Hi David,
Apparently, your STAR file rlnImageName entries and your MRC stack size do
not agree anymore. Perhaps in using a bigger box size you may have
extracted a few less particles (those near the edge of the micrographs),
so you cannot use old STAR files anymore?
HTH,
S
> Hi Sjors and other Relion users,
>
> I'm trying to complete a polishing run that failed at "+ Reconstructing
> two halves of shiny particles ... " stage, likely as a result of not
> having enough RAM available. After reducing the number of MPI and using
> the Continue Old Run option the run proceeds as normal:
>
> + Reading the input STAR file ...
> + Grouping all particles from the same micrographs ...
> + Using pixel size calculated from magnification and detector pixel size
> in the input STAR file: 1.72001
> + Fitting straight paths for beam-induced movements in all micrographs
> ...
> + Written out all fitted movements in STAR file:
> Refine3D_560box/22k_560box_ct29_ct29_data_run1_shiny_560box_resrange_30to14.star
> +
> Refine3D_560box/22k_560box_ct29_ct29_data_run1_shiny_560box_resrange_30to14_bfactors.star
> already exists: skipping calculation average of per-frame B-factors.
> + run1_shiny_560box_resrange_30to14.star already exists: skipping
> polishing of the particles.
>
> However, it falls down at the reconstruction stage with the following
> error message:
>
> readMRC: Image number 14 exceeds stack size 13
> File: ./src/rwMRC.h line: 189
>
> Do you have any idea as to what might be going wrong and how we can get
> past this sticking point? The only thing of note that is different to our
> previous successful polishing runs is box size; we're trying a 560 pixel
> box this time round, 320 worked in the past.
>
> Many thanks,
>
> David
>
--
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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