Try Buster! Pietro
Get Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Vera Pfanzagl <vera.pfanz...@boku.ac.at> Sent: Tuesday, July 13, 2021 3:33:04 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Problems with refining covalently linked heme cofactor Hello, I am trying to refine a heme protein which has the heme cofactor covalently linked to the protein at three positions (two ester linkages and a sulfilimin bond) (coot.png shows the atoms which should be in the sulfilimin bond). However as as coot cannot covalently link atoms between a cofactor and amino acids the atoms are displaced during the refinement and I don't know how to fix this. Also the heme b disintegrates if I run it through phenix and then try to refine it manually in coot. The hydrogen atoms just fly off. I can delete the hydrogens before running a manual refinement but this problem reappears after adding the hydrogens during phenix refine. I now tried to replace it with HEB from the coot monomer library (I cannot find the old HEM in the monomer library) and got once the same result (atoms are displaced) and in the second case I cannot even place HEB correctly as some atoms rearrange after refinement (heb_wierd.png) and two hydrogens are connected when I add it from the library (heb_withoutrefine.png) Thanks, Vera ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cpr159%40LEICESTER.AC.UK%7Ca04350bbcbf44bcaa51508d9460434df%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637617806161876681%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=UuvWfh0lsuE2cbhNJhqDJPA8U0SueiJdNWIhPRQhg%2BY%3D&reserved=0> ######################################################################## 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/
