Dear Xin, I don’t know of a dedicated tool that will do this for you. However, protein crystals have a well characterised range of density values, described by the Matthew’s coefficient (Vm). Vm values typically range from 1.6 to 3.5 Å3 of crystal volume per Da of protein. So given the molecular weight of your protein in Da, you can estimate the volume of crystal that each copy of the protein molecule will occupy. The crudest estimate of the unit cell parameters would be to take the cube root of that volume. A more sophisticated way of doing this would be to calculate the principal components of the radius of gyration tensor to give you a box around the molecule (as the previous poster suggested), then scale this volume up or down to give you a realistic Matthew’s coefficient. Kind regards, Joe
------------------------------------------------------ Dr Joseph J B Cockburn Group Leader and Lecturer in X-ray Crystallography The Astbury Centre for Structural Molecular Biology Faculty of Biological Sciences University of Leeds Leeds LS2 9JT UK +44 (0)113 3430758<tel:+441133430758> From: CCP4 bulletin board <[email protected]> on behalf of Zhang Xin <[email protected]> Date: Monday, 10 November 2025 at 06:29 To: [email protected] <[email protected]> Subject: [ccp4bb] Estimating a plausible unit cell from an AlphaFold model CAUTION: External Message. Use caution opening links and attachments. Dear all, I would like to ask a brief question. When only an AlphaFold-predicted PDB model is available and no diffraction data yet, is there any existing tool to estimate a reasonable unit cell (assuming space group P1)? If there are recommended tools or common practices for this, I would appreciate any suggestions. Best regards, Xin ________________________________ 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/
