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CCPEM  September 2018

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Subject:

Re: Ewald sphere correction in RELION

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Fri, 7 Sep 2018 16:32:00 +0100

Content-Type:

text/plain

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text/plain (58 lines)

Hi,

Magnification anisotropy correction and Ewald sphere correction are
different concepts.

Unfortunately RELION 3.0 does not support magnification anisotropy
estimation and correction.
We are working for it but it will not be included in version 3.0.

For Ewald sphere correction, please use relion_reconstruct:

relion_reconstruct --i run_data.star --o half1.mrc --subset 1 --angpix 1.23
 --ctf --ewald --mask_diameter 560 --sectors 2 --width_mask_edge 5 --sym I1

Then repeat this for the other half (--subset 2) as well.

See the paper (https://doi.org/10.1016/j.ultramic.2017.11.001)
for the meanings of mask_diameter, sectors and width_mask_edge.

Best regards,

Takanori Nakane

> Dear Community,
>
> Has anyone had any experience with applying ewald sphere correction in
> relion 3.0?
> I understand that this feature is still in beta but I would like to give
> it
> a go. Would be helpful to have some guidance on its usage.
> Specifically, does the program automatically calculate the magnification
> anisotropy *a la* jspr or does it need to be determined at the scope and
> then the correct values applied during the reconstruction?
>
> Cheers,
> pranav
>
> --
> Pranav Shah
> Postdoctoral Research Fellow.
>
> Hogle Lab
> Harvard Medical School
> 240 Longwood Avenue
> Boston, MA 02115
> (617) 432-4360 (fax)
> (617) 432-3839 (lab)
>
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