Ah that's right, I had forgotten about this supplementary video. I even read this paper again not too long ago. It's working better than the HexAuFoil paper suggests it should, that's interesting to see. But it might not be generally applicable to all datasets? especially of lower resolution.
________________________________ From: Tomas Malinauskas <tomas.malinaus...@gmail.com> Sent: Monday, March 17, 2025 6:07:22 PM To: Guillaume Gaullier Cc: CCP4BB@JISCMAIL.AC.UK Subject: Dose-dependent evolution of the cryo-EM density of the disulfide bond (Re: [ccp4bb] Query Regarding Additional Density Near Disulfide Bond in Cryo-EM Structure Hi Guillaume, Regarding your suggested experiment, something similar is presented in Supplementary Video 2 in the following paper: https://www.nature.com/articles/s41586-020-2829-0 Best wishes, Tomas On Mon, Mar 17, 2025 at 4:03 PM Guillaume Gaullier <guillaume.gaull...@kemi.uu.se> wrote: > > Hello, > > > Sorry to hijack this discussion, but does someone know if reduction of a > disulphide could be a manifestation of radiation damage? Especially in > cryoEM, since we're shooting electrons at it. > > > One way to test this would be to do a rough zero-dose extrapolation (repeat > motion correction with fewer and fewer frames, use the particle coordinates > and orientations determined with the full dose to extract particle images and > do reconstructions from the micrographs obtained with fewer frames) and see > if this feature appears with accumulated dose. But this is tricky to do if > motion correction is not perfect. At least according to the paper that > introduced HexAuFoil grids: https://doi.org/10.1126/science.abb7927 ; but I > don't know if anyone has tried even without these grids. > > > Cheers, > > > Guillaume > > ________________________________ > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Artem > Evdokimov <artem.evdoki...@gmail.com> > Sent: Monday, March 17, 2025 4:50:37 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Query Regarding Additional Density Near Disulfide Bond > in Cryo-EM Structure > > To me this looks like a mixture of oxidized and reduced states of the S-S > bond. Hard to say with any certainty seeing as the (optical) resolution is > modest. > > Artem > > - Cosmic Cats approve of this message > > > On Mon, Mar 17, 2025 at 8:18 AM Devbrat Kumar <devformed...@gmail.com> wrote: >> >> Hello Everyone, >> >> I am worried about the density of the disulfide bond in the cryo-EM >> structure that I am analyzing. The experimental map shows the expected >> density for the disulfide bond involving two cysteine residues, but in >> addition, I see some unexplained density, which I do not know how to >> interpret. >> >> I have attached the figure for your reference. Does anyone have experience >> with such extra density around a disulfide bond in their structures? Any >> thoughts would be greatly appreciated. >> >> Thanks for your attention and assistance. >> >> Warm regards >> Devbrat kumar >> Postdoctoral Fellow >> IITD, In >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen > avsändaren och vet att innehållet är säkert. > CAUTION: Do not click on links or open attachments unless you recognise the > sender and know the content is safe. > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det > att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan > du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. > For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
