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<p style="margin-top:0;margin-bottom:0">Hi Sjors, <br>
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<p style="margin-top:0;margin-bottom:0">Thank you for the really helpful update. That does sound very promising.
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<p style="margin-top:0;margin-bottom:0">Best,<br>
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<div style="font-family:Tahoma; font-size:13px">Kimberley Gibson<br>
<br>
Research Associate, Charles Sindelar Lab<br>
<br>
Dept. Molecular Biophysics and Biochemistry<br>
Yale University<br>
<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Sjors Scheres <scheres@mrc-lmb.cam.ac.uk><br>
<b>Sent:</b> Thursday, June 7, 2018 3:25:24 PM<br>
<b>To:</b> Gibson, Kimberley<br>
<b>Cc:</b> Steinar Halldorsson; 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> Re: [3dem] Missing wedge masking in RELION</font>
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<div class="PlainText">Hi Kimberley, Steinar,<br>
The way this is done is published: see Bharat et al, Structure 2016.<br>
Kimberley, yes you are right, and we are on this one! We are working with<br>
the Briggs group to generate better 3D CTFs for subsequent use in relion<br>
refinement and classification. Hopefully more about this some time in the<br>
medium-future.<br>
HTH,<br>
Sjors<br>
<br>
<br>
>>From personal experience, after using RELION to perform subvolume<br>
>> averaging on a structure with an extreme preferred orientation - that<br>
>> even tomography would struggle to overcome - I found that RELION did tend<br>
>> to overcompensate the missing wedge. Upon looking at the 3D FTs of our<br>
>> averaged structure, we noticed that much of the Fourier space was filled<br>
>> in and we were rather optimistic about the results. I would approach<br>
>> these results a little more cautiously now as I believe that RELION was<br>
>> blurring together certain features which are now more resolvable using<br>
>> other programs that do apply wedge masking. This is something that could<br>
>> be discussed for future updates to RELION and incorporated into the<br>
>> pipeline, hopefully.<br>
><br>
> Sincerest regards,<br>
><br>
> Kimberley Gibson<br>
><br>
> Research Associate, Charles Sindelar Lab<br>
><br>
> Dept. Molecular Biophysics and Biochemistry<br>
> Yale University<br>
><br>
> ________________________________<br>
> From: 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Steinar Halldorsson<br>
> <steinar.halldorsson@crick.ac.uk><br>
> Sent: Wednesday, June 6, 2018 5:32:58 AM<br>
> To: 3dem@ncmir.ucsd.edu<br>
> Subject: [3dem] Missing wedge masking in RELION<br>
><br>
><br>
> Dear Tomography folks<br>
><br>
><br>
> A question regarding sub-tomogram averaging in Relion, how does the<br>
> software treat the missing wedge? Wishful thinking, but does it in any way<br>
> automatically apply a mask to the individual particles? Is there a way (or<br>
> will there be a way in the next versions) to apply such a mask?<br>
><br>
><br>
> Many thanks,<br>
><br>
> Steinar<br>
><br>
> The Francis Crick Institute Limited is a registered charity in England and<br>
> Wales no. 1140062 and a company registered in England and Wales no.<br>
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<br>
-- <br>
Sjors Scheres<br>
MRC Laboratory of Molecular Biology<br>
Francis Crick Avenue, Cambridge Biomedical Campus<br>
Cambridge CB2 0QH, U.K.<br>
tel: +44 (0)1223 267061<br>
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