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CCPEM  March 2015

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Subject:

Re: movie processing

From:

Sjors Scheres <[log in to unmask]>

Reply-To:

Sjors Scheres <[log in to unmask]>

Date:

Sun, 22 Mar 2015 10:04:44 -0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (75 lines)

that's correct. Use this for particle extraction.
HTH, S
> Hi Sjors,
>
> Thanks for your reply. I contacted with our IT and they said I did run out
> of RAM. Do you mind giving me a clue to average every 3 movie frames
> upon particle
> extraction in RELON? I guess I should use --avg_movie_frames 3.
>
> Thanks,
>
> On Sat, Mar 21, 2015 at 6:03 AM, Sjors Scheres <[log in to unmask]>
> wrote:
>
>> Hi Yan,
>> You may be running out of RAM. Try averaging every 3 movie frames upon
>> particle extraction. That way you end up with 20 frames, which is a more
>> reasonable number.
>> HTH,
>> S
>> > Hi all,
>> >
>> > I was trying to run movie processing in RELION 1.3 by using the
>> command :
>> >
>> > relion_refine_mpi --o Refine3D/movie_60f_7f_ct26 --continue
>> > Refine3D/cont_run1_ct12_it026_optimiser.star --solvent_mask
>> > run1_class001_mask.mrc --oversampling 1 --healpix_order 2
>> > --auto_local_healpix_order 4 --offset_range 5 --offset_step 2
>> > --realign_movie_frames particles_ori_60f_movie_subset.star
>> > --movie_frames_running_avg 7 --sigma_off 1 --skip_rotate
>> --skip_maximize
>> >  --j 1
>> >
>> > Job was stuck at the step of 'Expanding current model for movie
>> frames'
>> > for
>> > about 9 hours and then was killed by signal 9 like the following:
>> >
>> --------------------------------------------------------------------------
>> > orterun noticed that process rank 6 with PID 91141 on node
>> > gcomp-08.cryoem.lsi.umich.edu exited on signal 9 (Killed).
>> >
>> --------------------------------------------------------------------------
>> >
>> > There are 60 frames each micrographs and in total 52K particles for
>> movie
>> > processing. 16Gb RAM was assigned to each thread.
>> >
>> > Any advice would be much appreciated.
>> >
>> > Thanks a lot,
>> > Yan
>> >
>>
>>
>> --
>> 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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