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Dear Daniel Adams I suggest you to run "analysis Data for MR" then, see the Patterson peak height in .log file and cross check using native Patterson map at the given coordinates (where pseudotranslation is present) at 5-6 sigma. Any non-origin peak in native Patterson map, which is more than 0.15 fraction of the origin peak, might suggest the presence of pseudo-translation. You can get few molecules in the asymmetric unit using pseudo-translation information in MOLREP and other molecules in the asymmetric unit can be generated manually by applying pseudo-translation (if two molecules are related by pseudo-translation) vector using MOLEMAN2 or any other program. Then these molecules can be used for rigid body refinement to confirm the solution is correct or not. If you are looking for pseudo-translation then you have to look at Kappa=0 in self-rotation, if two molecules related by pseudo-translation then orientation is same, but self-rotation will not show the pseudo-translation peak. If I am wrong please correct me. Rajkumar --- Daniel Adams <[EMAIL PROTECTED]> wrote: > Dear bb, > I am trying to figure out SRF for P1 space group > dataset using Molrep. > The programme indicates the presence of > pseudotranlation however the peaks > heights are confusing me... > The output of MOLREP is follows: > > -- Fobs -- > ------------- > Fobs: resolution : 29.89 2.80 > Completeness of Fobs : 0.980 > B_overall of Fobs : 36.021 > Optical resolution : 2.005 > Anisotropic distribution of Structure Factors: > Ratio of Eigen values : 0.9627 0.4958 1.0000 > ------------- > Resolution will be used : 29.89 4.00 > ------------- > INFO: anisothermal correction of Fobs --- > --- Check Patterson for pseudo-translation --- > PST_limit : 0.125 of origin peak > INFO: pseudo-translation was detected. > Origin Patterson peak: P,P/sig : > 8748.844 140.071 > 1 Patterson. peak : p,P/sig : > 1694.444 27.128 > 2 Patterson peak : P,P/sig : > 809.574 12.961 > 3 Patterson peak : P,P/sig : > 649.761 10.403 > Peak 1: trans.vector /ort/ : 11.342 > 0.000 > 0.000 > trans.vector /frac/: 0.152 > 0.000 > 0.000 > Peak 2: trans.vector /ort/ : 22.779 > 0.000 > 0.000 > trans.vector /frac/: 0.306 > 0.000 > 0.000 > Peak 3: trans.vector /ort/ : 2.457 > 85.961 > 0.617 > trans.vector /frac/: 0.037 > 0.948 > 0.006 > INFO: use keyword: "PST". > > Sol_ Space group : P 1 > Sol_ No: 1 Sett: 1 > Sol_ Cell: 74.540 90.930 120.610 109.23 110.92 > 90.03 > > Sol_--- Self Rotation function --- > Sol_ > --- anisothermal correction of Fobs --- > Radius of integration : 35.00 > Resmin,Resmax : 29.89 4.00 > --- rfcoef for Fobs. --- > distance limit : 2.000 / grad / > > Number of RF peaks : 30 > theta phi chi alpha > beta gamma > Rf Rf/sigma > Sol_RF 1 0.00 0.00 0.00 0.00 0.00 > 0.00 295.0 > 21.24 > Sol_RF 2 172.27 -88.17 180.00 91.83 15.45 > 88.17 159.1 > 11.46 > Sol_RF 3 97.66 90.33 180.00 270.33 164.69 > 269.67 137.9 > 9.93 > Sol_RF 4 90.00 -179.40 180.00 313.80 180.00 > 132.60 121.4 > 8.74 > Sol_RF 5 163.40 -25.19 180.00 154.81 33.19 > 25.19 118.4 > 8.53 > Sol_RF 6 142.86 -89.96 180.00 90.04 74.28 > 89.96 98.14 > 7.07 > Sol_RF 7 162.97 -90.08 180.00 89.92 34.05 > 90.08 97.46 > 7.02 > Sol_RF 8 148.91 -90.06 180.00 89.94 62.18 > 90.06 96.48 > 6.95 > Sol_RF 9 95.89 -89.67 180.00 90.33 168.23 > 89.67 95.26 > 6.86 > Sol_RF 10 180.00 0.00 180.00 180.00 0.00 > 0.00 94.75 > 6.82 > Sol_RF 11 173.15 91.79 180.00 271.79 13.70 > 268.21 94.34 > 6.79 > Sol_RF 12 157.43 91.67 179.98 271.67 45.14 > 268.33 94.29 > 6.79 > Sol_RF 13 89.66 1.71 28.37 271.79 28.37 > 88.38 94.23 > 6.78 > Sol_RF 14 90.34 -178.29 28.37 91.62 28.37 > 268.21 94.23 > 6.78 > Sol_RF 15 135.06 -89.96 180.00 90.04 89.88 > 89.96 93.13 > 6.70 > Sol_RF 16 121.29 89.44 180.00 269.44 117.43 > 270.56 93.11 > 6.70 > Sol_RF 17 165.19 90.06 180.00 270.06 29.61 > 269.94 92.96 > 6.69 > Sol_RF 18 106.06 -89.84 180.00 90.16 147.88 > 89.84 92.83 > 6.68 > Sol_RF 19 88.53 0.14 46.03 270.76 46.02 > 90.49 92.34 > 6.65 > Sol_RF 20 91.47 -179.86 46.03 89.51 46.02 > 269.24 92.34 > 6.65 > Sol_RF 21 112.75 -89.54 180.00 90.46 134.51 > 89.54 92.16 > 6.64 > Sol_RF 22 109.99 90.00 180.00 270.00 140.01 > 270.00 91.80 > 6.61 > Sol_RF 23 89.89 -179.85 120.54 90.34 120.54 > 270.04 91.11 > 6.56 > Sol_RF 24 90.11 0.15 120.54 269.96 120.54 > 89.66 91.11 > 6.56 > Sol_RF 25 90.00 0.10 155.48 270.11 155.48 > 89.90 90.13 > 6.49 > Sol_RF 26 90.00 -179.90 155.48 90.10 155.48 > 269.89 90.13 > 6.49 > Sol_RF 27 150.73 89.77 180.00 269.77 58.54 > 270.23 89.47 > 6.44 > Sol_RF 28 115.82 89.94 180.00 269.94 128.37 > 270.06 89.27 > 6.43 > Sol_RF 29 135.80 90.11 180.00 270.11 88.39 > 269.89 88.69 > 6.38 > Sol_RF 30 90.24 -0.07 65.22 269.77 65.22 > 89.91 88.37 > 6.36 > > My question is: > 1. Is there really a three pseudotranslationally > related molecules ? > my asymmetric unit have 12 molecules (50% solvent > content) and > biochemically data indicates either hexameric or > tetrameric assembly. > 2. What is the best way to figure out the > pseudotranslation ? > 3. When I do SRF for data containing PST, should I > expect SRF for all > molecules or for 1 molecule. I understand that > orientation of PST related > molecules should be same. > > Thanks in advance. > > Cheers > > Dan > E.Rajakumara Graduate Student. Protein Crystallography Lab. Centre for Cellular and Molecular Biology. Hyderabad-500 007 India. Phone No. +914027192835. Send instant messages to your online friends http://uk.messenger.yahoo.com
