There is some more info in the documentation of the corresponding command: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#mapstats
ChimeraX and Coot report different numbers probably because they have different defaults: ChimeraX computes statistics on the whole box (per its documentation, and unless you have cropped or masked or otherwise explicitly done something to the map), while Coot might use only the sub-region within a mask? Not sure what the default is for Coot, but Paul’s last message suggests that it might use a mask by default. The sure thing is that these numbers should come out identical (to rounding error maybe) if both programs compute them from the entire box, and you might be able to check this if you can convince Coot to consider the whole box. Cheers, Guillaume On 27 Sep 2024, at 11:42, anna anna <[email protected]<mailto:[email protected]>> wrote: Dear Paul, I am not expert of chimeraX.... here https://www.cgl.ucsf.edu/chimerax/docs/user/tools/mapstats.html I found this description: Map Statistics reports the minimum, maximum, and mean values, the standard deviation (SD) from the mean, and the root-mean-square (RMS) deviation from zero for volume data (map) models. Here is the output for my model: Map cryosparc_P9_J388_003_volume_map(1).mrc #1, minimum -0.255, maximum 0.4798, mean 0.0002941, SD 0.01472, RMS 0.01472 That's all I can say..... PS: I didn't know about moorhen, I am trying it right now! Il giorno gio 26 set 2024 alle ore 18:11 Paul Emsley <[email protected]<mailto:[email protected]>> ha scritto: Dear Ana, Coot calculates the map rmsd for cryo-EM reconstructions by ignoring the modal values. I suspect that this is not what ChimeraX does. Can you get ChimeraX to tell you what it thinks the map rmsd is? Ideally one should use a mask when calculating the cryo-EM rmsd. Paul. p.s. for a bit of fun, I thought I'd see if I could reproduce the style of representation using moorhen On 26/09/2024 16:30, anna anna wrote: Dear Colin, thank you for the explanation. I followed your advice and indeed, the map is almost identical in coot and chimera. <image.png> I would like to take this opportunity to ask for further clarification: as suggested by someone else, I should be able to calculate the map value by multiplying the rmsd value of the map by 5.5. The statistics of my map are (from chimera): Map cryosparc_P9_J388_003_volume_map(1).mrc #1, minimum -0.255, maximum 0.4798, mean 0.0002941, SD 0.01472, RMS 0.01472 so 0.01472 multiplied by 5.5 = 0.081 Do you have any idea to account for this difference? Thank you, Anna Il giorno gio 26 set 2024 alle ore 16:21 Colin Palmer - STFC UKRI <[email protected]<mailto:[email protected]>> ha scritto: 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 <[email protected]<mailto:[email protected]>> On Behalf Of anna anna Sent: Thursday, September 26, 2024 11:13 AM To: ccp4bb <[email protected]<mailto:[email protected]>> 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, ________________________________ 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. 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