- Industry - phenix-online.org

Workshop talks available online
by Nigel Moriarty 01 Apr '25

01 Apr '25

Folks I have published all the talks that have been released for distribution. https://www.phenix-online.org/workshops login: workshop password: phenix3py Cheers Nigel --- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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Workshop talks available online
by Nigel Moriarty 01 Apr '25

01 Apr '25

Folks I have published all the talks that have been released for distribution. https://www.phenix-online.org/workshops login: workshop password: phenix3p Cheers Nigel --- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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Industry Round is just starting.
by Nigel Moriarty 19 Mar '25

19 Mar '25

Feel free to join now. Join Zoom Meeting https://lbnl.zoom.us/j/91935895632?pwd=apavpMaMGbJ0FLXw9Q8rCECI8iAyng.1 <https://www.google.com/url?q=https://lbnl.zoom.us/j/91935895632?pwd%3Dapavp…> Meeting ID: 919 3589 5632 Passcode: 730330 Cheers Nigel --- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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Tomorrow - Industry Roundtable - 2025 Spring Phenix Developers Meeting
by Ashley Dawn 18 Mar '25

18 Mar '25

Dear Consortium Members, The* 2025 Spring Phenix Developers Meeting <https://phenix-online.org/workshops/mar-2025-lanl/index.html>* ends tomorrow with the *Industry Roundtable.* Wednesday, March 19 – Phenix Industry Session (USA Mountain Time) - 9:00 AM – 12:00 PM Industry Roundtable – conference of developers and industry to discuss the future directions of Phenix. This session will be devoted to a discussion of AlphaFold/RosettaFold and future directions. *Industry consortium members are encouraged to attend*. The Zoom information is below. Please join us for this interactive discussion. Best, Ashley Ashley Dawn (she/her/hers) Program Manager, Phenix Industrial Consortium <https://phenix-online.org/> Molecular Biophysics & Integrated Bioimaging (MBIB <https://biosciences.lbl.gov/mbib/>) Lawrence Berkeley Laboratory 510-486-5455 Join Zoom Meeting > https://lbnl.zoom.us/j/91935895632?pwd=apavpMaMGbJ0FLXw9Q8rCECI8iAyng.1 > <https://www.google.com/url?q=https://lbnl.zoom.us/j/91935895632?pwd%3Dapavp…> > > Meeting ID: 919 3589 5632 > Passcode: 730330 > > --- > > One tap mobile > +12133388477,,91935895632# US (Los Angeles) > +16692192599,,91935895632# US (San Jose) > > --- > > Dial by your location > • +1 213 338 8477 US (Los Angeles) > • +1 669 219 2599 US (San Jose) > • +1 669 900 6833 US (San Jose) > • +1 206 337 9723 US (Seattle) > • +1 253 215 8782 US (Tacoma) > • +1 346 248 7799 US (Houston) > • +1 602 753 0140 US (Phoenix) > • +1 720 928 9299 US (Denver) > • +1 971 247 1195 US (Portland) > • +1 470 250 9358 US (Atlanta) > • +1 470 381 2552 US (Atlanta) > • +1 646 518 9805 US (New York) > • +1 646 558 8656 US (New York) > • +1 651 372 8299 US (Minnesota) > • +1 786 635 1003 US (Miami) > • +1 267 831 0333 US (Philadelphia) > • +1 301 715 8592 US (Washington DC) > • +1 312 626 6799 US (Chicago) > > Meeting ID: 919 3589 5632 > > Find your local number: https://lbnl.zoom.us/u/adUP3eF75H > <https://www.google.com/url?q=https://lbnl.zoom.us/u/adUP3eF75H&sa=D&source=…> > > --- > > Join by SIP > • 91935895632(a)zoomcrc.com > > --- > > Join by H.323 > • 144.195.19.161 (US West) > • 206.247.11.121 (US East) > • 115.114.131.7 (India Mumbai) > • 115.114.115.7 (India Hyderabad) > • 159.124.15.191 (Amsterdam Netherlands) > • 159.124.47.249 (Germany) > • 159.124.104.213 (Australia Sydney) > • 159.124.74.212 (Australia Melbourne) > • 64.211.144.160 (Brazil) > • 159.124.168.213 (Canada Toronto) > • 159.124.196.25 (Canada Vancouver) > • 170.114.194.163 (Japan Tokyo) > • 147.124.100.25 (Japan Osaka) > > Meeting ID: 919 3589 5632 > Passcode: 730330 > > > > ────── > > > Reply allReplyForward

