- IHM-repval - salilab.org

This month's "large group" I/H methods meeting: agenda and connection details
by Brinda Vallat 06 Jun '17

06 Jun '17

Hello Everyone, This month's I/H methods meeting is fixed for Thursday, June 8 at 8AM PDT, 10AM CDT, 11AM EDT, 4PM BST, 5PM CEST and 12AM JST (June 9). The following have confirmed attendance via the doodle poll. *Confirmed attendees* Ben Webb (UCSF, US) Tom Goddard (UCSF, US) Brinda Vallat (RCSB, US) John Westbrook (RCSB, US) Aleks Gutmanas (PDBe, UK) Gert-Jan Bekker (PDBj, Japan) Mike Goodstadt (CNAG, Spain) Juergen (not sure if it is Juergen Haas from SIB, Switzerland or Juergen Koefinger from MPI, Germany - please clarify) If anyone else would like to join the meeting, please let me know. I encourage everyone to attend so as to make these meetings more effective. *Meeting agenda* 1. Update on I/H methods project - Ben Webb, Brinda Vallat 2. Live demo: Visualization of the Nup84 integrative model using ChimeraX - Tom Goddard 3. Open discussion - Everyone *Connection details* The meeting will be conducted in the same manner as last time. We will use BT for the voice call and joinme for screen sharing. We will not have any video. *For the BT voice call: * 1. Call the following number based on which country you are calling from: *US 18008681123UK 08000326469Germany 08001824096Japan 0120001425Switzerland 0800111051* *Spain ** 900816444* 2. Enter the participant code: *37910748#* 3. Say your name at the beep. *For the Joinme screen share: * 4. Go to http://join.me/rcsbmeeting <http://join.me/rcsbmeeting> Please let me know if you have any further questions. Thank you. -- 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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This month's "large group" integrative/hybrid modeling videoconference
by Ben Webb 01 Jun '17

01 Jun '17

Hi all - the monthly videoconference for the integrative/hybrid modeling project this month will be on Thursday June 8th: https://github.com/ihmwg/IHM-dictionary/wiki/Meetings The purpose of this meeting is to update everyone on our progress on the IHM dictionary. Tom Goddard from the ChimeraX team will also be demonstrating visualization of one of the example mmCIF IHM files with ChimeraX. 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/qtn8a43zw98df27s 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
by Brinda Vallat 07 Apr '17

07 Apr '17

Hello Everyone, Please find attached the meeting summary from yesterday's meeting. Please feel free to contact either Ben Webb, Tom Goddard or myself if you have any further questions or if you need any more information regarding the I/H methods dictionary, PDB-Dev or ChimeraX. The email addresses are included in the meeting summary. The summary also has the links to the various sited discussed during the meeting. Thank you once again for taking the time to attend the meeting. Our next meeting will be May, 2017. We'll contact you to fix a date and time convenient to everyone. Meanwhile, if you'd like to join our regular weekly Skype meeting, please let me know. The scheduled maintenance of the PDB-Dev website is now complete and the site is up and running currently. Regards, Brinda

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Thank you!
by Brinda Vallat 06 Apr '17

06 Apr '17

Hello Everyone, Thank you for taking the time to join the I/H methods meeting today. We look forward to working together to get more structures deposited into PDB-Dev. The PDB-Dev website (https://pdb-dev.rcsb.rutgers.edu) is currently down due to a scheduled maintenance for hardware upgrade. It is expected to be up in about 6 hours. In the meantime, all the examples on PDB-Dev can be also accessed on the Github site ( https://github.com/ihmwg/IHM-dictionary/tree/master/examples). Please feel free to clone/download the Git repository and visualize these structures with ChimeraX. If you encounter any problems. please reach out to me or Ben (ben(a)salilab.org) or Tom (goddard(a)cgl.ucsf.edu). The meeting summary from today will be updated on the Github repository wiki page (https://github.com/ihmwg/IHM-dictionary/wiki/Meetings). The next meeting will be roughly in a month. We will update you with the data and time as we get closer to the meeting. Thank you once again. -- Brinda Vallat RCSB Protein Data Bank 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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Fwd: mmCIF–modeling extension.pptx
by Brinda Vallat 06 Apr '17

06 Apr '17

---------- Forwarded message ---------- From: Jürgen Haas <juergen.haas(a)unibas.ch> Date: Thu, Apr 6, 2017 at 11:54 AM Subject: mmCIF–modeling extension.pptx To: Brinda Vallat <brinda.vallat(a)rcsb.org> -- Brinda Vallat RCSB Protein Data Bank 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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Update: Integrative/Hybrid modeling meeting
by Brinda Vallat 05 Apr '17

