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] <mailto:[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] <mailto:[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] <mailto:[email protected]> >> Sent from Proton Mail Android >> >> >> >> -------- Original Message -------- >> On 05/09/2025 10:40, Catherine Back >> <[email protected]> >> <mailto:[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 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/
