Thinking outside the box (groan), You could also use the PDB advanced search function and search by molecular weight using a range around the calculated mass with spacegroup either fixed as P1 or unfixed.
That will give you a list of similarly sized proteins with real packing environments and unit cells.. Cheers, Charlie. From: CCP4 bulletin board <[email protected]> On Behalf Of Oganesyan, Vaheh Sent: 10 November 2025 13:49 To: [email protected] Subject: Re: [ccp4bb] Estimating a plausible unit cell from an AlphaFold model WARNING: This message was sent by an external party. Report suspicious messages via the “Report Phishing” button in Outlook. Hi, I’m not sure why would you want to know that or how useful that information may be, but you can enter the AF model to DALI server and see if you get a set of scores that are considerably higher than others. Vaheh Get Outlook for iOS From: CCP4 bulletin board <C i This message needs your attention * No employee in your company has ever replied to this person. Powered by Mimecast CGBANNERINDICATOR Hi, I’m not sure why would you want to know that or how useful that information may be, but you can enter the AF model to DALI server and see if you get a set of scores that are considerably higher than others. Vaheh Get Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: CCP4 bulletin board <[email protected]<mailto:[email protected]>> on behalf of Joseph Cockburn <[email protected]<mailto:[email protected]>> Sent: Monday, November 10, 2025 7:19:32 AM To: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> Subject: Re: [ccp4bb] Estimating a plausible unit cell from an AlphaFold model 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]<mailto:[email protected]>> on behalf of Zhang Xin <[email protected]<mailto:[email protected]>> Date: Monday, 10 November 2025 at 06:29 To: [email protected]<mailto:[email protected]> <[email protected]<mailto:[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<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<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ________________________________ Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<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/
