I read somewhere (I don’t have the ref, sorry) that it is because the phases are directly measured in cryoEM (since it is an imaging technique), and they are often more accurate than the phases of crystallographic maps.
On this basis, if you can find a structure that has been solved both by cryoEM and crystallography with very accurate experimental phasing, and at comparable resolutions, then these two maps should look more similar in quality than what you would observe when comparing the same cryoEM map to a crystallographic map phased by MR. Cheers, Guillaume On 26 Sep 2024, at 18:56, Jon Cooper <[email protected]<mailto:[email protected]>> wrote: Another thing I am curious about is how a map can look good at 5.5 sigma because an X-ray one probably wouldn't unless it was atomic resolution. Don't worry if there isn't a simple explanation. Best wishes, Jon Cooper. [email protected]<mailto:[email protected]> Sent from Proton Mail Android -------- Original Message -------- On 26/09/2024 11:13, anna anna wrote: Dear all, I am depositing my first cryoEM structure and I am facing the following problem concerning the contour level of the map. Briefly, where do I find the value for the contour level to associate to the uploaded map in Coot? Long story: I worked with coot and I am happy with my map when I set the contour level at 0.115 V = 5.5 rmsd (actually "happy" is not the best definition, I feel quite uncomfortable with this "by feeling" assignment but, to what I understood, this is how it works...). Upon deposition, when I upload maps, a contour level is required but the values from coot are not accepted, I have to provide the contour level relative to the map value, like the one that you set in Chimera. Thus I opened the map in Chimera and I set a contour level "by eye" but the validation report revealed some problems: the total volume of the map is too low and too many residues are highlighted as out of density. Probably I should low the contour level but I don't want to go for a trial-and-error approach, there must be a way to convert the contour level from coot (the one that I used for modelling) in the one required for deposition! Any advice? Thank you, Anna ________________________________ 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 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/
