Jianhua,
The corrected FSC curve usually does not have a plateau that is much lower
than before the phase randomisation. A too tight mask that cuts protein
density or that has a too sharp edge will lead to over-correction. The dip
is probably caused by correlations in the signal because even without
masking the molecule lives only in the center of an otherwise empty box.
HTH,
S
> Hi Sjors,
>
> Thanks for the info. What's causing the correlations to 'spill over'? Is
> it the mask? I'm not sure what would be considered a mask that is too
> tight - wouldn't the corrected FSC always be lower than the masked FSC?
> And do we know that the lower FSC immediately after the 'dip' is not
> also due to the correlations 'spilling over'?
>
> Best regards,
> Jianhua
>
> On 2014-10-06 5:00 PM, Sjors Scheres wrote:
>> Hi Jianhua,
>> We see this artefact also sometimes, but you do not need to worry about
>> it. Probably it has to do with correlations "spilling over" into the
>> next
>> (1 or sometimes 2) resolution shell(s) after the phase-randomization,
>> leading thereby to an over-correction. We sometimes just omit that point
>> from the corrected curve. Perhaps I'll do something along those lines in
>> the next release. You should of course be very suspicious if the entire
>> corrected curve drops rapidly after the phase randomization, but just a
>> dip of 1 (or 2) shell(s) is OK. In your case, I would be more worried
>> about the corrected curve having a plateau that is much lower than the
>> near-1 value just after this dip. Are you sure your mask is not too
>> tight?
>> We often put a soft edge of up to 10 Angstroms on our masks.
>> HTH,
>> S
>>
>>> Hi Sjors and Relion users,
>>> I was curious as to what the 'corrected' FSC generated from Relion
>> post-processing means. The attached image shows FSC curves after
>> post-processing: one with just masked maps and the other is the
>>> corrected FSC. The corrected FSC shows a local minimum around the
>> resolution where phase randomization started. I didn't see this effect
>> in Chen et al, Ultramicroscopy 2013. What's causing the FSC dip and do
>> we need to worry about this?
>>> Best regards,
>>> Jianhua
>>
>
--
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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