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Day 2 - 2025 Spring Phenix Developers Meeting - March 17-19
by Ashley Dawn 17 Mar '25

17 Mar '25

Dear Consortium Members, The* 2025 Spring Phenix Developers Meeting <https://phenix-online.org/workshops/mar-2025-lanl/index.html>* continues tomorrow with another day of talks. Tuesday, March 18 – Talks (USA Mountain Time) - 09:00 – 09:05 AM Paul D. Adams, Welcome - 09:05 – 09:30 AM Laura Pacoste, Developing electron diffraction methods to probe oxidation states in metalloenzymes (virtual) - 09:30 – 09:55 AM Airlie McCoy, phasertng updates (virtual) - 09:55 – 10:20 AM Pavel Afonine, I. Nuances, New Tools, and Methods for Visualizing and Validating Subtle Structural Details.II. Atomic Model Refinement Gets More Accurate: Combining Aspherical Density Models with Quantum-Based Restraints - 10:20 – 10:45 AM Alisia Fadini, AlphaFold as a Prior: Guiding Protein Structure Prediction Using Experimental Data with ROCKET - 10:45 – 11:00 AM Break - 11:00 – 11:25 AM Oleg Sobolev, Automatically Finding the Best Reference Model - 11:25 – 11:50 AM Nigel W. Moriarty, Paradigm Shift for Ligands in Phenix - Part Deux - 11:50 – 12:15 PM Christopher Williams, Further details of low-pLDDT AlphaFold2 predictions Please also join us on Wednesday for the Industry session 9am-12pm. The Zoom information is below. Best, Ashley Ashley Dawn (she/her/hers) Program Manager, Phenix Industrial Consortium <https://phenix-online.org/> Molecular Biophysics & Integrated Bioimaging (MBIB <https://biosciences.lbl.gov/mbib/>) Lawrence Berkeley Laboratory 510-486-5455 Join Zoom Meeting https://lbnl.zoom.us/j/91935895632?pwd=apavpMaMGbJ0FLXw9Q8rCECI8iAyng.1 <https://www.google.com/url?q=https://lbnl.zoom.us/j/91935895632?pwd%3Dapavp…> Meeting ID: 919 3589 5632 Passcode: 730330 --- One tap mobile +12133388477,,91935895632# US (Los Angeles) +16692192599,,91935895632# US (San Jose) --- Dial by your location • +1 213 338 8477 US (Los Angeles) • +1 669 219 2599 US (San Jose) • +1 669 900 6833 US (San Jose) • +1 206 337 9723 US (Seattle) • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 602 753 0140 US (Phoenix) • +1 720 928 9299 US (Denver) • +1 971 247 1195 US (Portland) • +1 470 250 9358 US (Atlanta) • +1 470 381 2552 US (Atlanta) • +1 646 518 9805 US (New York) • +1 646 558 8656 US (New York) • +1 651 372 8299 US (Minnesota) • +1 786 635 1003 US (Miami) • +1 267 831 0333 US (Philadelphia) • +1 301 715 8592 US (Washington DC) • +1 312 626 6799 US (Chicago) Meeting ID: 919 3589 5632 Find your local number: https://lbnl.zoom.us/u/adUP3eF75H <https://www.google.com/url?q=https://lbnl.zoom.us/u/adUP3eF75H&sa=D&source=…> --- Join by SIP • 91935895632(a)zoomcrc.com --- Join by H.323 • 144.195.19.161 (US West) • 206.247.11.121 (US East) • 115.114.131.7 (India Mumbai) • 115.114.115.7 (India Hyderabad) • 159.124.15.191 (Amsterdam Netherlands) • 159.124.47.249 (Germany) • 159.124.104.213 (Australia Sydney) • 159.124.74.212 (Australia Melbourne) • 64.211.144.160 (Brazil) • 159.124.168.213 (Canada Toronto) • 159.124.196.25 (Canada Vancouver) • 170.114.194.163 (Japan Tokyo) • 147.124.100.25 (Japan Osaka) Meeting ID: 919 3589 5632 Passcode: 730330 ──────

