- IHM-repval - salilab.org

New PDB-Dev Beta Site
by Brinda Vallat 11 Feb '20

11 Feb '20

Hello Everyone, We are happy to inform you that the beta version of a new and improved PDB-Dev website is now available at https://pdb-dev-beta.wwpdb.org. In addition to providing dynamic and responsive web pages, the PDB-Dev web interface now includes two new features. 1. We provide a new search service that facilitates the retrieval of structures archived in PDB-Dev. Simple text search using macromolecular names, entry identifiers, experimental data types, author names, citation, software and several other keywords are now supported. Boolean search is also supported. Search results can be downloaded as csv or excel files. 2. We have individual entry pages for released entries. The entry pages highlight key details about the structure and provide links to related data residing in other repositories as well as the ability to download the structure. We request you to review the beta site and provide us your feedback. We plan to move the beta site into production by the end of February, 2020. Please send any comments or suggestions by February 24th to pdb-dev(a)mail.wwpdb.org. Thank you. Best regards, The PDB-Dev Team

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BPS 2019 satellite meeting
by Brinda Vallat 21 Dec '18

21 Dec '18

Hello Everyone, We are organizing a Workshop titled "Working towards federating structural models and data <https://www.biophysics.org/2019meeting/program/satellite-meetings/working-t…>". The Workshop is focused on creating an interoperating network of structural biology model and data repositories that will enable the archiving of integrative structural models and associated experimental data. The day-long Workshop will be held as a Satellite Meeting at the 2019 Biophysical Society Meeting on March 1, 2019 at the Baltimore Convention Center, 1 W Pratt St, Baltimore, MD 21201, USA. If you are interested in attending the Workshop, please visit the website <https://www.biophysics.org/2019meeting/program/satellite-meetings/working-t…> to register. Space is limited and on a first-come, first-serve basis. The $75 fee covers workshop registration and lunch. Registration closes on January 28, 2019. Please let me know if you have any questions. Season's greetings and best wishes for a very Happy New Year! Brinda -- BRINDA VALLAT, Ph.D. RCSB Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.445.4948 | E: brinda.vallat(a)rcsb.org

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Reminder: IHM "large" group meeting today
by Brinda Vallat 13 Sep '18

13 Sep '18

Hello Everyone, The next "large" group IHM meeting is today at 8:00 AM PDT / 10:00 AM CDT / 11:00 AM EDT / 4:00 PM BST / 5:00 PM CEST / 12:00 AM JST (Friday, September 14th). *Attendees* (based on the doodle poll <https://doodle.com/poll/im4zh8dzfudr4hfq>) 1. Ben Webb 2. Tom Goddard 3. Mikael Trellet 4. Brian Jimenez 5. Aleks Gutmanas 6. Kumaran Baskaran 7. John Westbrook 8. Brinda Vallat Please feel free to join the meeting even if you didn't sign up using the doodle poll. *Agenda: * 1. Update on current structures in PDB-Dev <https://pdb-dev.wwpdb.org/> 2. Update on the IHM-dictionary <https://github.com/ihmwg/IHM-dictionary>, MA-dictionary <https://github.com/ihmwg/MA-dictionary> and the FLR-dictionary <https://github.com/ihmwg/FLR-dictionary> 3. Update on the Python-IHM <https://github.com/ihmwg/python-ihm> library 4. Support for IHM-dictionary in HADDOCK <https://haddock.science.uu.nl/> 5. Open discussion *Connection details: * We will use *Zoom* for audio and screen sharing. There will be no video. The use of *Zoom* may require installation of new software (see "First time setup instructions for Zoom" below). To join the meeting, click on this link at the scheduled time from PC, Mac, Linux, iOS or Android: https://zoom.us/j/386263131 Meeting ID: 386 263 131 *First time setup instructions for Zoom* - Open a browser and visit https://zoom.us/test <https://www.google.com/url?q=https%3A%2F%2Fzoom.us%2Ftest&sa=D&ust=15271036…> - Click the Join button - Firefox - In Firefox, you’ll get a window to Launch Application - Close this window, and on the webpage click the link to download & run Zoom - Download and run the installer to install Zoom - The Zoom application will launch and join the test meeting - Chrome - Click the link to download & run Zoom - Download and run the installer to install Zoom - The Zoom application will launch and join the test meeting Please let me know if you have any questions in this regard. Thank you, Brinda -- BRINDA VALLAT, Ph.D. RCSB Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.445.4948 | E: brinda.vallat(a)rcsb.org

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Reminder: IHM "large" group meeting tomorrow
by Brinda Vallat 12 Sep '18

