Hi Tim The absolute peak height doesn't only depend on the element, it also depends on a number of other things, most notably the resolution and the B factor (i.e. peaks are broader and peak heights are lower at lower resolution and higher B factor), and of course the occupancy factor in the case of partial occupancy. So I'm not clear how one would know what peak height to expect just by looking at the map: one would have to do quite a complicated calculation involving a Fourier transform of the scattering curve. It's the volume integral of the electron density under the peak that's directly related to the element type, not the peak height. The range of resolution and B factor for small molecules is much less than for macromolecules, so your method of element identification is likely to be much more reliable in the former case.
Cheers -- Ian On Mon, 2 May 2022 at 12:15, Tim Gruene <tim.gru...@univie.ac.at> wrote: > Hi Ian, > > this is the custom I was educated with. However, small molecule people > seem confused when a map contour level is described with an rsmd (which > to me makes some sense). When refining a structure with shelxl, the > peak height of the maxima of the difference map corresponds quite well > to the element one is expecting, i.e. the absolute value of the peak > height can be used to guess the missing atom type (e.g. '8' for a > properly ordered oxygen from a water molecule). > > Also COOT has been displaying the map countour level with the unit > e/A^3, and I seem to remember Paul's recommendation to use this unit, > rather than the rmsd, which is displayed in brackets. > > Cheers, > Tim > > On Mon, 2 May 2022 09:48:30 +0100 Ian Tickle <ianj...@gmail.com> wrote: > > > Hi Tim > > > > F000 is customarily not included in MX electron density for the > > reason you mention. This doesn't matter because the contour levels > > are completely arbitrary anyway, i.e. you choose a level that shows > > the features you expect to see. This can be misleading of course > > since there may be significant features at lower density than you > > expected due to thermal motion / disorder or maybe H atoms; however > > including F000 would not change that. > > > > Cheers > > > > -- Ian > > > > > > On Mon, 2 May 2022 at 07:45, Tim Gruene <tim.gru...@univie.ac.at> > > wrote: > > > > > Hello readers, > > > > > > how does Coot calculate the absolute map levels, i.e. the contour > > > level given as [e/A^3]? i always thought (rather from hear-say) > > > that F000 was necessary for the absolute level. With a small > > > molecule structure, F000 can be calculated from a complete model, > > > but with solvent channels, the number of disordered electron is not > > > known, is it? > > > > > > Thanks a lot for a clarification! > > > > > > Best, > > > Tim > > > > > > > > > -- > > > -- > > > Tim Gruene > > > Head of the Centre for X-ray Structure Analysis > > > Faculty of Chemistry > > > University of Vienna > > > > > > Phone: +43-1-4277-70202 > > > > > > GPG Key ID = A46BEE1A > > > > > > > ######################################################################## > > > > > > 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/ > > > > > > > -- > -- > Tim Gruene > Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A > ######################################################################## 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/
