Hi All, Garib and others have mentioned most of it! For the sake of completeness, here are my two cents:
- Inoptimal position: Sometimes repulsion restraints may push it off the peak. Defining coordination restraints usually solves this (in Phenix, at least). - ADP: You may consider refining anisotropic just for Fe, even if the resolution doesn’t seem plausible. - f′ and f″: These can indeed contribute, so refine them! For that, you’ll need to use anomalous data, not merged F+/F−. - Refinement cycles: The refinement may not be converging, so try tripling the number of cycles. If none of this helps, don’t discount Fourier ripples (though does not look like it in this case!)! Remember, Fe is heavier than the rest of your “protein atoms” (C/N/O/H), meaning that both the signal and any noise around it are amplified and stand out more prominently in the map than for other atoms. Other atoms may have ± peaks of the same nature, but you don’t see them at your typical contouring levels (you will see them if you lower the contour level!). Good luck! Pavel On Fri, Sep 5, 2025 at 5:03 AM Garib Murshudov < [email protected]> wrote: > In my experience there could be several reasons for green densities around > metal atoms: > > 1) occupancy. In this case it is unlikely to be a problem > 2) effect of f’ if it is strong. It is visible at higher resolution more > than at low resolutions. > 3) B vallues, isotropic or anisotropic. B value of the metal should be > very similar to that of the well defined surrounding atoms > 4) Multiple positions due to mixtures of charges and coordination > geometries > > Regards > Garib > > On 5 Sep 2025, at 12:47, Ezra Peisach < > [email protected]> wrote: > > CAUTION: This email originated from outside of the LMB: > *[email protected] <[email protected]>-.* > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > If you think this is a phishing email, please forward it to > [email protected] > > > -- > > I know you mentioned that this was not an anomalous map, but what at > wavelength were your data collected at? Fe has a significant f" at CuKalpha > (1.54..) wavelength. > > > > > On 9/5/25 7:37 AM, Jon Cooper wrote: > > I would check the iron occupancy in case it is less than 1.0 and that your > Fe has the left-shift in the PDB file otherwise it might be treated as a > fluorine? Good old pdb format. > > Best wishes, Jon Cooper. > [email protected] > > Sent from Proton Mail Android > > > -------- Original Message -------- > On 05/09/2025 10:40, Catherine Back > <[email protected]> > <[email protected]> wrote: > > Good morning, > > I am currently solving a structure containing four heme b molecules (res > 1.7 Å), each coordinated by two histidines. The refinement is looking good, > but the output from refinement has marked the Fe ions of each heme with > positive density (green) in the FoFc difference map - see image. Any ideas > why? I used the Monomer Library in Coot to add hemes ('HEM') in. Is it > something to do with the oxidation state of the Fe? And if so, is there > anything I can do about it? > > Best wishes, > Catherine > > Dr Catherine R. Back (she/her) > Senior Post-doctoral Research Associate > School of Biochemistry > University of Bristol > UK > > > > ------------------------------ > > 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 > > > > ------------------------------ > > 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/