12 Sep '18

Hello Everyone, The next "large" group IHM meeting is on Thursday, September 13th at 8:00 AM PDT / 10:00 AM CDT / 11:00 AM EDT / 4:00 PM BST / 5:00 PM CEST / 12:00 AM JST (Friday, September 14th). *Attendees* (based on the doodle poll <https://doodle.com/poll/im4zh8dzfudr4hfq>) 1. Ben Webb 2. Tom Goddard 3. Mikael Trellet 4. Brian Jimenez 5. Aleks Gutmanas 6. Kumaran Baskaran 7. John Westbrook 8. Brinda Vallat Please feel free to join the meeting even if you didn't sign up using the doodle poll. *Agenda: * 1. Update on current structures in PDB-Dev <https://pdb-dev.wwpdb.org/> 2. Update on the IHM-dictionary <https://github.com/ihmwg/IHM-dictionary>, MA-dictionary <https://github.com/ihmwg/MA-dictionary> and the FLR-dictionary <https://github.com/ihmwg/FLR-dictionary> 3. Update on the Python-IHM <https://github.com/ihmwg/python-ihm> library 4. Support for IHM-dictionary in HADDOCK <https://haddock.science.uu.nl/> 5. Open discussion *Connection details: * We will use *Zoom* for audio and screen sharing. There will be no video. The use of *Zoom* may require installation of new software (see "First time setup instructions for Zoom" below). To join the meeting, click on this link at the scheduled time from PC, Mac, Linux, iOS or Android: https://zoom.us/j/386263131 Meeting ID: 386 263 131 *First time setup instructions for Zoom* - Open a browser and visit https://zoom.us/test <https://www.google.com/url?q=https%3A%2F%2Fzoom.us%2Ftest&sa=D&ust=15271036…> - Click the Join button - Firefox - In Firefox, you’ll get a window to Launch Application - Close this window, and on the webpage click the link to download & run Zoom - Download and run the installer to install Zoom - The Zoom application will launch and join the test meeting - Chrome - Click the link to download & run Zoom - Download and run the installer to install Zoom - The Zoom application will launch and join the test meeting Please let me know if you have any questions in this regard. Thank you, Brinda -- BRINDA VALLAT, Ph.D. RCSB Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.445.4948 | E: brinda.vallat(a)rcsb.org

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IHM "large" group meeting: schedule, agenda and connection details
by Brinda Vallat 10 Sep '18

10 Sep '18

Hello Everyone, The next "large" group IHM meeting is on Thursday, September 13th at 8:00 AM PDT / 10:00 AM CDT / 11:00 AM EDT / 4:00 PM BST / 5:00 PM CEST / 12:00 AM JST (Friday, September 14th). *Attendees* (based on the doodle poll <https://doodle.com/poll/im4zh8dzfudr4hfq>) 1. Ben Webb 2. Tom Goddard 3. Mikael Trellet 4. Brian Jimenez 5. Aleks Gutmanas 6. Kumaran Baskaran 7. John Westbrook 8. Brinda Vallat Please feel free to join the meeting even if you didn't sign up using the doodle poll. *Agenda: * 1. Update on current structures in PDB-Dev <https://pdb-dev.wwpdb.org/> 2. Update on the IHM-dictionary <https://github.com/ihmwg/IHM-dictionary>, MA-dictionary <https://github.com/ihmwg/MA-dictionary> and the FLR-dictionary <https://github.com/ihmwg/FLR-dictionary> 3. Update on the Python-IHM <https://github.com/ihmwg/python-ihm> library 4. Support for IHM-dictionary in Haddock <https://haddock.science.uu.nl> 5. Open discussion *Connection details: * We will use *Zoom* for audio and screen sharing. There will be no video. The use of *Zoom* may require installation of new software (see "First time setup instructions for Zoom" below). To join the meeting, click on this link at the scheduled time from PC, Mac, Linux, iOS or Android: https://zoom.us/j/386263131 Meeting ID: 386 263 131 *First time setup instructions for Zoom* - Open a browser and visit https://zoom.us/test <https://www.google.com/url?q=https%3A%2F%2Fzoom.us%2Ftest&sa=D&ust=15271036…> - Click the Join button - Firefox - In Firefox, you’ll get a window to Launch Application - Close this window, and on the webpage click the link to download & run Zoom - Download and run the installer to install Zoom - The Zoom application will launch and join the test meeting - Chrome - Click the link to download & run Zoom - Download and run the installer to install Zoom - The Zoom application will launch and join the test meeting Please let me know if you have any questions in this regard. Thank you, Brinda -- BRINDA VALLAT, Ph.D. RCSB Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.445.4948 | E: brinda.vallat(a)rcsb.org

