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CCPEM  February 2014

CCPEM February 2014

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Subject:

Re: Refinement_with_movies_error

From:

Sjors Scheres <[log in to unmask]>

Reply-To:

Sjors Scheres <[log in to unmask]>

Date:

Thu, 27 Feb 2014 09:17:59 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (118 lines)

Hi Matteo,
Apparently, the movie particles have not been extracted using the exact 
same coordinate files as for the "average particles". This is crucial. 
Make sure you follow exactly this page: 
http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Process_movies
HTH, S


On 02/27/2014 08:37 AM, Matteo Allegretti wrote:
> Dear Sjors,
> I am encountering an error when I try to launch autorefine "continue old
> run" with movies. Actually the image number in the error reported below
> change...
> What would you suggest?
>
> Another question: can the grouping procedure be coupled with the movie-
> refinement?
>
> Thank you so much,
> Matteo
>
>   Expectation iteration 21
> 10.93/50.82 min ............~~(,_,">master encountered error: readMRC:
> Image number 73 exceeds stack size 72
> File: ./src/rwMRC.h line: 189
> +++ RELION: command line arguments (with defaults for optional ones
> between parantheses) +++
> ====== Continue options =====
>                           --continue : _optimiser.star file of the
> iteration after which to continue
> ====== General options =====
>                        --o (OLD_ctX) : Output rootname
>                         --iter (OLD) : Maximum number of iterations to perform
>                   --tau2_fudge (OLD) : Regularisation parameter (values
> higher than 1 give more weight to the data)
>              --flatten_solvent (OLD) : Switch on masking on the references?
>                 --solvent_mask (OLD) : User-provided mask for the references
>                --solvent_mask2 (OLD) : User-provided secondary mask
>                          --tau (OLD) : STAR file with input tau2-spectrum
> (to be kept constant)
>            --particle_diameter (OLD) : Diameter of the circular mask that
> will be applied to the experimental images (in Angstroms)
>         --join_random_halves (false) : Join previously split random halves
> again (typically to perform a final reconstruction).
> ====== Re-align movie frames =====
>            --realign_movie_frames () : Input STAR file with the movie frames
>                --nr_frames_prior (5) : Number of movie frames to calculate
> running-average priors
>       --movie_frames_running_avg (3) : Number of movie frames in each
> running average
> ====== Orientations =====
>                 --oversampling (OLD) : Adaptive oversampling order to
> speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
>                --healpix_order (OLD) : Healpix order for the angular
> sampling rate on the sphere (before oversampling):
> hp2=15deg, hp3=7.5deg, etc
>                     --psi_step (OLD) : Angular sampling (before
> oversampling) for the in-plane angle (default=10deg for
> 2D, hp sampling for 3D)
>                 --offset_range (OLD) : Search range for origin offsets (in
> pixels)
>                  --offset_step (OLD) : Sampling rate for origin offsets (in
> pixels)
>     --auto_local_healpix_order (OLD) : Minimum healpix order (before
> oversampling) from which auto-refine procedure will use local searches
>                    --sigma_ang (OLD) : Stddev on all three Euler angles for
> local angular searches (of +/- 3 stddev)
>                    --sigma_rot (OLD) : Stddev on the first Euler angle for
> local angular searches (of +/- 3 stddev)
>                   --sigma_tilt (OLD) : Stddev on the first Euler angle for
> local angular searches (of +/- 3 stddev)
>                    --sigma_psi (OLD) : Stddev on the in-plane angle for
> local angular searches (of +/- 3 stddev)
>                    --sigma_off (OLD) : Stddev. on the translations
> ====== Corrections =====
>                        --scale (OLD) : Switch on intensity-scale
> corrections on image groups
>                         --norm (OLD) : Switch on normalisation-error
> correction
> ====== Computation =====
>                              --j (1) : Number of threads to run in parallel
> (only useful on multi-core machines)
>                         --pool (OLD) : Number of images to be processed
> together
>                  --cpus_per_node (8) : Maximum number of models for which
> the FT can be set simultaneously (decrease in case of
> memory problems in this step)
>                           --verb (1) : Verbosity (1=normal, 0=silent)
> ====== Expert options =====
>           --strict_highres_exp (OLD) : Resolution limit (in Angstrom) to
> restrict probability calculations in the expectation step
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
>
>
> --
>
> Matteo Allegretti
> PhD candidate
>
> Max Planck Institut für Biophysik
> Max-von-Laue-Straße 3
> D-60438 Frankfurt am Main
> Office: +49-69-6303-3015

-- 
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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