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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