Re: [ccp4bb] oligomer ligand building
Hi Changyi, I'm not sure if this will answer your question, but it is likely that the cif file you are reading into Refmac is not in the correct format from Hic-Cup. I would suggest reading your coordinate file for the ligand into the Dundee server which will output a cif formats for refinement programs. Scroll down to the Refmac output and save as a .cif, and then read this file into your next round of refinement with Refmac. After this round, Refmac will generate a new cif library containing this ligand. I hope this helps. Cheers, Paul
[ccp4bb] Molecular replacement question
Hello fellow crystallographers, I am trying molecular replacement for a protein crystal dataset that has very high sequence similarity to the search model with several predicted flexible loop regions; however, all attempts at finding a solution have not produce very ideal starting solutions using Phaser and Molrep (CC = 0.3 and Z-score = 5). I am very confident that the unit cell parameters are C2 84.027 120.565 108.272 90.00 104.71 90.00, and there appears to be no evidence of twinning. The Matthews calculation predicts from anywhere from 2-4 monomers in the ASU, and calculation of the SRF in Molrep does not identify any peaks in higher order symmetry except for the expected crystallographic two-fold for C2. Below is the table from the calculated SRF in molrep. Any advice would be greatly appreciated. #thetaphichi alpha beta gamma Rf Rf/sigma Sol_RF 1 0.000.000.000.000.000.00 870.5 21.59 Sol_RF 258.61 -10.17 180.00 169.83 -117.23 10.17 162.5 4.03 Sol_RF 366.02 -0.00 180.00 180.00 -132.030.00 161.1 4.00 Sol_RF 458.42 -9.54 180.00 170.46 -116.859.54 159.8 3.96 Sol_RF 5 149.840.00 180.00 -180.00 60.320.00 156.0 3.87 Sol_RF 658.96 -5.52 180.00 174.48 -117.915.52 151.5 3.76 Sol_RF 765.59 20.95 180.00 20.95 131.18 159.05 143.9 3.57 Sol_RF 890.00 -98.96 180.000.00 180.00 17.92 142.9 3.55 Sol_RF 956.53 15.78 180.00 15.78 113.07 164.22 142.0 3.52 Sol_RF 1071.10 -19.94 180.00 160.06 -142.20 19.94 141.6 3.51 Sol_RF 1171.28 29.78 180.00 29.78 142.55 150.22 140.4 3.48 Sol_RF 1265.22 -15.88 180.00 164.12 -130.44 15.88 139.2 3.45 Sol_RF 1368.84 -0.00 180.00 180.00 -137.670.00 138.0 3.42 Sol_RF 1432.51 -180.00 180.00 -180.00 65.02 -0.00 137.9 3.42 Sol_RF 1575.02 -28.84 180.00 151.16 -150.04 28.84 134.7 3.34 Sol_RF 1671.69 -20.99 180.00 159.01 -143.37 20.99 133.0 3.30 Sol_RF 1792.13 101.46 179.93 102.35 -175.74 79.42 130.9 3.25 Sol_RF 18 107.89 144.73 179.79 145.06 -144.22 35.61 128.8 3.19 Sol_RF 1987.45 -78.19 180.00 101.81 -174.90 78.19 128.1 3.18 Sol_RF 2038.570.69 30.36 102.66 -18.79 -78.71 122.4 3.04 Sol_RF 2126.77 174.59 176.58 172.68 53.523.49 120.5 2.99 Sol_RF 22 116.66 178.08 175.143.49 126.48 187.32 120.5 2.99 Sol_RF 2375.56 -41.35 180.00 138.65 -151.12 41.35 119.8 2.97 Sol_RF 2466.12 36.35 180.00 36.35 132.24 143.65 116.6 2.89 Sol_RF 2583.87 71.62 180.00 71.62 167.74 108.38 114.7 2.85 Sol_RF 2669.24 -12.37 180.00 167.63 -138.48 12.37 112.3 2.79 Sol_RF 2759.75 15.26 172.297.64 119.07 157.12 112.2 2.78 Sol_RF 28 120.25 -164.74 172.29 22.88 119.07 172.36 112.2 2.78 Sol_RF 2996.68 -70.99 180.00 109.01 -166.63 70.99 110.9 2.75 Sol_RF 3063.23 -44.73 180.00 135.27 -126.47 44.73 108.9 2.70 Cheers, Paul Holland
