Thanks, I'll check them out.
*Dr. Amit Gaur, * *Department of Biomedical Science,* *College of Medicine,* *Florida State University,* *1115 W Call St, Tallahassee, FL,32304* On Mon, Jul 13, 2026 at 10:42 AM Pavel Afonine <[email protected]> wrote: > Hi, > phenix.refine can try to add ions automatically as part of refinement. Try > it out to get a 2nd opinion. The method it uses is described here: > https://pmc.ncbi.nlm.nih.gov/articles/PMC3975891/ > Good luck! > > Pavel > > > 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/
