Hi,
OK, the log indicates that multibody refinement itself has finished
successfully.
What happens if you run relion_flex_analyse from the command line?
The command is in the note.txt and should look like:
`which relion_flex_analyse` --PCA_orient --model
MultiBody/job092/run_model.star --data MultiBody/job092/run_data.star
--bodies bodies.star --o MultiBody/job092/analyse --do_maps --k 5
> Also, a combined map of two bodies together is not produced - should it
> be?, or it needs to made separately, e.g. in Chimera?
This is intended. There is no combined map.
Best regards,
Takanori Nakane
> Dear Takanori,
>
> This is the end of "run.out" file:
>
> ?Auto-refine: Refinement has converged, stopping now...
> ?Auto-refine: + Final reconstruction from all particles is saved as:
> MultiBody/job1110/run_ct15_class001.mrc
> ?Auto-refine: + Final model parameters are stored in:
> MultiBody/job1110/run_ct15_model.star
> ?Auto-refine: + Final data parameters are stored in:
> MultiBody/job1110/run_ct15_data.star
> ?Auto-refine: + Final resolution (without masking) is: 3.40645
> ?Auto-refine: + But you may want to run relion_postprocess to mask the
> unfil.mrc maps and calculate a higher resolution FSC
>
> Last files produced:
>
> run_ct15_half2_body001_unfil.mrc
> run_ct15_half2_body002_unfil.mrc
> run_ct15_half1_body001_unfil.mrc
> run_ct15_half1_body002_unfil.mrc
> run_ct15_data.star
> run_ct15_body001.mrc
> run_ct15_body002.mrc
> run_ct15_body001_angdist.bild
> run_ct15_body002_angdist.bild
> run_ct15_model.star
> run_ct15_sampling.star
> run.out
>
> After that there is no CPU activity, so it does not go into PCA step.
>
> Also, a combined map of two bodies together is not produced - should it
> be?, or it needs to made separately, e.g. in Chimera?
>
> Thanks for your help!
>
> Leonid
>
> Prof. Leonid Sazanov
> IST Austria
> Am Campus 1
> A-3400 Klosterneuburg
> Austria
>
> Phone: +43 2243 9000 3026
> E-mail: [log in to unmask]
>
> On 12/08/18 21:08, Takanori Nakane wrote:
>> Hi,
>>
>> Yes, it should work without GPU.
>>
>> A MultiBody job proceeds in two steps.
>>
>> (1) multi-body refinement itself (relion_refine_mpi)
>> (2) PCA analysis (relion_flex_analyser)
>>
>> Could you please look at the log file and see which step failed?
>> Did the first step say "refinement has converged" and produce
>> relevant STAR files?
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2018/08/12 16:30, Leonid Sazanov wrote:
>>> Hi, great new features in Relion3.0!
>>>
>>> A question - after running multibody refinement we don't get out the
>>> results of PCA analysis, even though this option is set to "yes" in
>>> GUI. The program stops but is not marked as finished. Is it supposed
>>> to be working in CPU version of 3.0beta (the only one we have working
>>> so far)?
>>>
>>> Many thanks!
>>>
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>>
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