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The next "large group" integrative/hybrid modeling videoconference
by Ben Webb 05 Sep '18

05 Sep '18

Hi all - we will be having a videoconference for the integrative/hybrid modeling project next month, on Thursday September 13th: https://github.com/ihmwg/IHM-dictionary/wiki/Meetings We will update everyone on our progress on the IHM and related dictionaries, with a look at the current set of depositions in the PDB-Dev database, and also have some open discussion time - anyone from the group can raise any issues they may be having with the design of the dictionary, deposition of models, and so on. Please fill out the Doodle poll to let us know your availability, so we can schedule the call at a time that most people can make: https://doodle.com/poll/im4zh8dzfudr4hfq Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Meeting summary from the May 24th IHM meeting
by Brinda Vallat 13 Jun '18

13 Jun '18

Hello Everyone, The summary of the May 24th IHM meeting is available here <https://github.com/ihmwg/IHM-dictionary/wiki/IHM-Meeting-Summary-May-24-2018>. As requested, the presentations are available for download from the the meeting summary page. Apologies for the delay in sending out this email although the meeting summary was updated on the GitHub wiki page soon after the meeting. Thank you, Brinda -- Brinda Vallat RCSB Center for Integrative Proteomics Research Rutgers, The State University of New Jersey 174 Frelinghuysen Rd Piscataway NJ 08854-8076 Email: brinda.vallat(a)rcsb.org Phone: 848-445-4948

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Reminder: "Large" group IHM meeting: Agenda and Connection details
by Brinda Vallat 23 May '18

23 May '18

Hello Everyone, The next "Large" group IHM meeting is on Thursday, May 24th at 7:00 AM PDT / 9:00 AM CDT / 10:00 AM EDT / 3:00 PM BST / 4:00 PM CEST / 11:00 PM JST. *Attendees* (based on the doodle poll <https://doodle.com/poll/uddhrpu5mr3msqaq>) 1. Ben Webb 2. Tom Goddard 3. Mikael Trellet 4. Juergen Koefinger 5. Aleks Gutmanas 6. Gert-Jan Bekker 7. John Westbrook 8. Brinda Vallat Anyone is welcome to join the meeting, even if your name is not in the above list. *Agenda: * 1. Update on the IHM-dictionary <https://github.com/ihmwg/IHM-dictionary> and PDB-Dev <https://pdb-dev.wwpdb.org/> 2. Update on the Python-IHM <https://github.com/ihmwg/python-ihm> library 3. Open discussion *Connection details: * We will use *Zoom* for audio and screen sharing. There will be no video. Please note that we will use different AV technology compared to past meetings and this may require installation of new software (see "First time setup instructions for Zoom" below). To join the meeting, click on this link at the scheduled time: https://zoom.us/j/460121642 Meeting ID: 460121642 *First time setup instructions for Zoom* - Open a browser and visit https://zoom.us/test <https://www.google.com/url?q=https%3A%2F%2Fzoom.us%2Ftest&sa=D&ust=15271036…> - Click the Join button - Firefox - In Firefox, you’ll get a window to Launch Application - Close this window, and on the webpage click the link to download & run Zoom - Download and run the installer to install Zoom - The Zoom application will launch and join the test meeting - Chrome - Click the link to download & run Zoom - Download and run the installer to install Zoom - The Zoom application will launch and join the test meeting Please let me know if you have any questions in this regard. Thank you, Brinda

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Reminder: "Large" group IHM meeting: Agenda and Connection details
by Brinda Vallat 21 May '18

