Hi, I agree that in MX there is a standard way to calculate the rms over the asymmetric unit. This provides a similar expected rms level when comparing features between many many different crystals. However, I would like to add that there can still be some variability from the expected rms peak height of features for crystals with very high or very low solvent content. If your crystal falls into the tails of the solvent content distribution, you will be including either very large or very small regions of relatively flat solvent in your map rms used for normalization. Regards, Mitch
On Wed, Jul 15, 2026 at 5:56 AM Clemens Vonrhein < [email protected]> wrote: > Hi, > > On Tue, Jul 14, 2026 at 02:04:02PM -0700, Dale Tronrud wrote: > > What people almost universally do is simply calculate the rms value of > > the map which is an rms deviation assuming the the "true value" is zero. > > Out of interest: I understand the computation of "the" rms value for a > crystallographic map covering a multiple of the asymmetric unit - > which is standardising this computation to a large extent. But how > does one do this with EM maps? The map is in some kind of arbitrary > box and could be masked/non-masked ... so a rms value adequate for > visualising one map could be completely different for another map just > because of those technicalities, right? > > I don't even pretend to understand the scale of those maps or any > other procedure that resulting in them, but is htere any standard > procedure that allows users to come up with a "typical" rms value that > would allow some kind of equal footling comparison between e..g > deposited EM maps? The rms level at which the lowest B TRP/PHE/TYR > shows a hole (just to pick "something" probably rather silly)? > > Any pointer for my education about Cryo-EM SOPs would be highly > appreciated! > > Cheers > > Clemens > > PS: we have the same problem in MX when dealing with deposited > non-crystallographic maps (like event maps in an abritrary P1 cell > with some padding around a masked density) ... as soon as we don't > have a defined standard volume (asymmetric unit) using the > resulting rms becomes an arbitrary choice in itself I guess. > > > > > > While you might be able to convince yourself that the rms value of a > Fo-Fc > > map is related to its "error level" (although don't say that in the > presence > > of James Holton!) no on can argue that the rms value of a density (or > > potential) map has any relation to the standard deviation of that map. > > > > So, Coot labels the quantity an rms. I, personally, hope that others > > would become honest about their calculation and use that term too. > > > > Dale Tronrud > > > > On 7/14/2026 6:45 AM, Morici, Martino wrote: > > > Hi folks > > > > > > > > > I am working on a CryoEM map of a ribosome (specifically a 70S .mrc > from > > > Relion, looking at both the 3Drefined map focus-refined with a mask on > > > the 30S and the corresponding Relion postprocessed map with the same > > > mask). > > > > > > My aim is evaluating which parts of a ligand´s density appear at > > > lower/higher threshold. > > > > > > > > > In the field, the sigma is used (The ligand is visible at X sigma etc). > > > > > > Coot shows RMSD while scrolling. > > > > > > I did some homework and it seems to me that a certain value Y rmsd in > > > Coot is basically equivalent to the corresponding X sigma. > > > > > > > > > However, before publishing this and writing it down, I wanted your > > > opinion if effectively X and Y are the same, and if not how to > > > understand their correlation. > > > > > > > > > I am asking because I am not sure whether the way I processed these > maps > > > may affect the X/Y correlation. > > > > > > > > > Thank you so much > > > > > > - M. > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > To unsubscribe from the COOT list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1> > > > > > > > ######################################################################## > > > > To unsubscribe from the COOT list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > > > This message was issued to members of www.jiscmail.ac.uk/COOT, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > -- > > *-------------------------------------------------------------- > * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com > * Global Phasing Ltd., 9 Journey Campus, Castle Park > * Cambridge CB3 0AX, UK www.globalphasing.com > *-------------------------------------------------------------- > > ######################################################################## > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