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Day 1 - 2025 Spring Phenix Developers Meeting - March 17-19
by Ashley Dawn 17 Mar '25

17 Mar '25

Dear Consortium Members, The* 2025 Spring Phenix Developers Meeting <https://phenix-online.org/workshops/mar-2025-lanl/index.html>* is this week *March 17-19, 2025 *in Santa Fe, NM and online. Here's today's talks (USA Mountain Time) Monday, March 17 – Talks - 09:00 – 09:05 AM Paul D. Adams, Introduction - 09:05 – 09:30 AM Dorothee Liebschner, Current status of DiSCaMB integration/Overview of MicroED models. - 09:30 – 09:55 AM Paulina Dominiak, Aspherical scattering factors in refinement of biomacromolecules - 09:55 – 10:20 AM Malgorzata Biczysko, Quantum refinement with machine learning: AQuaRef - 10:20 – 10:35 AM Break - 10:35 – 11:00 AM Tom Terwilliger, Is there a best assignment of side-chain alternative conformations to conformers? - 11:00 – 11:25 AM David Case, Creating and evaluating ensemble atomic models - 11:25 – 11:45 AM Billy Poon, Phenix updates - 11:45 - 12:10 PM Jane Richardson, Opportunities and concerns in RNA modeling - 12:10 – 12:30 PM Christopher Schlicksup, Exploration of per-atom real space refinement weight There will be more talks tomorrow and an Industry Roundtable on Wednesday. Please join us. The Zoom information is below. Thank you, Ashley > >> Join Zoom Meeting >> https://lbnl.zoom.us/j/91935895632?pwd=apavpMaMGbJ0FLXw9Q8rCECI8iAyng.1 >> <https://www.google.com/url?q=https://lbnl.zoom.us/j/91935895632?pwd%3Dapavp…> >> >> Meeting ID: 919 3589 5632 >> Passcode: 730330 >> >> --- >> >> One tap mobile >> +12133388477,,91935895632# US (Los Angeles) >> +16692192599,,91935895632# US (San Jose) >> >> --- >> >> Dial by your location >> • +1 213 338 8477 US (Los Angeles) >> • +1 669 219 2599 US (San Jose) >> • +1 669 900 6833 US (San Jose) >> • +1 206 337 9723 US (Seattle) >> • +1 253 215 8782 US (Tacoma) >> • +1 346 248 7799 US (Houston) >> • +1 602 753 0140 US (Phoenix) >> • +1 720 928 9299 US (Denver) >> • +1 971 247 1195 US (Portland) >> • +1 470 250 9358 US (Atlanta) >> • +1 470 381 2552 US (Atlanta) >> • +1 646 518 9805 US (New York) >> • +1 646 558 8656 US (New York) >> • +1 651 372 8299 US (Minnesota) >> • +1 786 635 1003 US (Miami) >> • +1 267 831 0333 US (Philadelphia) >> • +1 301 715 8592 US (Washington DC) >> • +1 312 626 6799 US (Chicago) >> >> Meeting ID: 919 3589 5632 >> >> Find your local number: https://lbnl.zoom.us/u/adUP3eF75H >> <https://www.google.com/url?q=https://lbnl.zoom.us/u/adUP3eF75H&sa=D&source=…> >> >> --- >> >> Join by SIP >> • 91935895632(a)zoomcrc.com >> >> --- >> >> Join by H.323 >> • 144.195.19.161 (US West) >> • 206.247.11.121 (US East) >> • 115.114.131.7 (India Mumbai) >> • 115.114.115.7 (India Hyderabad) >> • 159.124.15.191 (Amsterdam Netherlands) >> • 159.124.47.249 (Germany) >> • 159.124.104.213 (Australia Sydney) >> • 159.124.74.212 (Australia Melbourne) >> • 64.211.144.160 (Brazil) >> • 159.124.168.213 (Canada Toronto) >> • 159.124.196.25 (Canada Vancouver) >> • 170.114.194.163 (Japan Tokyo) >> • 147.124.100.25 (Japan Osaka) >> >> Meeting ID: 919 3589 5632 >> Passcode: 730330 >> >> >> *If you would like to add company members to subscribe to our industry >> partners listserv, please email industry-join(a)phenix-online.org >> <industry-join(a)phenix-online.org> with “subscribe” (no quotes) as the >> subject line and nothing in the body. By subscribing, you will receive >> information about developer meetings, workshops, and industry-focused >> sessions that happen a few times a year. If you no longer want to receive >> these emails, you may choose to use "unsubscribe" in the subject line. This >> is not a discussion listserv. If you have software questions, >> please email help(a)phenix-online.org <help(a)phenix-online.org>.* >> >>

