Hi Laura,
The last column (FSC between phase-randomized maps) has way too high
values, indicating that your mask is too tight. The options mentioned by
Celia in the previous message can be used to make it wider and/or
softer, such that you'll decrease the convolution artefacts of the mask.
That way, your resolution estimates would be back up again. I recommend
reading the Chen et al paper in Ultramicroscopy on the
phase-randomization approach.
HTH,
Sjors
On 01/11/2016 10:57 AM, Laura van Bezouwen wrote:
> Hi Sjors,
>
> Here the data from the star file
>
> Best,
> Laura
>
> data_fsc
>
> loop_
> _rlnSpectralIndex #1
> _rlnResolution #2
> _rlnAngstromResolution #3
> _rlnFourierShellCorrelationCorrected #4
> _rlnFourierShellCorrelationUnmaskedMaps #5
> _rlnFourierShellCorrelationMaskedMaps #6
> _rlnCorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps #7
> 0 0.001001 999.000000 1.000000 1.000000
> 1.000000 1.000000
> 1 0.001842 542.880003 1.000000 0.999738
> 1.000000 1.000000
> 2 0.003684 271.440001 0.999994 0.999719
> 0.999994 0.999994
> 3 0.005526 180.960001 0.999967 0.998216
> 0.999967 0.999969
> 4 0.007368 135.720001 0.999885 0.997291
> 0.999885 0.999884
> 5 0.009210 108.576001 0.999671 0.994004
> 0.999671 0.999661
> 6 0.011052 90.480000 0.999273 0.993902
> 0.999273 0.999265
> 7 0.012894 77.554286 0.999054 0.992794
> 0.999054 0.999062
> 8 0.014736 67.860000 0.999113 0.990347
> 0.999113 0.999136
> 9 0.016578 60.320000 0.999216 0.989517
> 0.999216 0.999248
> 10 0.018420 54.288000 0.999231 0.989563
> 0.999231 0.999244
> 11 0.020262 49.352728 0.999039 0.988129
> 0.999039 0.999030
> 12 0.022104 45.240000 0.998628 0.984196
> 0.998628 0.998612
> 13 0.023946 41.760000 0.998092 0.982134
> 0.998092 0.998144
> 14 0.025788 38.777143 0.997232 0.982614
> 0.997232 0.997216
> 15 0.027630 36.192000 0.995824 0.980549
> 0.995824 0.995725
> 16 0.029472 33.930000 0.991772 0.966970
> 0.991772 0.991592
> 17 0.031314 31.934118 0.986715 0.952258
> 0.986715 0.986613
> 18 0.033156 30.160000 0.984583 0.948087
> 0.984583 0.984855
> 19 0.034999 28.572632 0.981506 0.936454
> 0.981506 0.982097
> 20 0.036841 27.144000 0.971712 0.905649
> 0.971712 0.972574
> 21 0.038683 25.851429 0.958617 0.871192
> 0.958617 0.960381
> 22 0.040525 24.676364 0.949232 0.859541
> 0.949232 0.952200
> 23 0.042367 23.603478 0.937576 0.810476
> 0.937576 0.940890
> 24 0.044209 22.620000 0.077404 0.747890
> 0.925552 0.919305
> 25 0.046051 21.715200 0.271748 0.681754
> 0.912621 0.880016
> 26 0.047893 20.880000 0.414872 0.663891
> 0.903159 0.834496
> 27 0.049735 20.106667 0.353391 0.572984
> 0.884437 0.821279
> 28 0.051577 19.388572 0.151467 0.464235
> 0.855019 0.829140
> 29 0.053419 18.720000 0.000000 0.350038
> 0.808089 0.811492
> 30 0.055261 18.096000 0.032382 0.285495
> 0.789182 0.782127
> 31 0.057103 17.512258 0.131669 0.335029
> 0.788716 0.756678
> 32 0.058945 16.965000 0.128011 0.369962
> 0.768948 0.735029
> 33 0.060787 16.450909 0.052803 0.388005
> 0.753959 0.740243
> 34 0.062629 15.967059 0.139929 0.386406
> 0.749383 0.708609
> 35 0.064471 15.510857 0.202783 0.371727
> 0.743122 0.677781
> 36 0.066313 15.080000 0.208281 0.325347
> 0.726189 0.654156
> 37 0.068155 14.672433 0.212430 0.274756
> 0.708241 0.629545
> 38 0.069997 14.286316 0.198512 0.275890
> 0.705103 0.632063
> 39 0.071839 13.920000 0.216018 0.320212
> 0.700515 0.617995
> 40 0.073681 13.572000 0.214331 0.297769
> 0.690331 0.605854
> 41 0.075523 13.240976 0.138881 0.237556
> 0.659936 0.605090
> 42 0.077365 12.925714 0.000000 0.160701
> 0.569820 0.579063
> 43 0.079207 12.625116 0.000000 0.145217
> 0.487059 0.546045
> 44 0.081049 12.338182 0.000000 0.110821
> 0.482422 0.520803
> 45 0.082891 12.064000 0.068225 0.170635
