Hi,
Thank you very much for this report.
I updated relion_reconstruct to give an error if --mask_diameter was not
specified with --ewald.
Best regards,
Takanori Nakane
> Hi all,
>
> I have found this issue too. It can be rectified by applying the
> --mask_diameter option. If you don’t apply a mask, the result is a
> featureless blob.
>
> Best,
> Charles
>
> On Fri, 26 Oct 2018 at 9:21 pm, David Bhella <[log in to unmask]>
> wrote:
>
>> Hi,
>>
>> I also have an ewald sphere question - I too have a map around 2.8
>> angstroms from refine3D after CTF refinement, but when I add ?ewald to
>> the
>> relion_reconstruct command I just get a white sphere.
>>
>> According to post-process the resolution is great - goes to Nyquist,
>> Marin
>> would love it…
>> I am however having some trouble interpreting the map :-)
>>
>> Images attached for with and without ?ewald
>>
>> Suggestions for how to not mess this up would be gratefully received!
>>
>> D.
>>
>> Dr David Bhella
>> Director - Scottish Centre for Macromolecular Imaging
>>
>> MRC-University of Glasgow Centre for Virus Research
>> Sir Michael Stoker Building
>> Garscube Campus
>> 464 Bearsden Road
>> <https://maps.google.com/?q=464+Bearsden+Road+%0D%0AGlasgow+G61+1QH+%0D%0AScotland+(UK&entry=gmail&source=g>
>> Glasgow G61 1QH
>> <https://maps.google.com/?q=464+Bearsden+Road+%0D%0AGlasgow+G61+1QH+%0D%0AScotland+(UK&entry=gmail&source=g>
>> Scotland (UK
>> <https://maps.google.com/?q=464+Bearsden+Road+%0D%0AGlasgow+G61+1QH+%0D%0AScotland+(UK&entry=gmail&source=g>
>> )
>>
>> Telephone: 0141-330-3685
>> Skype: d.bhella
>>
>>
>> On 26 Oct 2018, at 10:51, Tasuku HAMAGUCHI <[log in to unmask]> wrote:
>>
>> Dear all,
>>
>> I obtained a 3D structure of a spherical virus with a diameter of about
>> 300 A by RELION-3 beta.
>> 3D auto refine and postprocess produced a 2.88 A resolution map.
>>
>> Then, I tried relion_reconstruct --ewald with and without
>> --reverse_curvature as,
>>
>> relion_reconstruct --i Refine3D/job172/run_data.star --o
>> reverse_half1.mrc
>> --subset 1 --angpix 1.24 --ctf --ewald --mask_diameter 400 --sectors 2
>> --width_mask_edge 5 --sym I1 --reverse_curvature
>>
>> Here Refine3D/job172/run_data.star is output from 3D auto refine.
>>
>> Postprocessing the resulting maps showed 2.91A and 3.05A resolutions
>> with
>> and without --reverse_curvature, respectively.
>>
>> So I think Ewald sphere correction is effective, but the resolution by
>> relion_reconstruct --ewald is lower than by auto refine (with no Ewald
>> sphere correction).
>> I wonder if there is a way to improve the resolution of the original 3D
>> auto-refined map (2.88 A resolution) by Ewald sphere correction.
>>
>> Thank you in advance,
>> Best regards,
>>
>> Tasuku
>>
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> --
> _________________
>
> *Charles Bayly-Jones*
> BSc(ScSchProg)(Hons)
>
> *PhD Candidate*
> *Teaching Associate*
>
> *Monash Biomedicine Discovery Institute*
> *Department of Biochemistry and Molecular Biology*
> Level 2, Building 77
> 23 Innovation Walk
> Clayton VIC 3800
> Australia
>
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