If my memory serves right you can introduce it via coot place it in the correct electron density and see whether your Rfactor goes down in refinement and you also I believe need to do a occupancy refinement in Phenix, hope this helps.
Best Sourav Sourav Roy,PhD Research Assistant Professor Dept of Biochemistry and Molecular Biophysics Kansas State University Phone No: 785-532-0673, email: [email protected] 141 Chalmers Hall, 1717 Claflin Road Manhattan, KS,66506 Lab: 317 Ackert Hall, Office: 323 Ackert Hall On Mon, Jul 13, 2026 at 8:03 AM amit gaur < [email protected]> wrote: > Hi All, > > I am currently trying to model calcium and sodium ions in Coot, but I am > encountering atomic clashes after placing them. Based on the electron > density, I am confident that these sites are occupied. > > Has anyone experienced this before or have any suggestions on how to > handle these clashes? I would appreciate any advice. > > Thank you! > > *Amit Gaur, * > *Department of Biomedical Science,* > *College of Medicine,* > *Florida State University,* > *1115 W Call St, Tallahassee, FL,32304 > <https://www.google.com/maps/search/1115+W+Call+St,+Tallahassee,+FL,32304?entry=gmail&source=g>* > > > > > ------------------------------ > > 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/
