[3dem] Missing wedge masking in RELION

[Gibson, Kimberley]

Hi Sjors,


Thank you for the really helpful update. That does sound very promising.


Best,


Kimberley Gibson

Research Associate, Charles Sindelar Lab

Dept. Molecular Biophysics and Biochemistry
Yale University

________________________________
From: Sjors Scheres <scheres at mrc-lmb.cam.ac.uk>
Sent: Thursday, June 7, 2018 3:25:24 PM
To: Gibson, Kimberley
Cc: Steinar Halldorsson; 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] Missing wedge masking in RELION

Hi Kimberley, Steinar,
The way this is done is published: see Bharat et al, Structure 2016.
Kimberley, yes you are right, and we are on this one! We are working with
the Briggs group to generate better 3D CTFs for subsequent use in relion
refinement and classification. Hopefully more about this some time in the
medium-future.
HTH,
Sjors


>>From personal experience, after using RELION to perform subvolume
>> averaging on a structure with an extreme preferred orientation - that
>> even tomography would struggle to overcome - I found that RELION did tend
>> to overcompensate the missing wedge. Upon looking at the 3D FTs of our
>> averaged structure, we noticed that much of the Fourier space was filled
>> in and we were rather optimistic about the results. I would approach
>> these results a little more cautiously now as I believe that RELION was
>> blurring together certain features which are now more resolvable using
>> other programs that do apply wedge masking. This is something that could
>> be discussed for future updates to RELION and incorporated into the
>> pipeline, hopefully.
>
> Sincerest regards,
>
> Kimberley Gibson
>
> Research Associate, Charles Sindelar Lab
>
> Dept. Molecular Biophysics and Biochemistry
> Yale University
>
> ________________________________
> From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Steinar Halldorsson
> <steinar.halldorsson at crick.ac.uk>
> Sent: Wednesday, June 6, 2018 5:32:58 AM
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Missing wedge masking in RELION
>
>
> Dear Tomography folks
>
>
> A question regarding sub-tomogram averaging in Relion, how does the
> software treat the missing wedge? Wishful thinking, but does it in any way
> automatically apply a mask to the individual particles? Is there a way (or
> will there be a way in the next versions) to apply such a mask?
>
>
> Many thanks,
>
> Steinar
>
> The Francis Crick Institute Limited is a registered charity in England and
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--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
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