Hi Laurence,
You can limit the resolution in the E-step using the corresponding
option on the Optimisation tab. Not sure that will solve your problem
though.
I would probably proceed into 3D, and then solve the classification
problem there. It might sort itself out in 3D (where more particles are
"averaged" together, or you may try the relion_particle_symmetry_expand
program, as explained in section 4.7 of our chapter in Meth Enzym:
http://dx.doi.org/10.1016/bs.mie.2016.04.012
HTH,
Sjors
On 01/03/2018 04:14 PM, Laurence Pearl wrote:
> Can anyone point me at any case studies and/or effective protocols for 2D classification of particles that are overall asymmetric, but have a highly symmetry and well ordered major sub-component. Standard 2D classification using RELION produces class averages showing superb detail for the symmetric sub-structure, even to the level of evident secondary structure, but results in the asymmetric components becoming partly symmetrised and consequently blurred. These are also the parts of the complex likely to show the greatest conformational variability anyway.
>
> My instinct as an old-time crystallographer steeped in Blow and Rossman rotation functions, is to restrict the 2D classification to much lower resolution, where the internal symmetry would be blurred out and the overall asymmetric shape would be more dominant in defining the relative orientations. However there are no obvious resolution filters in the RELION 2D GUI.
>
> There may well be much more effective/cleverer ways of achieving this.
>
> All suggestions welcome.
>
> --------------------------------------------------------------------------------
> Laurence H. Pearl PhD FRS FMedSci
>
> Professor of Structural Biology
> Genome Damage and Stability Centre
> School of Life Sciences, University of Sussex
> Brighton, BN1 9RQ, UK
>
> +44-(0)1273 678349
> --------------------------------------------------------------------------------
> "Live Modestly and do Serious Things .."
> - Dorothy Crowfoot Hodgkin
> --------------------------------------------------------------------------------
>
>
>
>
--
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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