Hi,
> _rlnCurrentResolution 5.460674
> _rlnPixelSize 2.700000
This indicates that you have reached the Nyquist frequency.
Please re-extract particles with a smaller pixel size.
Best regards,
Takanori Nakane
On 2019/02/03 17:30, sunyeping wrote:
> Hello Dr. Nakane,
>
> The first part of the run_model.star from Refine3D is:
>
>
> data_model_general
>
> _rlnReferenceDimensionality 3
> _rlnDataDimensionality 2
> _rlnOriginalImageSize 180
> _rlnCurrentResolution 5.460674
> _rlnCurrentImageSize 180
> _rlnPaddingFactor 2.000000
> _rlnIsHelix 0
> _rlnFourierSpaceInterpolator 1
> _rlnMinRadiusNnInterpolation 10
> _rlnPixelSize 2.700000
> _rlnNrClasses 1
> _rlnNrBodies 1
> _rlnNrGroups 181
> _rlnTau2FudgeFactor 1.000000
> _rlnNormCorrectionAverage 0.645256
> _rlnSigmaOffsets 0.834530
> _rlnOrientationalPriorMode 1
> _rlnSigmaPriorRotAngle 0.234375
> _rlnSigmaPriorTiltAngle 0.234375
> _rlnSigmaPriorPsiAngle 0.234375
> _rlnLogLikelihood 1.140314e+09
> _rlnAveragePmax 0.342304
>
>
> data_model_classes
>
> loop_
> _rlnReferenceImage #1
> _rlnClassDistribution #2
> _rlnAccuracyRotations #3
> _rlnAccuracyTranslations #4
> _rlnEstimatedResolution #5
> _rlnOverallFourierCompleteness #6
> Refine3D/job068/run_class001.mrc 1.000000 0.223000 0.161000 5.400000 1.000000
>
>
> data_model_class_1
>
> loop_
> _rlnSpectralIndex #1
> _rlnResolution #2
> _rlnAngstromResolution #3
> _rlnSsnrMap #4
> _rlnGoldStandardFsc #5
> _rlnFourierCompleteness #6
> _rlnReferenceSigma2 #7
> _rlnReferenceTau2 #8
> _rlnSpectralOrientabilityContribution #9
> 0 0.000000 999.000000 999.000000 1.000000 1.000000 4.558077e-09 0.012246 0.000000
> 1 0.002058 486.000000 999.000000 1.000000 1.000000 2.661997e-08 0.018962 1.313120e-07
> 2 0.004115 243.000000 999.000000 1.000000 1.000000 2.087823e-08 0.002319 8.637322e-07
> 3 0.006173 162.000000 999.000000 1.000000 1.000000 1.548740e-08 0.002378 2.491402e-06
> 4 0.008230 121.500000 999.000000 1.000000 1.000000 1.207707e-08 3.570124e-04 1.070988e-05
>
> Best regards,
> Yeping Sun
>
>
> ------------------------------------------------------------------
> From:Takanori Nakane <[log in to unmask]>
> Sent At:2019 Feb. 4 (Mon.) 00:04
> To:孙业平 <[log in to unmask]>; CCPEM <[log in to unmask]>
> Subject:Re: [ccpem] The "Postprocessing::run ERROR: FSC curve never drops below randomize_fsc_at." problem
>
> Hi,
>
> Please show me the FSC table in the first part of your run_model.star
> from Refine3D.
>
> Best regards,
>
> Takanori Nakane
>
> On 2019/02/03 14:57, sunyeping wrote:
>> Dear All,
>> I post this problem yesterday but haven't got any anwer. I think I should give more detail.
>>
>> In the Refine3D, I get the warning message as following:
>>
>> WARNING: FSC dipped below 0.5 and rose again. Using higher resolution of 8.37931 A, instead of 9 A.
>> This is not necessarily a bad thing. Often it is caused by too tight masks.
>> WARNING: FSC dipped below 0.5 and rose again. Using higher resolution of 8.67857 A, instead of 9.34615 A.
>> This is not necessarily a bad thing. Often it is caused by too tight masks.
>> WARNING: FSC dipped below 0.5 and rose again. Using higher resolution of 5.65116 A, instead of 6.1519 A.
>> This is not necessarily a bad thing. Often it is caused by too tight masks.
>> WARNING: FSC dipped below 0.5 and rose again. Using higher resolution of 5.65116 A, instead of 5.92683 A.
>> This is not necessarily a bad thing. Often it is caused by too tight masks.
>> I have tried to increase the mask
>>
>> In PostProcess job, I got the following error message in the run.err file:
>>
>> in: /home/cryoem/softwares/Relion30Beta/relion/src/postprocessing.cpp, line 1152
>> === Backtrace ===
>> /home/cryoem/softwares/Relion30Beta/relion/build/bin/relion_postprocess(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x423f01]
>> /home/cryoem/softwares/Relion30Beta/relion/build/bin/relion_postprocess(_ZN14Postprocessing3runEv+0xbaa) [0x44896a]
>> /home/cryoem/softwares/Relion30Beta/relion/build/bin/relion_postprocess(main+0x62) [0x419a02]
>> /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f729de9db35]
>> /home/cryoem/softwares/Relion30Beta/relion/build/bin/relion_postprocess() [0x419f6f]
>> ==================
>> ERROR:
>> Postprocessing::run ERROR: FSC curve never drops below randomize_fsc_at.
>>
>> And the message int the run.out file of the PostProcess job is:
>>
>>
>> == Reading input half-reconstructions:
>> + half1-map: Refine3D/job068/run_half1_class001_unfil.mrc
>> + half2-map: Refine3D/job068/run_half2_class001_unfil.mrc
>> == Using a user-provided mask ...
>> + input mask: MaskCreate/job077/mask.mrc
>> == Masking input maps ...
>> + randomize phases beyond: -486 Angstroms
>>
>> Do you know how is this " "Postprocessing::run ERROR: FSC curve never drops below randomize_fsc_at." problem" caused and how to solve it?
>> I will be grateful if you can help me with this.
>>
>> Best Regards.
>> Yeping
>>
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>>
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