Dear Sjors,
Thanks, will try to find such set.
I can comment that this is rather small protein (~200 kDa) compared to
our other larger targets, which do work in polishing.
Best,
Leo
Prof. Leonid Sazanov
IST Austria
Am Campus 1
A-3400 Klosterneuburg
Austria
Phone: +43 2243 9000 3026
E-mail: [log in to unmask]
Web: https://ist.ac.at/research/life-sciences/sazanov-group/
On 26/10/2018 07:27, Sjors Scheres wrote:
> Dear Leo,
> You can help with this by searching for the smallest subset of your data
> that still reproduces the error, and then share that test case with us.
> Small is an important word, as we cannot transfer large amounts of data
> and run long jobs for many test cases.
> Please be patient though. Our team works very hard, and the people
> involved volunteer to provide user feedback.
> Best,
> Sjors
>
>
>
> Sent from my phone.
>
> -------- Original message --------
> From: Leonid Sazanov <[log in to unmask]>
> Date: 23/10/2018 20:32 (GMT+09:00)
> To: [log in to unmask]
> Subject: Re: [ccpem] Bayesian Polishing b-factor fitting error
>
> Dear Takanori,
>
> Tried the latest fix (877139d9dd)
>
> Still get the error after frame 9, and this time b-factors for the first
> 9 frames seem to make less sense than before, so it got worse in a way.
>
> What exactly is the problem here, can you describe it briefly, please?
>
> Thanks for your efforts!
>
> Here are new B-factors:
>
> # RELION; version 3.0-beta-2
>
> data_perframe_bfactors
>
> loop_
> _rlnMovieFrameNumber #1
> _rlnBfactorUsedForSharpening #2
> _rlnFittedInterceptGuinierPlot #3
> 0 -1.01236 0.003240
> 1 -11.50108 0.001786
> 2 -16.51618 -0.02748
> 3 -22.32118 -0.01753
> 4 -28.48895 -0.00305
> 5 -31.38510 -0.02080
> 6 -34.23007 -0.01237
> 7 -40.68527 0.020047
> 8 -45.91777 0.041472
> 9 -49.76217 0.125882
> 10 -8.80873e+10 -inf
> 11 -8.80873e+10 -inf
>
> And here are previous on the same data:
>
> # RELION; version 3.0-beta-2
>
> data_perframe_bfactors
>
> loop_
> _rlnMovieFrameNumber #1
> _rlnBfactorUsedForSharpening #2
> _rlnFittedInterceptGuinierPlot #3
> 0 -11.23603 0.049748
> 1 -0.08144 -0.21510
> 2 -0.08144 -0.25988
> 3 -1.65827 -0.30094
> 4 -6.20297 -0.29457
> 5 -12.73199 -0.27411
> 6 -18.13065 -0.24068
> 7 -21.96097 -0.23674
> 8 -26.33093 -0.20546
> 9 -29.74517 -0.11742
> 10 -8.80873e+10 -inf
> 11 -8.80873e+10 -inf
>
> Prof. Leonid Sazanov
> IST Austria
> Am Campus 1
> A-3400 Klosterneuburg
> Austria
>
> Phone: +43 2243 9000 3026
> E-mail: [log in to unmask]
>
> On 19/10/18 20:15, Takanori Nakane wrote:
> > Hi,
> >
> > Jasenko made two more commits (0ad988f, 294ce0d) after I posted
> > here yesterday. Did you try that? If the problem persists,
> > we need more time to investigate. This is not an easy bug to fix.
> >
> > Best regards,
> >
> > Takanori Nakane
> >
> > On 2018/10/19 17:37, Leonid Sazanov wrote:
> >> Dear all,
> >>
> >> We tried this fix, but still get the same error at the same frame.
> >> Please let us know what else can be tried.
> >>
> >> Many thanks,
> >> Leonid
> >>
> >> Prof. Leonid Sazanov
> >> IST Austria
> >> Am Campus 1
> >> A-3400 Klosterneuburg
> >> Austria
> >>
> >> Phone: +43 2243 9000 3026
> >> E-mail: [log in to unmask]
> >> Web: https://ist.ac.at/research/life-sciences/sazanov-group/
> >>
> >> On 17/10/2018 18:55, Takanori Nakane wrote:
> >>> Dear all,
> >>>
> >>> Jasenko made a workaround for this issue.
> >>> This is the latest commit (d9686b9) on our public repository.
> >>>
> >>> Please re-compile the program and 'continue' the job.
> >>> If the trajectories also contain NaNs, it might still produce
> >>> broken particles. If you notice it (i.e. Refine3D crashing),
> >>> please let us know.
> >>>
> >>> Best regards,
> >>>
> >>> Takanori Nakane
> >>>
> >>>> Dear Liz,
> >>>>
> >>>> No, we did not.
