Hello, you can also use anomalous scattering to identify the element type, either by collecting data above and below absorption edges, or in cases edges can't be accessed, e.g. sodium, by refining f".
Check out this paper and our webpage in case you are interested in an experimental approach. https://journals.iucr.org/d/issues/2024/10/00/gin5001/index.html https://www.diamond.ac.uk/Instruments/Mx/I23.html Best regards, Armin ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Martin Mal? <[email protected]> Sent: Monday, July 13, 2026 17:37 To: [email protected] <[email protected]> Subject: Re: [ccp4bb] Question About Modeling Calcium and Sodium in Coot Dear Amit Gaur, You can have a look on our work on the MetalCoord program: https://github.com/Lekaveh/MetalCoordAnalysis https://journals.iucr.org/d/issues/2024/12/00/von5002/index.html It can also give you external distance and angle restraints which can be used in refmac, servalcat, phenix.refine or Coot. In Coot 0.9, select Calculate -> Modules -> Restraints, and then Restraints -> Read Extra Refmac Restraints... In Coot 1, click on the + with arrow in the right top corner and select Restraints, and then Restraints -> Import Restraints... Good luck! Please keep us updated how it goes. Cheers, Martin On 13/07/2026 14:02, amit gaur 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 ________________________________ 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/
