the resolution of realign
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Dear Niko,
I am wondering how can I judge the resolution? Should I use part_FSC or FSC? In your paper 2016, your suggest to use part_FSC. If I use part_FSC, it is still above 0.143 at 6A. But I can not see transmembrane alpha helix in my map.
Best regards,
Chao
C NO. RESOL RING RAD FSPR FSC Part_FSC Part_SSNR Rec_SSNR CC EXP. C SIG C ERFC TOTVOX C 2 264.50 0.0040 0.56 1.000 1.000 47.8584 573.35 0.0000 0.0000 0.0000 0.00 17 C 3 132.25 0.0080 0.40 1.000 1.000 42.1346 576.24 0.0000 0.0000 0.0000 0.00 41 C 4 88.17 0.0120 0.65 1.000 1.000 21.5776 452.95 0.0000 0.0000 0.0000 0.00 89 C 5 66.12 0.0160 0.89 1.000 1.000 10.7431 316.61 0.0000 0.0000 0.0000 0.00 129 C 6 52.90 0.0200 1.09 0.999 1.000 7.2377 267.54 0.0000 0.0000 0.0000 0.00 225 C 7 44.08 0.0240 1.78 0.998 1.000 3.7936 165.87 0.0000 0.0000 0.0000 0.00 253 C 8 37.79 0.0280 1.57 0.998 1.000 3.9090 184.98 0.0000 0.0000 0.0000 0.00 393 C 9 33.06 0.0320 2.28 0.997 1.000 2.9107 140.63 0.0000 0.0000 0.0000 0.00 461 C 10 29.39 0.0360 2.96 0.994 1.000 2.2620 102.07 0.0000 0.0000 0.0000 0.00 613 C 11 26.45 0.0400 5.06 0.984 0.999 1.5797 59.69 0.0000 0.0000 0.0000 0.00 713 C 12 24.05 0.0440 10.30 0.943 0.998 1.1075 31.32 0.0000 0.0000 0.0000 0.00 845 C 13 22.04 0.0480 21.04 0.808 0.992 0.7283 15.75 0.0000 0.0000 0.0000 0.00 1025 C 14 20.35 0.0520 29.35 0.705 0.986 0.5131 11.86 0.0000 0.0000 0.0000 0.00 1229 C 15 18.89 0.0560 22.96 0.780 0.991 0.5224 14.45 0.0000 0.0000 0.0000 0.00 1313 C 16 17.63 0.0600 22.57 0.788 0.991 0.5054 14.80 0.0000 0.0000 0.0000 0.00 1585 C 17 16.53 0.0640 25.86 0.741 0.988 0.4702 13.00 0.0000 0.0000 0.0000 0.00 1701 C 18 15.56 0.0680 30.77 0.675 0.984 0.4316 11.07 0.0000 0.0000 0.0000 0.00 2021 C 19 14.69 0.0720 36.11 0.613 0.979 0.3913 9.67 0.0000 0.0000 0.0000 0.00 2181 C 20 13.92 0.0760 37.46 0.604 0.978 0.3998 9.47 0.0000 0.0000 0.0000 0.00 2473 C 21 13.22 0.0800 39.26 0.578 0.976 0.3976 8.99 0.0000 0.0000 0.0000 0.00 2697 C 22 12.60 0.0840 45.23 0.494 0.966 0.3312 7.59 0.0000 0.0000 0.0000 0.00 2949 C 23 12.02 0.0880 53.52 0.402 0.952 0.2716 6.30 0.0000 0.0000 0.0000 0.00 3237 C 24 11.50 0.0920 58.04 0.354 0.942 0.2586 5.68 0.0000 0.0000 0.0000 0.00 3577 C 25 11.02 0.0960 61.08 0.313 0.931 0.2456 5.18 0.0000 0.0000 0.0000 0.00 3761 C 26 10.58 0.1000 66.89 0.248 0.907 0.2105 4.41 0.0000 0.0000 0.0000 0.00 4249 C 27 10.17 0.1040 67.28 0.245 0.905 0.2106 4.37 0.0000 0.0000 0.0000 0.00 4465 C 28 9.80 0.1080 70.96 0.210 0.887 0.1927 3.96 0.0000 0.0000 0.0000 0.00 4937 C 29 9.45 0.1120 75.80 0.155 0.844 0.1667 3.29 0.0000 0.0000 0.0000 0.00 5013 C 30 9.12 0.1160 76.59 0.144 0.832 0.1613 3.15 0.0000 0.0000 0.0000 0.00 5677 C 31 8.82 0.1200 80.25 0.106 0.777 0.1355 2.64 0.0000 0.0000 0.0000 0.00 5773 C 32 8.53 0.1240 79.60 0.112 0.789 0.1437 2.73 0.0000 0.0000 0.0000 0.00 6489 C 33 8.27 0.1280 79.12 0.117 0.797 0.1498 2.80 0.0000 0.0000 0.0000 0.00 6653 C 34 8.02 0.1320 76.45 0.146 0.835 0.1716 3.18 0.0000 0.0000 0.0000 0.00 7229 C 35 7.78 0.1360 69.18 0.226 0.896 0.2270 4.15 0.0000 0.0000 0.0000 0.00 7561 C 36 7.56 0.1400 60.62 0.320 0.933 0.2925 5.27 0.0000 0.0000 0.0000 0.00 8033 C 37 7.35 0.1440 52.34 0.418 0.955 0.3663 6.51 0.0000 0.0000 0.0000 0.00 8469 C 38 7.15 0.1480 46.81 0.482 0.965 0.4198 7.41 0.0000 0.0000 0.0000 0.00 8889 C 39 6.96 0.1520 45.28 0.501 0.967 0.4430 7.69 0.0000 0.0000 0.0000 0.00 9441 C 40 6.78 0.1560 45.65 0.497 0.967 0.4436 7.63 0.0000 0.0000 0.0000 0.00 9965 C 41 6.61 0.1600 49.73 0.446 0.960 0.4038 6.89 0.0000 0.0000 0.0000 0.00 10309 C 42 6.45 0.1640 60.22 0.325 0.934 0.3172 5.33 0.0000 0.0000 0.0000 0.00 11033 C 43 6.30 0.1680 75.15 0.162 0.850 0.2010 3.37 0.0000 0.0000 0.0000 0.00 11433 C 44 6.15 0.1720 85.19 0.052 0.619 0.1092 1.80 0.0000 0.0000 0.0000 0.00 12169 C 45 6.01 0.1760 88.41 0.017 0.342 0.0620 1.02 0.0000 0.0000 0.0000 0.00 12561 C 46 5.88 0.1800 90.17 -0.001 -0.023 0.0133 0.22 0.0000 0.0000 0.0000 0.00 13157 C 47 5.75 0.1840 89.66 0.004 0.101 0.0293 0.47 0.0000 0.0000 0.0000 0.00 13553
It sometimes happens that the
It sometimes happens that the FSC is not a reliable resolution measure. For example, if there is a large alignment error of the particles, the FSC may increase at higher resolution because if blurring of the signal and noise at higher resolution. This problem seems to be fairly common across different software packages and appears to be a general problem of the FSC. You will have to find other ways to estimate your resolution, for example by comparing your map with a model.
Fsc / helices
Hi chaoqi,
What percentage of your protein is NOT in the transmembrane region? I.e. The fraction of mass outside the membrane.
Did you try to estimate local
Did you try to estimate local resolution, e.g. with resmap?
From my experience the Part_FSC is a good indicator of the global resolution and comparable to what Relion tells you after masking.
Resmap should not differ substantially, if so something is wrong.