> 0.543809 0.510407
> 46 0.084733 11.801739 0.140923 0.210082
> 0.572328 0.502172
> 47 0.086575 11.550638 0.184768 0.197557
> 0.561240 0.461797
> 48 0.088417 11.310000 0.090499 0.090526
> 0.485879 0.434722
> 49 0.090259 11.079184 0.009623 0.099761
> 0.418816 0.413169
> 50 0.092101 10.857600 0.058183 0.115648
> 0.417853 0.381890
> 51 0.093943 10.644706 0.069282 0.095211
> 0.404335 0.359994
> 52 0.095785 10.440000 0.035125 0.025660
> 0.368706 0.345725
> 53 0.097627 10.243019 0.013108 0.048567
> 0.352646 0.344048
> 54 0.099469 10.053333 0.000000 0.086889
> 0.341105 0.343989
> 55 0.101312 9.870546 0.000000 0.060966
> 0.336228 0.342042
> 56 0.103154 9.694286 0.012317 0.050740
> 0.319587 0.311102
> 57 0.104996 9.524211 0.035141 0.048257
> 0.310946 0.285850
> 58 0.106838 9.360000 0.083133 0.053748
> 0.319367 0.257653
> 59 0.108680 9.201356 0.069603 0.060859
> 0.289653 0.236512
> 60 0.110522 9.048000 0.039160 0.012992
> 0.243690 0.212866
> 61 0.112364 8.899672 0.028978 0.042030
> 0.215449 0.192036
> 62 0.114206 8.756129 0.000000 0.029583
> 0.174534 0.194375
> 63 0.116048 8.617143 0.000000 0.056930
> 0.175615 0.204439
> 64 0.117890 8.482500 0.000000 0.023297
> 0.208175 0.215546
> 65 0.119732 8.352000 0.000000 0.027420
> 0.197074 0.215896
> 66 0.121574 8.225455 0.005812 0.032989
> 0.205541 0.200897
> 67 0.123416 8.102687 0.017306 0.065378
> 0.202685 0.188644
> 68 0.125258 7.983529 0.005446 0.031938
> 0.192049 0.187624
> 69 0.127100 7.867826 0.000000 0.012513
> 0.171204 0.171413
> 70 0.128942 7.755429 0.009350 0.026444
> 0.167451 0.159593
> 71 0.130784 7.646197 0.002465 0.019367
> 0.159180 0.157102
> 72 0.132626 7.540000 0.000000 0.023295
> 0.120196 0.155948
> 73 0.134468 7.436712 0.000000 0.024605
> 0.104188 0.140570
> 74 0.136310 7.336216 0.000000 0.007806
> 0.131533 0.134491
> 75 0.138152 7.238400 0.037193 0.006969
> 0.158783 0.126286
> 76 0.139994 7.143158 0.050622 0.026536
> 0.167537 0.123150
> 77 0.141836 7.050390 0.004045 0.034147
> 0.135955 0.132446
> 78 0.143678 6.960000 0.000000 -0.002035
> 0.093391 0.161158
>
> 2016-01-11 11:30 GMT+01:00 Celia Plisson-Chastang <
> [log in to unmask]>:
>
>> Hi Laura,
>>
>> If you use the automask option of postprocess, you might have to "loosen"
>> the mask by playing around with the --inimask_threshold, --extend_inimask
>> and --width_mask_edge values you use.
>> Also, if your raw fsc curve is not weird looking, you can try to randomize
>> the phases at a lower resolution, ie lower fsc value (the default value of
>> phase randomizing correspond to the resolution where FSC=0.8), with the
>> option --randomize_at_fsc.
>> hope it helps!
>> all the best
>> celia
>>
>>
>>
>> Le Lundi 11 Janvier 2016 10:18 CET, Laura van Bezouwen <
>> [log in to unmask]> a écrit:
>>
>>> Hi,
>>>
>>> I was wondering if somebody could help with my mask. I made several masks
>>> to run on my particle. One mask really helped but another mask not. The
>>> results were very surprising. I did a 3D classification with the mask and
>>> took the best class for my 3D refinement. After my 3D refinement I had a
>>> resolution of 12.6 Å but after postprocessing I ended up with a
>> resolution
>>> of 23.6 Å. Making a difference mask in Chimera didn't help. Does anybody
>>> knows what is going on? And how I can improve my results
>>>
>>> Thanks for the help,
>>>
>>> Best,
>>>
>>> Laura
>> --
>> --
>> Dr Célia Plisson-Chastang
>> Laboratoire de Biologie Moléculaire Eucaryote
>> UMR CNRS 5099-Université Paul Sabatier Toulouse III
>> Bâtiment IBCG, 118 Route de Narbonne
>> 31062 Toulouse Cedex, France
>>
>> Telephone : +33(0)5 61 33 59 50
>> Fax : +33(0)5 61 33 58 86
>>
>>
>>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
|
