We've encountered similar problems: probably related to hardware trouble
when writing the movies originally to disc. If it's just one or two
missing frames in a few movies you may also "rescue" those by just
adding the last frame of it multiple times. You could use
relion_stack_create (or any other MRC stack handling program) to do this.
HTH, S
On 04/03/2014 12:08 PM, Radostin Danev wrote:
> Hi Sjors,
>
> Thank you for your quick response!
>
> I checked and indeed, a few movies have less frames than the rest. I will
> remove them from the .star files and try again.
>
> Rado
>
>
> -----Original Message-----
> From: Collaborative Computational Project in Electron cryo-Microscopy
> [mailto:[log in to unmask]] On Behalf Of Sjors Scheres
> Sent: 03 April 2014 12:42
> To: [log in to unmask]
> Subject: Re: [ccpem] Refine with movies error
>
> Hi Rado,
>
> All particles in your movie.star file have to have the same number of movie
> frames. This is currently not the case in your data. If you have different
> exposure times (and thus frame numbers) in one data set, I would recommend
> using the highest number of frames they have in common.
>
> If you think your data all should have the same number of frames, then have
> a close look at all your movies to double check for errors.
>
> HTH,
> S
>
> On 04/03/2014 10:51 AM, Radostin Danev wrote:
>> Hi everyone,
>>
>> I searched the archives but did not find a similar problem reported
>> before, so here it goes ...
>>
>> I am trying to refine with movies. Continuing from a previous
>> non-movie 3D refinement which used grouped particles gave me the following
> error:
>> .............
>>
>> + Slave 125 runs on host = hpcl3009.biochem.mpg.de
>> + Slave 126 runs on host = hpcl3009.biochem.mpg.de
>> + Slave 127 runs on host = hpcl3009.biochem.mpg.de
>> =================
>> Expanding current model for movie frames...
>> MlModel::expandToMovieFrames ERROR: unequal number of frames in
>> groupgroup_20
>> File: src/ml_model.cpp line: 553
>> MlModel::expandToMovieFrames ERROR: unequal number of frames in
>> groupgroup_20
>> File: src/ml_model.cpp line: 553
>> MlModel::expandToMovieFrames ERROR: unequal number of frames in
>> groupgroup_20
>> File: src/ml_model.cpp line: 553
>> MlModel::expandToMovieFrames ERROR: unequal number of frames in
>> groupgroup_20
>> File: src/ml_model.cpp line: 553
>> ----------------------------------------------------------------------
>> ---- MPI_ABORT was invoked on rank 51 in communicator MPI_COMM_WORLD
>> with errorcode 1.
>>
>> .............
>>
>> Thinking that it is a problem with the grouping I then tried to
>> continue from a 3D refinement which used the non-grouped original
>> particles.star file.
>> This seemed to work but then it gave the following error:
>>
>> ............
>>
>> =============================
>> Oversampling= 1 NrHiddenVariableSamplingPoints= 3924566016
>> OrientationalSampling= 0.234375 NrOrientations= 107600
>> TranslationalSampling= 1.125 NrTranslations= 196
>> =============================
>> Expectation iteration 34
>> 1.02/13.72 hrs ....~~(,_,"> exp_thisparticle_sumweight= -nan [oo]
>> exp_part_id= 13697exp_iimage=11
>> group_id= 87 mymodel.scale_correction[group_id]= 0.831255
>> exp_ipass= 0
>> sampling.NrDirections(0, true)= 3259 sampling.NrDirections(0, false)=
> 535
>> sampling.NrPsiSamplings(0, true)= 768 sampling.NrPsiSamplings(0, false)=
> 26
>> mymodel.sigma2_noise[exp_ipart]=
>> 0.04963
>> 0.001015
>> (skipped a lot of numbers)
>> 9.566e-06
>> 8.995e-06
>>
>> wsum_model.sigma2_noise[exp_ipart]=
>> 0
>> 0
>> (skipped a lot of numbers) 0
>> 0
>> 0
>>
>> written out Mweight.spi
>> exp_thisparticle_sumweight= -nan
>> exp_min_diff2[exp_ipart]= 9.9e+100
>> slave 125 encountered error: ERROR!!! zero sum of weights....
>> File: src/ml_optimiser.cpp line: 3929
>> +++ RELION: command line arguments (with defaults for optional ones
>> +++ between
>> parantheses) +++
>>
>> ..........
>>
>> What could be the problem?
>>
>> Thanks!
>>
>> Rado
> --
> 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
--
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
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