Hi Matt,
This makes sense: you provided the refinement program with a 2D reference,
which prompted it to perform a 2D refinement. For those of you interested
in getting the best possible 2D class averages (not often needed, but who
knows), one can use this same procedure intentionally.
HTH,
Sjors
> I’ve solved my own problem if anyone is interested…
> When I scaled the model I used proc2D instead of proc3D accidentally
> generating a 2D volume as the model…
> When I did it properly using relion_image_handler everything worked fine.
>
>
>
>
> --
> Matthew Iadanza
> Postdoctoral Research Fellow
> Ranson and Radford Labs
> Astbury Center for Structural Molecular Biology
> University of Leeds
> Leeds, LS2 9JT United Kingdom
> [log in to unmask]<mailto:[log in to unmask]>
>
>
>
>
> On 25 Oct 2016, at 15:37, Matthew Iadanza
> <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> I've encountered a strange problem. I'm running a 3D auto refine on a set
> of particles, when the job converges and finishes I get the following in
> the log as expected:
>
>
> Auto-refine: Refinement has converged, stopping now...
> Auto-refine: + Final reconstruction from all particles is saved as:
> Refine3D/job097/run_class001.mrc
> Auto-refine: + Final model parameters are stored in:
> Refine3D/job097/run_model.star
> Auto-refine: + Final data parameters are stored in:
> Refine3D/job097/run_data.star
> Auto-refine: + Final resolution (without masking) is: 8.83333
> Auto-refine: + But you may want to run relion_postprocess to mask the
> unfil.mrc maps and calculate a higher resolution FSC
>
> but the job doesn't move to the finished list and when I look in the
> Refine3D directory the file run_class001.mrc is not there. Instead I see
> the following files:
> run_half1_class001_unfil.mrc
> run_half2_class001_unfil.mrc
>
> which are 2D class averages rather than the expected 3D halfmaps.
>
> The following files are produced in the last iteration:
> Refine3D/job097/run_it019_data.star
> Refine3D/job097/run_it019_half1_classes.mrcs
> Refine3D/job097/run_it019_half1_model.star
> Refine3D/job097/run_it019_half2_classes.mrcs
> Refine3D/job097/run_it019_half2_model.star
> Refine3D/job097/run_it019_optimiser.star
> Refine3D/job097/run_it019_sampling.star
>
> All of the mrcs files are 2D it almost looks like the program is confused
> and at least partially doing a 2D refinement.
>
> Any help would be appreciated.
> Matt I
>
>
--
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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