> >>>> I really hope developers will answer something, since now there are at
> >>>> least three groups experiencing this problem.
> >>>> Best wishes,
> >>>> Leonid
> >>>>
> >>>> Prof. Leonid Sazanov
> >>>> IST Austria
> >>>> Am Campus 1
> >>>> A-3400 Klosterneuburg
> >>>> Austria
> >>>>
> >>>> Phone: +43 2243 9000 3026
> >>>> E-mail: [log in to unmask]
> >>>> Web: https://ist.ac.at/research/life-sciences/sazanov-group/
> >>>>
> >>>> On 13/10/2018 22:42, Liz Kellogg wrote:
> >>>>> Hi Leonid,
> >>>>>
> >>>>> I'm experiencing the same issues. Did you ever get the issue
> >>>>> resolved?
> >>>>> Thanks
> >>>>>
> >>>>> Liz
> >>>>>
> >>>>> On Sat, Oct 13, 2018 at 10:42 AM Leonid Sazanov <[log in to unmask]
> >>>>> <mailto:[log in to unmask]>> wrote:
> >>>>>
> >>>>> Dear Takanori and Jasenko,
> >>>>>
> >>>>> We still have not resolved this problem (reported by Domen
> >>>>> below),
> >>>>> which seems to happen to others as well.
> >>>>> Does polishing normally work for K2 superresolution images if
> >>>>> they
> >>>>> have binned 2X in motioncor2?
> >>>>> It seems that if we increase memory available the errors
> >>>>> change but
> >>>>> in the end it is always segmentation fault, and always on
> >>>>> frame 10.
> >>>>> Now we used 250 GB memory and still have this error.
> >>>>> Would be great to resolve it.
> >>>>> Many thanks
> >>>>> Best wishes,
> >>>>> Leonid
> >>>>>
> >>>>>
> >>>>> Hi,
> >>>>>
> >>>>>
> >>>>> Thanks for your suggestion. I have checked the directories
> >>>>> but my
> >>>>> FCC files are all of the same size as well (29344 bytes).
> >>>>>
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> Domen
> >>>>>
> >>>>> On 29-Sep-18 0:48, Zhaoming Su wrote:
> >>>>> >
> >>>>> > Hi Takanori and Jasenko,
> >>>>> >
> >>>>> >
> >>>>> > My FCC files have the same size.
> >>>>> >
> >>>>> >
> >>>>> >
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103863_Data_10103657_10103658_20180910_1942_FCC_w0.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103863_Data_10103657_10103658_20180910_1942_FCC_w1.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103863_Data_10103667_10103668_20180910_1938_FCC_cc.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103863_Data_10103667_10103668_20180910_1938_FCC_w0.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103863_Data_10103667_10103668_20180910_1938_FCC_w1.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103571_10103572_20180910_1945_FCC_cc.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103571_10103572_20180910_1945_FCC_w0.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103571_10103572_20180910_1945_FCC_w1.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103579_10103580_20180910_1946_FCC_cc.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103579_10103580_20180910_1946_FCC_w0.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103579_10103580_20180910_1946_FCC_w1.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103589_10103590_20180910_1946_FCC_cc.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103589_10103590_20180910_1946_FCC_w0.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103589_10103590_20180910_1946_FCC_w1.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103603_10103604_20180910_1943_FCC_cc.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103603_10103604_20180910_1943_FCC_w0.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103603_10103604_20180910_1943_FCC_w1.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103612_10103613_20180910_1943_FCC_cc.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103612_10103613_20180910_1943_FCC_w0.mrc
> >>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
> >>>>> FoilHole_10103864_Data_10103612_10103613_20180910_1943_FCC_w1.mrc
> >>>>> >
> >>>>> >
> >>>>> > Best,
> >>>>> >
> >>>>> >
> >>>>> > Zhaoming Su, Ph.D.
> >>>>> >
> >>>>> > Research Scientist, Bioengineering
> >>>>> >
> >>>>> > Stanford University
> >>>>> > From: Takanori Nakane <[log in to unmask]
> >>>>> <mailto:[log in to unmask]>>
> >>>>> > Sent: Friday, September 28, 2018 3:14:59 PM
> >>>>> > To: Zhaoming Su; [log in to unmask]
> >>>>> <mailto:[log in to unmask]>
> >>>>> > Cc: Jasenko Zivanov
> >>>>> > Subject: Re: [ccpem] Bayesian Polishing b-factor fitting
> >>>>> error
> >>>>> >
> >>>>> > 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]
> >>>>> <mailto:[log in to unmask]>>
> >>>>> on behalf of Domen Kampjut <[log in to unmask]
> >>>>> <mailto:[log in to unmask]>>
> >>>>> > > Sent: Friday, September 28, 2018 7:45:40 AM
> >>>>> > > To: [log in to unmask] <mailto:[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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