Treating the iron (Fe) as fluorine (F) is roughly equivalent having the iron occupancy at (9/26) or 0.34 approx ;-0
Best wishes, Jon Cooper. [email protected] Sent from Proton Mail Android -------- Original Message -------- On 05/09/2025 13:03, Garib Murshudov 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]. >> 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 >> [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]>](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 ######################################################################## 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/
