As an alternative to CASTp3.0, try the MOLEonline tool (currently v 2.5). Provides nice channel/pocket characterization (and uses vy cool geometry!). Also, CAVER is an option. Happy excavating!
Miranda L Lynch, PhD Research Scientist, Research Foundation of UB UB/Hauptman-Woodward Institute 700 Ellicott Street Buffalo, NY 14203 Research Assistant Professor, Dept. of Structural Biology Jacobs School of Medicine and Biomedical Sciences University at Buffalo, The State University of New York 955 Main Street, Suite 5120 Buffalo, NY 14203 ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of CCP4BB automatic digest system <[email protected]> Sent: Friday, July 24, 2026 7:01 PM To: [email protected] <[email protected]> Subject: CCP4BB Digest - 23 Jul 2026 to 24 Jul 2026 (#2026-167) There are 6 messages totaling 4054 lines in this issue. Topics of the day: 1. Post-Doc position in Luebeck, Germany 2. Support for Diamond Light Source and UK National Research Infrastructure (2) 3. Protein cavity volume calculation (3) ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570138911%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=MHHWvzGm3WAOr01BsJSRuZuDzmRHPvcmyScAsSgEUBU%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570181171%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=qPVIEkANNJuG39jAb7ECHXh2WlgaSRkwiubaYbiJohY%3D&reserved=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570209836%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=vlOS9hy13OVwup%2BnrFSpl4vFLwV9dJ3JUtxuO4NIbIo%3D&reserved=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570227186%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Mv%2Btwzhog5neg9EIGQcQwVSVW%2FvL%2F9LJDbMPp9m6NfM%3D&reserved=0<https://www.jiscmail.ac.uk/policyandsecurity/> ---------------------------------------------------------------------- Date: Fri, 24 Jul 2026 11:41:03 +0000 From: Thomas Krey <[email protected]> Subject: Post-Doc position in Luebeck, Germany Dear colleagues, Are you a Crystallographer and interested in viruses? The Krey lab is looking for a motivated Postdoc to join our mission in fighting the Hepatitis E Virus! Help us design the next generation of antiviral inhibitors using structural biology. https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.b-ite.com%2Frecruitingmanager%2Fjob-postings%2Fshare%2Fq5RCqGZsTOLiZPKte09I5xUTCjw42YGv1mzf7J0rnrpb4U1iOg254dcqkO8LHTJ1&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570248976%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=mW9%2B10isYC3uh6JIDSKtDF2Lq4gbVU%2FTFMkfYW58wCY%3D&reserved=0<https://www.b-ite.com/recruitingmanager/job-postings/share/q5RCqGZsTOLiZPKte09I5xUTCjw42YGv1mzf7J0rnrpb4U1iOg254dcqkO8LHTJ1> Best wishes Thomas Prof. Dr. Thomas Krey [University of Luebeck] University of Lübeck Institute of Biochemistry phone: +49-451-3101-3100 fax: +49-451-3101-3104 e-mail: [email protected]<mailto:[email protected]> https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.biochem.uni-luebeck.de%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570275719%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=TAhpsZjz9uPOit8URONShr%2BMPxqhn%2B9mKjWeSjsl%2Bzw%3D&reserved=0<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.biochem.uni-luebeck.de%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570293999%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=NyEbsDvP%2BiEHKuw2b2DYRh3QAZiHnbRoSuyYA%2FQ%2FV%2Bk%3D&reserved=0><http://www.biochem.uni-luebeck.de/> Ratzeburger Allee 160 23562 Lübeck Germany ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570309970%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=nxX4r2iaGZAZG4oTfsp6cEnJmgccED6wRbh31G6eo14%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570330905%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=%2F2Qm1JNaX3uWZ4DVaw211F3sLI%2F8rVKEAZWZX4boolY%3D&reserved=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570366232%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=pZ1YRYYw%2Bu5UqV4SS%2BaFC9c2S%2BMLBSoXeenreq34tnE%3D&reserved=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fp&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570384629%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=d49ccUx%2Bc8a2eNH39sZHzh2Tae1RAcWH6wKDlWyFJ5I%3D&reserved=0<https://www.jiscmail.ac.uk/p> ------------------------------ Date: Fri, 24 Jul 2026 12:11:42 +0000 From: Colin Levy <[email protected]> Subject: Support for Diamond Light Source and UK National Research Infrastructure Dear CCP4 Community, Many of you will be aware of recent announcements concerning funding pressures affecting several UK national research facilities, including Diamond Light Source, ISIS Neutron and Muon Source, and the Central Laser Facility. As a member of the Diamond User Committee (DUC), I wanted to draw attention to an open letter that has been prepared on behalf of the user community in response to these developments. A link to the letter is available at the bottom of this message. Diamond is a critical component of the UK structural biology ecosystem. Every year, thousands of researchers rely on access to its beamlines for macromolecular crystallography, cryo-EM, spectroscopy, imaging, and a wide range of multidisciplinary research programmes. The facility underpins not only fundamental discovery science but also translational research, industrial collaboration and biotechnology. The proposed budget reductions raise concerns about the long-term impact on user access and facility capability. While the precise implications will depend on how the reductions are implemented, potential consequences may include: * Reduced beamtime availability and increased competition for access. * Delays in facility upgrades and future capability development. * Reduced technical and scientific support available to users. * Constraints on staffing, training, and expertise retention. * Reduced flexibility to respond to emerging scientific opportunities. * Potential impacts on the UK's international competitiveness in science and