Ooo, thanks for this Martin.
Dr Catherine R. Back (she/her) Senior Post-doctoral Research Associate School of Biochemistry University of Bristol UK [email protected] ________________________________ From: Martin Malý <[email protected]> Sent: 08 September 2025 17:23 To: Catherine Back <[email protected]>; [email protected] <[email protected]> Subject: Re: [ccp4bb] Green density over Fe in heme Dear Catherine, Regardless with program you use for refinement, I would recommend to use dictionary from the monomer library for HEM from the very latest CCP4 version (9.0.010). All the metal-containing monomers were recently updated and fixed with the help of the MetalCoord program. You can also get the library directly from GitHub: https://github.com/MonomerLibrary/monomers However, this will most likely not solve your particular problem with the peak in diff. density. Anyway, the refinement should be more stable and reported geometry outliers more relevant. Best regards, Martin On 05/09/2025 13:50, Catherine Back wrote: Hi All, Many thanks for all your suggestions. I've had some direct replies as well as all the ones from the BB. * The occupancies were definitely 1.0 * I'll refine anisotropically from now on. * The Bfactors for two of the Fe-atoms were abnormally high, which contributed to the density. I've altered them and they've gone back down to similar levels to the surrounding atoms. * The collection wavelength was 0.976 Å. * I was using Phenix Refine, though I tried Refmac first. There is still a little positive density in the area of the Fe, but the structure is well refined, so possibly this is just amplifying any tiny errors? Cheers, Catherine Dr Catherine R. Back (she/her) Senior Post-doctoral Research Associate School of Biochemistry University of Bristol UK ________________________________ From: CCP4 bulletin board <[email protected]><mailto:[email protected]> on behalf of Jon Cooper <[email protected]><mailto:[email protected]> Sent: 05 September 2025 13:17 To: [email protected]<mailto:[email protected]> <[email protected]><mailto:[email protected]> Subject: Re: [ccp4bb] Green density over Fe in heme 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]<mailto:[email protected]> Sent from Proton Mail Android -------- Original Message -------- On 05/09/2025 13:03, Garib Murshudov <[email protected]><mailto:[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]><mailto:[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 ________________________________ 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/
