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the resolution of realign

3 replies [Last post]
chaoqi
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Joined: 27 Jul 2017

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
tarek
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Joined: 7 Mar 2016
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.

himesb
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Joined: 26 Jul 2017
Fsc / helices

Hi chaoqi,

What percentage of your protein is NOT in the transmembrane region? I.e. The fraction of mass outside the membrane.

niko
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Joined: 5 May 2009
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.