innovation. It is important to emphasise that this is not simply an issue for frequent Diamond users. National facilities such as Diamond form part of the research infrastructure that supports a significant proportion of UK bioscience, physical sciences, engineering, environmental science, and industrial research. Their strength depends upon sustained engagement and support from the communities they serve. The Diamond User Committee is encouraging researchers, facility users, students, principal investigators, and research leaders to support the open letter and consider how best to make their views known through appropriate channels. Clear evidence of the scientific, economic, and societal value delivered by Diamond and other national facilities will be essential in informing future discussions. For many of us, Diamond has been central to scientific advances, student training, collaborative research, and grant success. If these facilities have played an important role in your work, now is an important time to ensure that the value of that contribution is visible. Open Letter in Response to Funding Pressures Affecting Diamond Light Source<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopenletter.earth%2Fopen-letter-in-response-to-funding-pressures-affecting-diamond-light-source-ee231c6e&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570425226%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ElCaqT7FPD7GqUM4FXofgrZu2Jt2Ef6fZAz1Yk85Raw%3D&reserved=0<https://openletter.earth/open-letter-in-response-to-funding-pressures-affecting-diamond-light-source-ee231c6e>> With best wishes, Colin Dr. Colin W. Levy [email protected] Expert Technical Specialist (XRD) Manchester Institute of Biotechnology, Faculty of Science & Engineering Tel: +44 (0) 161 529 4380 The University of Manchester [cid:2e02cb8b-dbf8-4123-a3e1-c35f7c51d3ec] ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570456388%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=TJ07SvyVSq0Cv%2FBK03NWOYAZQGhVmxbLXnwQmnghIrk%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570478752%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=VNjyVTO3rYYRjVMY%2FjNLXCr3CDwc64Mp1NBlGOyfVQ0%3D&reserved=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570495119%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=8oMMQxjJBtSvsLO2Io1nE1g1ct1OWTaYZ2RkM8%2Bi2GY%3D&reserved=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570517916%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=pPKzYUGln4zuXH2Fgwfhmk8qCIcvkwYMjrpQnP1BjJo%3D&reserved=0<https://www.jiscmail.ac.uk/policyandsecurity/> ------------------------------ Date: Fri, 24 Jul 2026 14:54:41 +0200 From: Jon Hughes <[email protected]> Subject: Re: Support for Diamond Light Source and UK National Research Infrastructure brexit forever! jh Am 24. Juli 2026 14:11:42 MESZ schrieb Colin Levy <[email protected]>: >Dear CCP4 Community, >Many of you will be aware of recent announcements concerning funding pressures >affecting several UK national research facilities, including Diamond Light >Source, ISIS Neutron and Muon Source, and the Central Laser Facility. >As a member of the Diamond User Committee (DUC), I wanted to draw attention to >an open letter that has been prepared on behalf of the user community in >response to these developments. A link to the letter is available at the >bottom of this message. >Diamond is a critical component of the UK structural biology ecosystem. Every >year, thousands of researchers rely on access to its beamlines for >macromolecular crystallography, cryo-EM, spectroscopy, imaging, and a wide >range of multidisciplinary research programmes. The facility underpins not >only fundamental discovery science but also translational research, industrial >collaboration and biotechnology. >The proposed budget reductions raise concerns about the long-term impact on >user access and facility capability. While the precise implications will >depend on how the reductions are implemented, potential consequences may >include: > > * Reduced beamtime availability and increased competition for access. > * Delays in facility upgrades and future capability development. > * Reduced technical and scientific support available to users. > * Constraints on staffing, training, and expertise retention. > * Reduced flexibility to respond to emerging scientific opportunities. > * Potential impacts on the UK's international competitiveness in science > and innovation. > >It is important to emphasise that this is not simply an issue for frequent >Diamond users. National facilities such as Diamond form part of the research >infrastructure that supports a significant proportion of UK bioscience, >physical sciences, engineering, environmental science, and industrial >research. Their strength depends upon sustained engagement and support from >the communities they serve. >The Diamond User Committee is encouraging researchers, facility users, >students, principal investigators, and research leaders to support the open >letter and consider how best to make their views known through appropriate >channels. Clear evidence of the scientific, economic, and societal value >delivered by Diamond and other national facilities will be essential in >informing future discussions. >For many of us, Diamond has been central to scientific advances, student >training, collaborative research, and grant success. If these facilities have >played an important role in your work, now is an important time to ensure that >the value of that contribution is visible. >Open Letter in Response to Funding Pressures Affecting Diamond Light >Source<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopenletter.earth%2Fopen-letter-in-response-to-funding-pressures-affecting-diamond-light-source-ee231c6e&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570535359%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=XCAFZ2kQNLDgPeZeN3elGzN%2F8D0Ok0TuDAWODSZUom4%3D&reserved=0<https://openletter.earth/open-letter-in-response-to-funding-pressures-affecting-diamond-light-source-ee231c6e>> >With