Hi Dani,
Did you repair the bug in your relion version as indicated here:
http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Known_issue#Movie-extraction_with_first_frame_not_being_number_1
In general, we always use all frames. B-factor weighting will just
downweight the highest freqs in the first few frames, but there often is
still a lot of useful information in those early frames.
Also, did you check how the plots of B and scale-factors in the
_bfactors.star file look?
HTH,
S
> Hello,
>
> I am trying to do a Particle polishing step in the relion processing of a
> set of virus particles. The extraction of the movie particles (from frame
> 3 to frame 21 of 24 frames) and the refinement of that movie particles
> (using a running window of 5) seems to work nicely. Then, when I run the
> particle polishing (with a running window of 5, a Stddev on particle
> distance of 300, and performing b-factor weighting with highres-limit 6 A
> and lowres-limit 20A), all the shiny particles that I obtain in
> shiny.star are black (seems to be 0 in all their pixels). However, If i
> run exactly the same particle polishing without b-factor weighting, I
> obtain a nice-looking set of shiny particles. Thus, the problem seems to
> be the b-factor weighing.... Any idea? Should I try different parameters?
>
> Thanks in advance,
>
> Kind Regards,
>
> Daniel
>
--
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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