21 May '18

Hello Everyone, The next "Large" group IHM meeting is on Thursday, May 24th at 7:00 AM PDT / 9:00 AM CDT / 10:00 AM EDT / 3:00 PM BST / 4:00 PM CEST / 11:00 PM JST. *Attendees* (based on the doodle poll <https://doodle.com/poll/uddhrpu5mr3msqaq>) 1. Ben Webb 2. Tom Goddard 3. Mikael Trellet 4. Juergen Koefinger 5. Aleks Gutmanas 6. Gert-Jan Bekker 7. John Westbrook 8. Brinda Vallat Anyone is welcome to join the meeting, even if your name is not in the above list. *Agenda: * 1. Update on the IHM-dictionary <https://github.com/ihmwg/IHM-dictionary> and PDB-Dev <https://pdb-dev.wwpdb.org/> 2. Update on the Python-IHM <https://github.com/ihmwg/python-ihm> library 3. Open discussion *Connection details: * We will use *Zoom* for audio and screen sharing. There will be no video. Please note that we will use different AV technology compared to past meetings and this may require installation of new software (see "First time setup instructions for Zoom" below). To join the meeting, click on this link at the scheduled time: https://zoom.us/j/460121642 Meeting ID: 460121642 *First time setup instructions for Zoom* - Open a browser and visit https://zoom.us/test <https://www.google.com/url?q=https%3A%2F%2Fzoom.us%2Ftest&sa=D&ust=15271036…> - Click the Join button - Firefox - In Firefox, you’ll get a window to Launch Application - Close this window, and on the webpage click the link to download & run Zoom - Download and run the installer to install Zoom - The Zoom application will launch and join the test meeting - Chrome - Click the link to download & run Zoom - Download and run the installer to install Zoom - The Zoom application will launch and join the test meeting Please let me know if you have any questions in this regard. Thank you, Brinda On Fri, May 18, 2018 at 3:29 PM, Brinda Vallat <brinda.vallat(a)rcsb.org> wrote: > Hello Everyone, > > The next "Large" group IHM meeting is on Thursday, May 24th at 7:00 AM PDT > / 9:00 AM CDT / 10:00 AM EDT / 3:00 PM BST / 4:00 PM CEST / 11:00 PM JST. > > *Attendees* (based on the doodle poll > <https://doodle.com/poll/uddhrpu5mr3msqaq>) > > 1. Ben Webb > 2. Tom Goddard > 3. Mikael Trellet > 4. Juergen Koefinger > 5. Aleks Gutmanas > 6. Gert-Jan Bekker > 7. John Westbrook > 8. Brinda Vallat > > Anyone is welcome to join the meeting, even if your name is not in the > above list. > > *Agenda: * > > 1. Update on the IHM-dictionary <https://github.com/ihmwg/IHM-dictionary> > and PDB-Dev <https://pdb-dev.wwpdb.org/> > 2. Update on the Python-IHM <https://github.com/ihmwg/python-ihm> library > 3. Open discussion > > *Connection details: * > > We will use Zoom for audio and screen sharing. There will be no video. > Please note that we will use different AV technology compared to past > meetings. > > To join the meeting, click on this link at the scheduled time: > https://zoom.us/j/460121642 > Meeting ID: 460121642 > > Please let me know if you have any questions in this regard. > > Thank you, > Brinda > > > -- > Brinda Vallat > > RCSB > Center for Integrative Proteomics Research > Rutgers, The State University of New Jersey > 174 Frelinghuysen Rd > Piscataway NJ 08854-8076 > Email: brinda.vallat(a)rcsb.org > Phone: 848-445-4948 > > -- Brinda Vallat RCSB Center for Integrative Proteomics Research Rutgers, The State University of New Jersey 174 Frelinghuysen Rd Piscataway NJ 08854-8076 Email: brinda.vallat(a)rcsb.org Phone: 848-445-4948

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"Large" group IHM meeting: Agenda and Connection details
by Brinda Vallat 18 May '18

18 May '18

Hello Everyone, The next "Large" group IHM meeting is on Thursday, May 24th at 7:00 AM PDT / 9:00 AM CDT / 10:00 AM EDT / 3:00 PM BST / 4:00 PM CEST / 11:00 PM JST. *Attendees* (based on the doodle poll <https://doodle.com/poll/uddhrpu5mr3msqaq>) 1. Ben Webb 2. Tom Goddard 3. Mikael Trellet 4. Juergen Koefinger 5. Aleks Gutmanas 6. Gert-Jan Bekker 7. John Westbrook 8. Brinda Vallat Anyone is welcome to join the meeting, even if your name is not in the above list. *Agenda: * 1. Update on the IHM-dictionary <https://github.com/ihmwg/IHM-dictionary> and PDB-Dev <https://pdb-dev.wwpdb.org/> 2. Update on the Python-IHM <https://github.com/ihmwg/python-ihm> library 3. Open discussion *Connection details: * We will use Zoom for audio and screen sharing. There will be no video. Please note that we will use different AV technology compared to past meetings. To join the meeting, click on this link at the scheduled time: https://zoom.us/j/460121642 Meeting ID: 460121642 Please let me know if you have any questions in this regard. Thank you, Brinda -- Brinda Vallat RCSB Center for Integrative Proteomics Research Rutgers, The State University of New Jersey 174 Frelinghuysen Rd Piscataway NJ 08854-8076 Email: brinda.vallat(a)rcsb.org Phone: 848-445-4948

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IHM-repval