best wishes, >Colin > >Dr. Colin W. Levy >[email protected] >Expert Technical Specialist (XRD) >Manchester Institute of Biotechnology, Faculty of Science & Engineering >Tel: +44 (0) 161 529 4380 >The University of Manchester > >[cid:2e02cb8b-dbf8-4123-a3e1-c35f7c51d3ec] > > >######################################################################## > >To unsubscribe from the CCP4BB list, click the following link: >https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311570557145%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=POUHhKEi8JKf%2BkT59FULP%2B%2FhWEEPHW05E8vN9daOu50%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > >This message was issued to members of 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https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571028897%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=DS%2FViRbrqxyKVB2vPw4hLt4f0KnHB5UpCzlAdkvxvnI%3D&reserved=0<https://www.jiscmail.ac.uk/policyandsecurity/> ------------------------------ Date: Fri, 24 Jul 2026 19:57:23 +0200 From: Xavier Brazzolotto <[email protected]> Subject: Protein cavity volume calculation Sorry for the bit off-list question, I would like to calculate a cavity volume using CASTp 3.0, but the server (https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsts.bioe.uic.edu%2Fcastp%2Fcalculation.html&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571104467%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=5elcrIqUf%2F4XgZiDs92zwE0MuEm1eEVjLfIc36Wq2Ow%3D&reserved=0<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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571166991%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Yp8%2FISquYnd%2FtKG9SGlCYwg9tFk0v2%2FXQJs6Xdj9hIM%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571209359%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=t5LyfdkeuvDdwetr9jnuxAFz8Hdb4UVGUMGhQvRpBnk%3D&reserved=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571244295%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=91ctrry5QeB5G1EpwQ%2B7t1QQp%2BfagA1dxmck5LSWCs8%3D&reserved=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571271764%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=H4P707TLlVs6UXvN4WqJpczLTnIg7msfDUQshXUWj2E%3D&reserved=0<https://www.jiscmail.ac.uk/policyandsecurity/> ------------------------------ Date: Fri, 24 Jul 2026 17:59:29 +0000 From: Jeffrey Bonanno <[email protected]> Subject: Re: Protein cavity volume calculation 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] From: CCP4 bulletin board <[email protected]> On Behalf Of Xavier Brazzolotto Sent: Friday, July 24, 2026 1:57 PM To: [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 (https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsts.bioe.uic.edu%2Fcastp%2Fcalculation.html&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571297725%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=xr4I%2Bss6cyh99lOpE89vdUos95%2FerSGSWqIC2me9Hno%3D&reserved=0<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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571321771%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=kx%2BoEdbfnkDvpnQbmMFFG58IYj3h4t34QQRThIdyRuM%3D&reserved=0<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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571352765%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=qquhRejmC2Uv9UV1GoieHeV2WT22omAE4HvzV81g3cc%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571410666%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=QPcsMWw4Nmd3dR5kXhJ%2BcxAloNGYrw2SBuU6KRPbkZ0%3D&reserved=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571465579%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=oInMxrUv%2BqvbEZ1fO3ASbk3nqP%2FFyXWWydg2ntA6O4I%3D&reserved=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571526816%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=SzRxyXWHCuoSS9ZztZwvxr4%2Bo%2BMHNgrygg%2FUC%2BkpHts%3D&reserved=0<https://www.jiscmail.ac.uk/policyandsecurity/> ------------------------------ Date: Fri, 24 Jul 2026 20:28:56 +0200 From: Xavier Brazzolotto <[email protected]> Subject: Re: 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 > (https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsts.bioe.uic.edu%2Fcastp%2Fcalculation.html&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571576316%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=eD3LScH37nubgiQfD9AMnaDEnkiyARynKgE7ZR3a6nk%3D&reserved=0<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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571612777%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=v4%2FQIAExGPn6EkyjgAiAveVrJRe8Y1UM%2BPFcVgSTHfQ%3D&reserved=0<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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571656603%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=zcgOWWq7nncfFRDz1p8LKqzCz%2BPdQM1v01lr3PvAVhw%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571719911%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=somJdeOewdHiYVKmOy9xYb86hvpfUBKGYdNRdNDlC%2B8%3D&reserved=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571769153%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ub55xp2YnZI0WqjFzijfkS%2BqHBtZocdc6wsUNLZNStg%3D&reserved=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://nam12.safelinks.protection.outlook.com/?url=https<http://https/>%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cmllynch2%40BUFFALO.EDU%7Cda726ee329dd49cff59a08dee9d7f932%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C639205311571802185%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=l%2FoIMDphr0h0BsV5T6G3tDjf6e6dROKnRV7HAY%2FIevc%3D&reserved=0 ------------------------------ End of CCP4BB Digest - 23 Jul 2026 to 24 Jul 2026 (#2026-167) ************************************************************* ######################################################################## 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/
