Dear Anna, The absolute map value that Coot displays – i.e. the 0.115 in your “0.115 V = 5.5 rmsd” – is the raw value from the map file, and should be equivalent to the “Level” shown in the Volume Viewer in Chimera or ChimeraX (as long as the step value is set to 1).
If you set the contour levels to the same number, the map should appear very similar in both programs. Note that when working with cryo-EM maps, you should usually ignore the rmsd value and focus only on the absolute values, because the rmsd will change if the map is masked, cropped or padded and the absolute values won’t. Also note that Coot changes the unit: if it thinks the map is from cryo-EM it shows “V” and if it thinks it is from crystallography it shows “e/A^3”. Sometimes it picks the wrong one, but it doesn’t matter and in both cases the values are the same. Best wishes, Colin From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of anna anna Sent: Thursday, September 26, 2024 11:13 AM To: ccp4bb <ccp4bb@jiscmail.ac.uk> Subject: [ccp4bb] contour level for cryoEM deposition: coot vs chimera 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/
