, z=0.3392 > using (3) the coordinate of "ATOM3 Ano 0.3713 0.1908 0.5000", we > got that > y=0.3454 > > But the questions are > (1)How to explain the peak of ATOM2 "0.5000 0.1902 0.3218 "? > (2)Why the harker positon (0,2y,2z) is missing? > > Thank you for you time! > Best! > Wei > > > > > > > > At 2013-01-26 00:58:29,"Ian Tickle" <[log in to unmask]> wrote: > > 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, <[log in to unmask]> 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" <[log in to unmask]> 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 <[log in to unmask]> 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 >>> >>> >>> >> >> >> > > >