Hi Dani,
Yes, please do re-extract and re-run the movie refinement. The B-factor
and scale intensity plots should be similar to the ones published in my
latest eLife paper.
HTH,
S
On 12/12/2014 09:07 AM, DANIEL.LUQUE.BUZO.40704 wrote:
> Hi Sjors,
>
> Thanks for your prompt answer
>
> No, I did not repair that bug.
>
> Once done, It is necesary to re-run the extraction of the movie particles
> and the refinement of these movie particles before perform the particle
> polishing, isn't it?
>
> I also did not ckecked _bfactors.star files. As I already deleted those
> files, I will check them once I re-run the process. How do they must
> look-like?
>
> Thanks!
>
> Kind Regards,
>
> Dani
>
> Quoting Sjors Scheres <[log in to unmask]>:
>
>> 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 267061http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>
--
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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