Sorry, I think the answer is on Colin's reply. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Sent from Proton Mail Android -------- Original Message -------- On 26/09/2024 17:56, Jon Cooper 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. > 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 ######################################################################## 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/