05 Apr '17

Hello Everyone, We have a few more members joining the meeting. The updated list is as follows: Ben Webb (UCSF, USA) Tom Goddard (UCSF, USA) Kumaran Baskaran (BMRB, USA) Emad Tajkhorshid (UIUC, USA) Ryan McGreevy (UIUC, USA) John Stone (UIUC, USA) Rocco Moretti (Vanderbilt, USA) John Westbrook (RCSB PDB, USA) Brinda Vallat (RCSB PDB, USA) Margaret Gabanyi (RCSB PDB, USA) Oliver Smart (PDBe, UK) Aleksandras Gutmanas (PDBe, UK) John Berrisford (PDBe, UK) Juergen Haas (SIB, Switzerland) Juergen Koefinger (Max Plank Institute, Germany) Hirofumi Suzuki (PDBj, Japan) Gert-Jan Bekker (PDBj, Japan) Please follow the instructions from the previous mail (below) to join the meeting via BT (for voice call) and Joinme (for screen share). The meeting time spans various time zones from California to Japan. As a reminder, the local times for the meeting are are: Thursday April 6th at 8AM PDT, 10AM CDT, 11AM EDT, 4PM BST, 5PM CEST and 12AM JST (April 7). Thank you, Brinda On Wed, Apr 5, 2017 at 1:47 PM, Brinda Vallat <brinda.vallat(a)rcsb.org> wrote: > Hello Everyone, > > The I/H methods meeting is scheduled for 8AM Pacific time tomorrow > (Thursday, April 6, 2017). > > *Meeting Agenda* > > 1. Overview of the current I/H methods dictionary and documentation. > Please follow the links below to access the dictionary and associated > documentation on Github. > https://github.com/ihmwg/IHM-dictionary > https://github.com/ihmwg/IHM-dictionary/blob/master/dictiona > ry_documentation/documentation.md > > Our goal is to gather feedback regarding the I/H methods dictionary. > > 2. Examples of I/H models from IMP (https://github.com/ihmwg/IHM- > dictionary/tree/master/examples) > > 3. Introduce the modeling dictionary, also available on Github ( > https://github.com/JuergenHaasSIB/modeling_dictionary). > > 4. Open discussion > > *Participants with confirmed attendance* > > Ben Webb (UCSF, USA) > Tom Goddard (UCSF, USA) > Kumaran Baskaran (BMRB, USA) > Emad Tajkhorshid (UIUC, USA) > John Westbrook (RCSB PDB, USA) > Brinda Vallat (RCSB PDB, USA) > Margaret Gabanyi (RCSB PDB, USA) > Oliver Smart (PDBe, UK) > Aleksandras Gutmanas (PDBe, UK) > John Berrisford (PDBe, UK) > Juergen Haas (SIB, Switzerland) > Juergen Koefinger (Max Plank Institute, Germany) > Hirofumi Suzuki (PDBj, Japan) > Gert-Jan Bekker (PDBj, Japan) > > I apologize if I have missed anyone. Please let me know and I'll add you > to the list. > > *How to join the meeting* > > Considering that the number of people attending this meeting has increased > over the last couple of days, it might be prudent to not use Skype as > originally planned. We will use BT (for voice) and Joinme (for screen > share) during the meeting. We will not have any video. Please follow the > instructions below to connect via BT and Joinme. > > *For the BT voice call: * > > 1. Call the following number based on which country you are calling from: > > > > > > *US 18008681123 <(800)%20868-1123>UK > 08000326469Germany 08001824096Japan > 0120001425Switzerland 0800111051* > > 2. Enter the participant code: *37910748#* > > 3. Say your name at the beep. > > *For the Joinme screen share: * > > 4. Go to http://join.me/rcsbmeeting <http://join.me/rcsbmeeting> > > Please let me know if you have any further questions. > > Thank you. > > -- > Brinda Vallat > > RCSB Protein Data Bank > 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 <(848)%20445-4948> > >

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Integrative/Hybrid modeling meeting tomorrow - agenda and connection details
by Brinda Vallat 05 Apr '17

