If you use ChimeraX, you can run KVFinder directly from the menu "Tools / Structure Analysis / Find Cavities" and this will get you an interactive visualization. Documentation: https://www.cgl.ucsf.edu/chimerax/docs/user/tools/findcavities.html
Cheers, Guillaume ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Xavier Brazzolotto <[email protected]> Sent: Friday, July 24, 2026 8:28:56 PM To: [email protected] Subject: Re: [ccp4bb] Protein cavity volume calculation The web server KVFinder does the job I want and is quite user-friendly Thank you all for your advices Xavier Le 24 juil. 2026 à 19:59, Jeffrey Bonanno <[email protected]> a écrit : We have used fpocket Jeffrey B. Bonanno, Ph.D. Department of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Avenue Bronx, NY 10461 off. 718-430-2452 fax. 718-430-8565 email [email protected]<mailto:[email protected]> From: CCP4 bulletin board <[email protected]<mailto:[email protected]>> On Behalf Of Xavier Brazzolotto Sent: Friday, July 24, 2026 1:57 PM To: [email protected]<mailto:[email protected]> Subject: [ccp4bb] Protein cavity volume calculation CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Report Message” button on the top right of the Outlook dashboard to report any suspicious emails. Sorry for the bit off-list question, I would like to calculate a cavity volume using CASTp 3.0, but the server (http://sts.bioe.uic.edu/castp/calculation.html) doesn’t seem to respond. Is the calculation service down permanently, or is there any other alternative? Xavier ________________________________ 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 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## 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/
