Then probably the error lies somewhere in the incorporation of the 
particles from the other program. Most likely, still some tweaks to the 
STAR file are needed. You could run the tutorial data in 1.4 and 
replicate _exactly_ the star files generated there.
HTH,
Sjors


On 09/20/2015 10:32 PM, Huy Bui wrote:
> Dear Sjors,
>
> I convert my particles from another program into Relion. That Star format
> is in Relion 1.3 because I wrote the conversion based on an old project.
> But the extraction using Relion 1.4 .  I refined it using local search
> until it converged using Relion 1.4. I extracted the particle movie stack
> in Relion 1.4. And try to do 3D refinement with movie frames by continueing
> the refinement from the last iteration of the previous refinement without
> any scripting on that.
>
> The header
>
> I checked the star file, it say rlnOriginalParticleName.
>
> Best,
> H
>
> A few lines of the particle_movie.star
>
> data_
>
> loop_
> _rlnMicrographName #1
> _rlnCoordinateX #2
> _rlnCoordinateY #3
> _rlnImageName #4
> _rlnDefocusU #5
> _rlnDefocusV #6
> _rlnDefocusAngle #7
> _rlnVoltage #8
> _rlnSphericalAberration #9
> _rlnAmplitudeContrast #10
> _rlnMagnification #11
> _rlnDetectorPixelSize #12
> _rlnCtfFigureOfMerit #13
> _rlnOriginalParticleName #14
> [log in to unmask]   921.000000  3450.000000
> [log in to unmask] 37038.140625
> 37512.000000    60.000000   300.000000     2.700000     0.100000
> 1.003580e+05    14.000000     0.074040 000001@Particles
> /Micrographs/00001_particles.mrcs
> [log in to unmask]  1022.000000  3510.000000
> [log in to unmask] 37038.140625
> 37512.000000    60.000000   300.000000     2.700000     0.100000
> 1.003580e+05    14.000000     0.074040 000002@Particles
> /Micrographs/00001_particles.mrcs
>
>
> The header of the particles star file after sum micrograph refinement
>
> data_images
>
> loop_
> _rlnVoltage #1
> _rlnDefocusU #2
> _rlnDefocusV #3
> _rlnDefocusAngle #4
> _rlnSphericalAberration #5
> _rlnDetectorPixelSize #6
> _rlnCtfFigureOfMerit #7
> _rlnMagnification #8
> _rlnAmplitudeContrast #9
> _rlnImageName #10
> _rlnCoordinateX #11
> _rlnCoordinateY #12
> _rlnMicrographName #13
> _rlnGroupNumber #14
> _rlnOriginXPrior #15
> _rlnOriginYPrior #16
> _rlnAngleRotPrior #17
> _rlnAngleTiltPrior #18
> _rlnAnglePsiPrior #19
> _rlnClassNumber #20
> _rlnNormCorrection #21
> _rlnLogLikeliContribution #22
> _rlnMaxValueProbDistribution #23
> _rlnNrOfSignificantSamples #24
> _rlnAngleRot #25
> _rlnAngleTilt #26
> _rlnAnglePsi #27
> _rlnOriginX #28
> _rlnOriginY #29
> _rlnRandomSubset #30
>    300.000000 37038.101562 37512.000000    60.000000     2.700000
>   14.000000     0.074040 1.003584e+05     0.100000
> [log in to unmask]
>    921.000000  3450.000000 Micrographs/00001.mrc            1    51.340000
> -13.540000  -161.949997    89.000000   150.339996            1     0.923720
> 1.021892e+05     0.003095          420  -162.033951    88.598114
> 150.391129   -57.743996   -18.992996            1
>
>
>
> On Sun, Sep 20, 2015 at 1:49 PM, Sjors Scheres <[log in to unmask]>
> wrote:
>
>> Hi Huy,
>> How were the particle and movie-particle star files generated? Also in
>> relion-1.4? Or did you perform any sort of scripting on it?
>> Also, did you see this on the WIki?
>>
>> http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Known_issue#Movie-refinement_does_not_work_with_particles_movie.star_file_made_in_release-1.3
>> In the header of the particles_movie.star rename rlnParticleName to
>> rlnOriginalParticleName.
>>
>> HTH,
>> Sjors
>>
>>
>>
>>> Dear Sjors and list,
>>>
>>> I am running the 3d refinement with movie frames (Falcon 2, 7 frames) in
>>> Relion 1.4
>>>
>>> mpirun -n 3 `which relion_refine_mpi` --o Refine3D/movie_ct27 --continue
>>> Refine3D/run2_bin1_ct25_it027_optimiser.star --solvent_mask mask512.mrc
>>> --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4
>>> --offset_range 5 --offset_step 2 --realign_movie_frames
>>> particles_movie.star --movie_frames_running_avg 1 --sigma_off 2
>>> --skip_rotate --skip_maximize  --j 3
>>>
>>>
>>> The errors I got is:
>>>
>>>   Expanding current model for movie frames...
>>>    12/  12 sec
>>>
>> ..........................................................~~(,_,">Experiment::expandToMovieFrames:
>>> ERROR: no movie frames selected. Check filenames of micrographs, movies
>>> and
>>> particle stacks!
>>>
>>>
>>> My micrograph and particle name and paths are exact as in guide line:
>>> Micrographs/00001.mrc
>>> Micrographs/00001_movie.mrcs
>>> ...
>>> Particles/Micrographs/00001_particles.mrcs
>>> Particles/Micrographs/00001_movie_particles.mrcs
>>> ...
>>>
>>> The star file definitely contains correct path.
>>>
>>> I searched the mailing list and saw that several people had the same
>>> problem. One get rid of it by naming correctly. Is there any way to check
>>> what is wrong?
>>>
>>> Best regards,
>>> Huy
>>>
>>
>> --
>> 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