Hi,
Yes, it is OK and FSC looks fine to me.
Takanori
On 2020/11/26 20:53, Victor Banerjee wrote:
> Does it mean OK to have such bumps at the 4.7A region? and the FSC is acceptable?
> -Victor
>
>
>
>
> On Thu, Nov 26, 2020 at 2:50 PM Takanori Nakane <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Yes.
>
> Takanori
>
> On 2020/11/26 19:18, Victor Banerjee wrote:
> >
> > Hi,
> > Just checking if this kind of bump in the green line is also acceptable? The map is refined and postproceed.
> > -Victor
> >
> >
> > On Thu, Nov 26, 2020 at 12:24 PM Reza Khayat <[log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>> wrote:
> >
> > Thanks!
> >
> > Reza Khayat, PhD
> > Associate Professor
> > City College of New York
> > Department of Chemistry and Biochemistry
> > New York, NY 10031
> >
> > ________________________________________
> > From: Takanori Nakane <[log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>>
> > Sent: Thursday, November 26, 2020 1:07 PM
> > To: Reza Khayat; [log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > Subject: [EXTERNAL] Re: [ccpem] Bump in FSC curves
> >
> > Hi,
> >
> > Because some CTF parameters (e.g. Cs) is defined assuming the right pixel size.
> > See
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www3.mrc-2Dlmb.cam.ac.uk_relion_index.php_Pixel-5Fsize-5Fissues&d=DwIG-g&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=Jyfz-YpMjUtIbokDFmZ3UMnIE5o6K4XUKZ0pYSn6l3Y&s=jQuIMopzoPDSd2-mfw-WIL_dlx2LXt4pagYeHGARyUw&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www3.mrc-2Dlmb.cam.ac.uk_relion_index.php_Pixel-5Fsize-5Fissues&d=DwIG-g&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=Jyfz-YpMjUtIbokDFmZ3UMnIE5o6K4XUKZ0pYSn6l3Y&s=jQuIMopzoPDSd2-mfw-WIL_dlx2LXt4pagYeHGARyUw&e=>
> >
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www3.mrc-2Dlmb.cam.ac.uk_relion_index.php_Pixel-5Fsize-5Fissues&d=DwIG-g&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=Jyfz-YpMjUtIbokDFmZ3UMnIE5o6K4XUKZ0pYSn6l3Y&s=jQuIMopzoPDSd2-mfw-WIL_dlx2LXt4pagYeHGARyUw&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__www3.mrc-2Dlmb.cam.ac.uk_relion_index.php_Pixel-5Fsize-5Fissues&d=DwIG-g&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=Jyfz-YpMjUtIbokDFmZ3UMnIE5o6K4XUKZ0pYSn6l3Y&s=jQuIMopzoPDSd2-mfw-WIL_dlx2LXt4pagYeHGARyUw&e=>>
> > .
> >
> > Takanori
> >
> > On 2020/11/26 18:04, Reza Khayat wrote:
> > > Why would an incorrect pixel size cause a bump in the FSC? The wrong pixel size will move the bump (left or right), but I just don't see
> why it
> > would create a bump. The pixel size is something we tell the computer to put the map on the laboratory point of reference. Perhaps I'm missing
> > something important....
> > >
> > > Reza Khayat, PhD
> > > Associate Professor
> > > City College of New York
> > > Department of Chemistry and Biochemistry
> > > New York, NY 10031
> > >
> > > ________________________________________
> > > From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>> on behalf of Marino
> > Jacopo (PSI) <[log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > > Sent: Thursday, November 26, 2020 10:27 AM
> > > To: [log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > > Subject: [EXTERNAL] Re: [ccpem] Bump in FSC curves
> > >
> > > I think it was already discussed somewhere it might be due to the detergent micelle. But I think Marta has a stronger feeling the
> initial pixel
> > size was off.
> > >
> > >
> > > -----Original Message-----
> > > From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>> On Behalf Of Basil
> > Greber
> > > Sent: Thursday, 26 November 2020 16:25
> > > To: [log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > > Subject: Re: [ccpem] Bump in FSC curves
> > >
> > > Hi Marta,
> > >
> > > This bump (the valley, not the hill) is common and not an indication of processing issues. It may arise from the reduced scattering power of
> > proteins in this frequency range.
> > >
> > > Best regards,
> > >
> > > Basil
> > >
> > >
> > >> Am 26.11.2020 um 15:16 schrieb Marta Sawicka <[log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>>:
> > >>
> > >> Dear cryo-EM folks,
> > >>
> > >> I have observed a strange bump in FSC curves, which always occurs in a region between 5.5-4.5 A. I see the same pattern regardless of a
> > protein I work with and data processing strategy. Having read what has been already discussed in relation to spikes in the FSC curves I
> suspect a
> > significant error in the pixel size to cause this bump. Also, having compared maps of the same protein coming from different microscopes, I
> needed
> > to rescale the pixel size by approximately 5% to get a correct fit. Based on the RELION wiki entry on the pixel size issues, I have redone
> > CtfRefine with estimation of the 4th order aberrations followed by another run to recalculate per-particle defocus. As far as I understand this
> > should make things consistent with a wrong pixel size and after I feed a correct “absolute” pixel size in PostProcessing, I should get FSC
> curves
> > without the bump. However, this is not the case and the FSCs look pretty much exactly the same. Is there something fundamental that I am
> missing
> > here? I would appreciate any ideas/suggestions.
> > >>
> > >> Many thanks,
> > >> Marta
> > >>
> > >> ########################################################################
> > >>
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> > >> <FSC.pdf>
> > >
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