Hi, It's important to also consider the coordination of your putative metal sites.
For example you could try Check my Metal: https://cmm.minorlab.org/ Or have a look at MESPEUS which is a database showing metal coordination in structures in the PDB https://mespeus.nchu.edu.tw/intro I was advised to be careful about assuming that metals present purely based on the electron density for the metal, bear in mind that occupancy or partial occupancy lighter metals can easily look like water molecules Best wishes, Mike From: CCP4 bulletin board <[email protected]> On Behalf Of Sourav Roy Sent: 13 July 2026 14:26 To: [email protected] Subject: Re: [ccp4bb] Question About Modeling Calcium and Sodium in Coot You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> 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]<mailto:[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]<mailto:[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 e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom. ######################################################################## 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/
