Hi Qiuye,

1. It should be OK to have some overlap. Probably better to use soft
edges to prevent artefacts.

2. Yes, I would suggest to use C2+helical symmetry, and only provide 1
operator that bring the red F onto the black F in your image.

3. I hope it will be OK, but we have admittedly not tried this ourselves...

Do check the operators using first relion_reconstruct with C2 and the
correct helical symmetry, followed by relion_localsym.

Have fun!

Sjors


On 5/12/21 9:03 PM, Qiuye Li wrote:
> Dear all,
> I'm currently working on the structure of a filament with four
> protofilaments. The top view can be simplified as the attached image.
> So far I have processed with C2 symmetry and got a map of ~3A. If the
> four protofilaments are indeed identical, one should improve the map
> with local symmetry imposed. Right now I briefly created four masks
> covering each protofilament and just started operator search, but my
> questions would be:
> 1. Does it matter if the mask covers another protofilament slightly,
> or missing small parts of its protofilament (eg. side chains,
> terminus)? Which way is safer? The interaction is really tight.
> 2. Should I use the C2 symmetry and helical symmetry option together
> with the local symmetry operator in 3D refinements? Or is it possible
> to force the overall C2 symmetry and helical symmetry in the local
> symmetry operator?
> 3. If the approach I mentioned here is not practical at all, are there
> other workarounds?
> Any inputs are highly appreciated, thanks!
>
> Best regards,
> Qiuye
>
>
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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
http://www2.mrc-lmb.cam.ac.uk/groups/scheres

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