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. jon.b.coo...@protonmail.com 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 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/
