Dear Chen,
This does not exist. I would encourage you to try symmetry expanding.
Good luck,
Sjors
> Dear EM community,
>
> I am just wondering whether there is a way to set up relion 3D
> classification/refine in such a way that local search is allowed to be
> performed surrounding multiple center points, with each center point
> related to the other center points by symmetry.
>
> I would like to perform this operation because I encountered a tricky case
> which can be simplified as the following. Let's assume the protein is a
> dimer A-A', but global search will align some A' to A. I hope I can apply
> the local search scheme proposed above in 3D classification, so that I
> would be able to get more properly aligned particles that if I simply do a
> standard local search. I understand that symmetry expansion can lead to a
> similar point, but I hope if possible I also have the opportunity to
> extract as much information as possible before symmetry expansion.
>
> I looked at the command line arguments for relion_refine_mpi, and I saw
> that there are arguments:
> --sigma_rot
> --sigma_tilt
> --sigma_psi
> I am thinking whether I could just set --sigma_rot to -1 and the other two
> to a certain local search range. Of course this will search all angular
> values for rot, which is not ideal, but maybe this is enough. And is there
> a better and more proper way of setting this up?
>
> I appreciate all the inputs.
>
> Best,
> Chen
>
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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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