Did you consider partial occupancy and or a mixture with phosphorylation? The residue SEP will solve your problem with covalent modification and its cif file can guide you in setting up a cif file for the vanadate serine modification (just replace all P with V and change the SEP to SEV or whatever).
Greetings Gottfried Am Dienstag, den 15-07-2025 um 04:52 schrieb Manjula Ramu: Dear CCP4 community, I am currently working on a structure that includes a vanadate (VO₄) moiety, and I am facing challenges with properly modeling and refining it in Coot and Refmac. Specifically, I would appreciate guidance on the following: – The best way to fit vanadate into the electron density (I see negative density in the same position) – How to handle potential covalent interactions with active site residues (e.g., serine) Any suggestions, relevant examples (PDBs or procedures), or workflow tips would be greatly appreciated. I am attaching the screenshots for you to look over. Thank you in advance for your support and expertise. ---------------------------------------------------- Thanks and Regards, Manjula [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 Links: ------ [1] https://www.nimhans.kar.nic.in/ ######################################################################## 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/
