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Subject:

Re: FSC calculation on C9 symmetry particle.

From:

Sjors Scheres <[log in to unmask]>

Reply-To:

Sjors Scheres <[log in to unmask]>

Date:

Wed, 9 May 2018 16:38:42 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (46 lines)

Dear Pu,

As long as you've refined in C9, the postprocessing will take the C9
symmetry into account. Often it is the mask used for post-processing
that causes problems. Is the red line in the generated pdf logfile (the
FSC between the phase-randomised maps) around zero beyond 4-4.5A
resolution? If not, that needs fixing.

HTH,

Sjors



On 05/09/2018 04:03 PM, Pu Qian wrote:
> Dear All,
>
> I'm working on a particle which have C9 symmetry but only has 100 kDa
> MW. RELION works well before 3D classification. However, Auto3D_refine
> always gives a resolution at 4.326A exactly whatever dataset size I
> changed from 160k to 50k. More strangely, when I run PostProcess, the
> resolution reported is 4.326A as well, exactly same as before.
> However, when I viewed 3D models before and after PostProcess,
> resolution was improved obviously. After post process, I can see side
> chains clearly, and even pigment molecules in the protein. Resolution
> of the map is definitely higher than before post process, around
> 3.5-3.7A roughly as I estimated. I viewed FSC, in high resolution
> region, it is quite noise. Is this because RELION does not use C9
> symmetry for FSC calculation?   
>
> Any advice is greatly appreciated. 
>
> Best regards
>
> Dr. Pu Qian
> The University of Sheffield
>
>

-- 
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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