Re: [ccp4bb] Green density over Fe in heme

[Lijun Liu]

It is very likely the occupancy of the iron not proper, or its b factor is refined/assigned too high.  The resolution is pretty good, so occ may be the issue?  By the way, which software did you use for the refinement? Sent from my iPhone On Sep 5, 2025, at 5:08 AM, Wim Burmeister <00012a5be754e48b-dmarc-requ...@jiscmail.ac.uk> wrote:  Hello, ou should try refinement of anisotropic temperature factors. Wim Le 05/09/2025 à 11:39, Catherine Back a écrit : 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 -- Wim Burmeister Professor Institut de Biologie Structurale (IBS) CIBB 71 avenue des Martyrs / CS 20192 38044 Grenoble Cedex 9, FRANCE E-mail: wim.burmeis...@ibs.fr Mobile:   +33 (0) 7 50 49 19 91    website Ce ne sont pas les faits qui rendent éco-anxieux, mais ce qu'on fait ou ne fait pas. Anonyme 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