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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