05 Apr '17

Hello Everyone, The I/H methods meeting is scheduled for 8AM Pacific time tomorrow (Thursday, April 6, 2017). *Meeting Agenda* 1. Overview of the current I/H methods dictionary and documentation. Please follow the links below to access the dictionary and associated documentation on Github. https://github.com/ihmwg/IHM-dictionary https://github.com/ihmwg/IHM-dictionary/blob/master/ dictionary_documentation/documentation.md Our goal is to gather feedback regarding the I/H methods dictionary. 2. Examples of I/H models from IMP ( https://github.com/ihmwg/IHM-dictionary/tree/master/examples) 3. Introduce the modeling dictionary, also available on Github ( https://github.com/JuergenHaasSIB/modeling_dictionary). 4. Open discussion *Participants with confirmed attendance* Ben Webb (UCSF, USA) Tom Goddard (UCSF, USA) Kumaran Baskaran (BMRB, USA) Emad Tajkhorshid (UIUC, USA) John Westbrook (RCSB PDB, USA) Brinda Vallat (RCSB PDB, USA) Margaret Gabanyi (RCSB PDB, USA) Oliver Smart (PDBe, UK) Aleksandras Gutmanas (PDBe, UK) John Berrisford (PDBe, UK) Juergen Haas (SIB, Switzerland) Juergen Koefinger (Max Plank Institute, Germany) Hirofumi Suzuki (PDBj, Japan) Gert-Jan Bekker (PDBj, Japan) I apologize if I have missed anyone. Please let me know and I'll add you to the list. *How to join the meeting* Considering that the number of people attending this meeting has increased over the last couple of days, it might be prudent to not use Skype as originally planned. We will use BT (for voice) and Joinme (for screen share) during the meeting. We will not have any video. Please follow the instructions below to connect via BT and Joinme. *For the BT voice call: * 1. Call the following number based on which country you are calling from: *US 18008681123 <(800)%20868-1123>UK 08000326469Germany 08001824096Japan 0120001425Switzerland 0800111051* 2. Enter the participant code: *37910748#* 3. Say your name at the beep. *For the Joinme screen share: * 4. Go to http://join.me/rcsbmeeting <http://join.me/rcsbmeeting> Please let me know if you have any further questions. Thank you. -- Brinda Vallat RCSB Protein Data Bank 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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This month's "large group" integrative/hybrid modeling Skype call
by Ben Webb 03 Apr '17

03 Apr '17

Hi all - the monthly Skype call for the integrative/hybrid modeling project this month will be on Thursday March 30th: https://github.com/ihmwg/IHM-dictionary/wiki/Meetings We generally hold these meetings at 9am Pacific time, but we appreciate that some people might like to attend but can't due to the time. I'll send out a Doodle poll shortly to you all so we can get a better idea of who wants to join and what time might work for a larger group. 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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Linking integrative models out to experimental data
by Ben Webb 13 Mar '17

13 Mar '17

Hi all, As you know, whenever we build an integrative or hybrid model we need to point to multiple sources of input experimental data. It doesn't make sense to embed that data directly in an mmCIF file because that would be very inefficient, so instead we need to link out to wherever the raw and/or processed experimental datasets are stored, ideally in a repository maintained by experts in the field (e.g. PDB, EMDB, SASBDB). I've summarized the kinds of data that we've been dealing with so far in our own modeling, with pointers to repositories where available, in the wiki: https://github.com/ihmwg/IHM-dictionary/wiki/External%20data Please take a look and add to it (or reply to this email). It seems likely that there are many modeling scenarios that neither RCSB nor the Sali lab have considered thus far. 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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wwPDB representation / validation group
by Andrej Sali 23 Feb '17

23 Feb '17

Hi all, As you know we meet weekly over Skype to discuss issues related to the representation and validation of integrative models: https://github.com/ihmwg/IHM-dictionary/wiki/Meetings <https://github.com/ihmwg/IHM-dictionary/wiki/Meetings> These meetings tend to focus on technical details related to the mmCIF dictionary. However, we're starting to have monthly meetings where we have a more high level discussion among a larger group of people. If you can only make an occasional meeting, we recommend these are the meetings you come to. The next such large-group meeting will be on February 23rd, 2017 at 9am Pacific time (noon Eastern). If you're interested in attending, please let Brinda Vallat at RCSB know, so she can add you to the Skype call: brinda.vallat(a)rcsb.org <mailto:brinda.vallat@rcsb.org> If this time is really inconvenient for you, please let Brinda know and we can look into other times. Best, Andrej -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org _______________________________________________ IHM-repval mailing list IHM-repval(a)salilab.org https://salilab.org/mailman/listinfo/ihm-repval

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