Hi Domen and Zhaoming,
I forward comments from Jasenko Zivanov (CC-ed),
the developer of Bayesian Polishing.
Please make sure all FCC files under the job directory
have the same size.
> Could it be that some of the (thousands of) partial FCC files (*_FCC_cc.mrc, *_FCC_w0/1.mrc) are damaged?
>
> Sjors changed the mrc-reader afterwards, so that it would refuse to load a corrupted image.
> That problem should be gone in the current version.
>
> I had observed a corrupted partial FCC file once myself.
> This could definitely introduce NaNs into the FCC computation.
>
> The way to diagnose this would be to check if there are unusually small files in the output-directory.
> All of them should be the same size.
Best regards,
Takanori Nakane
On 2018/09/28 17:34, Zhaoming Su wrote:
> Hi All,
>
> I have the exact problem on multiple data sets collected as packed mrc from EPU, except they all fail at the second frame...
>
> # RELION; version 3.0-beta-2
>
> data_perframe_bfactors
>
> loop_
> _rlnMovieFrameNumber #1
> _rlnBfactorUsedForSharpening #2
> _rlnFittedInterceptGuinierPlot #3
> 0 -0.04828 6.304424e-05
> 1 -5.15980e+10 -inf
> 2 -5.15980e+10 -inf
> 3 -5.15980e+10 -inf
> 4 -5.15980e+10 -inf
> 5 -5.15980e+10 -inf
> 6 -5.15980e+10 -inf
> 7 -5.15980e+10 -inf
> 8 -5.15980e+10 -inf
> 9 -5.15980e+10 -inf
> 10 -5.15980e+10 -inf
> 11 -5.15980e+10 -inf
> 12 -5.15980e+10 -inf
> 13 -5.15980e+10 -inf
> 14 -5.15980e+10 -inf
> 15 -5.15980e+10 -inf
> 16 -5.15980e+10 -inf
> 17 -5.15980e+10 -inf
> 18 -5.15980e+10 -inf
> 19 -5.15980e+10 -inf
> 20 -5.15980e+10 -inf
> 21 -5.15980e+10 -inf
> 22 -5.15980e+10 -inf
> 23 -5.15980e+10 -inf
> 24 -5.15980e+10 -inf
>
>
>
> Best,
>
>
> Zhaoming Su, Ph.D.
>
> Research Scientist, Bioengineering
>
> Stanford University
>
> ________________________________
> From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask]> on behalf of Domen Kampjut <[log in to unmask]>
> Sent: Friday, September 28, 2018 7:45:40 AM
> To: [log in to unmask]
> Subject: [ccpem] Bayesian Polishing b-factor fitting error
>
> Dear All,
>
> I keep running into an error when trying to polish particles in
> relion3.0. Polishing job starts normally and estimated per-particle
> motion for all micrographs look very reasonable judging from the .eps
> files in the Micrographs subfolder. Estimating B-factors fails after
> 10th frame though (see the bfactors.star output below) and the job
> terminates with segmantation fault. I only see this error in the dataset
> collected with a K2 camera as packed .mrc movies using EPU. Polishing of
> Falcon-III movies works fine. Also, if I limit the polishing job to the
> first 9 frames the job completes normally. Please let me know if anyone
> else observed the same error and what you would need to reproduce it.
>
> Many thanks and best wishes,
>
> Domen Kampjut
>
>
>
> --------------------------------------------------------------
>
> data_perframe_bfactors
>
> loop_
> _rlnMovieFrameNumber #1
> _rlnBfactorUsedForSharpening #2
> _rlnFittedInterceptGuinierPlot #3
> 0 -10.90545 0.048441
> 1 -0.08144 -0.21434
> 2 -0.08144 -0.26051
> 3 -3.19811 -0.29255
> 4 -5.69430 -0.29903
> 5 -12.85827 -0.27141
> 6 -19.60021 -0.24128
> 7 -22.26604 -0.23126
> 8 -28.06880 -0.19417
> 9 -30.55454 -0.11258
> 10 -8.80873e+10 -inf
> 11 -8.80873e+10 -inf
> 12 -8.80873e+10 -inf
> 13 -8.80873e+10 -inf
> 14 -8.80873e+10 -inf
> 15 -8.80873e+10 -inf
> 16 -8.80873e+10 -inf
> 17 -8.80873e+10 -inf
> 18 -8.80873e+10 -inf
> 19 -8.80873e+10 -inf
> 20 -8.80873e+10 -inf
> 21 -8.80873e+10 -inf
> 22 -8.80873e+10 -inf
> 23 -8.80873e+10 -inf
> 24 -8.80873e+10 -inf
> 25 -8.80873e+10 -inf
> 26 -8.80873e+10 -inf
> 27 -8.80873e+10 -inf
> 28 -8.80873e+10 -inf
> 29 -8.80873e+10 -inf
> 30 -8.80873e+10 -inf
> 31 -8.80873e+10 -inf
> 32 -8.80873e+10 -inf
> 33 -8.80873e+10 -inf
> 34 -8.80873e+10 -inf
> 35 -8.80873e+10 -inf
> 36 -8.80873e+10 -inf
> 37 -8.80873e+10 -inf
> 38 -8.80873e+10 -inf
> 39 -8.80873e+10 -inf
>
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