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Starts Tomorrow - 2025 Spring Phenix Developers Meeting - March 17-19
by Ashley Dawn 16 Mar '25

16 Mar '25

Dear Consortium Members, The* 2025 Spring Phenix Developers Meeting <https://phenix-online.org/workshops/mar-2025-lanl/index.html>* is this week *March 17-19, 2025 *in Santa Fe, NM and online. The Phenix Developers will host a series of talks on Monday and Tuesday, March 17 & 18. And, we will host an *Industry Roundtable discussion on Wednesday, March 19* in the morning (USA Mountain Time). This is a chance to ask questions and discuss any issues directly with the Developers. The agenda posted on the workshop website <https://phenix-online.org/workshops/mar-2025-lanl/index.html> (login:workshop, pswd:phenix3py) shows the complete schedule for those attending in person. Monday, March 17 – Talks - 09:00 – 09:05 AM *Paul D. Adams*, Introduction - 09:05 – 09:30 AM *Dorothee Liebschner*, Current status of DiSCaMB integration/Overview of MicroED models. - 09:30 – 09:55 AM *Paulina Dominiak*, Aspherical scattering factors in refinement of biomacromolecules - 09:55 – 10:20 AM *Malgorzata Biczysko*, Quantum refinement with machine learning: AQuaRef - 10:20 – 10:35 AM Break - 10:35 – 11:00 AM *Tom Terwilliger*, Is there a best assignment of side-chain alternative conformations to conformers? - 11:00 – 11:25 AM *David Case*, Creating and evaluating ensemble atomic models - 11:25 – 11:45 AM *Billy Poon*, Phenix updates - 11:45 - 12:10 PM *Jane Richardson*, Opportunities and concerns in RNA modeling - 12:10 – 12:30 PM *Christopher Schlicksup*, Exploration of per-atom real space refinement weight Tuesday, March 18 – Talks (USA Mountain Time) - 09:00 – 09:05 AM *Paul D. Adams*, Welcome - 09:05 – 09:30 AM *Laura Pacoste*, Developing electron diffraction methods to probe oxidation states in metalloenzymes (virtual) - 09:30 – 09:55 AM *Airlie McCoy*, phasertng updates (virtual) - 09:55 – 10:20 AM *Pavel Afonine*, I. Nuances, New Tools, and Methods for Visualizing and Validating Subtle Structural Details.II. Atomic Model Refinement Gets More Accurate: Combining Aspherical Density Models with Quantum-Based Restraints - 10:20 – 10:45 AM *Alisia Fadini*, AlphaFold as a Prior: Guiding Protein Structure Prediction Using Experimental Data with ROCKET - 10:45 – 11:00 AM Break - 11:00 – 11:25 AM *Oleg Sobolev*, Automatically Finding the Best Reference Model - 11:25 – 11:50 AM *Nigel W. Moriarty*, Paradigm Shift for Ligands in Phenix - Part Deux - 11:50 – 12:15 PM *Christopher Williams*, Further details of low-pLDDT AlphaFold2 predictions Wednesday, March 19 – Phenix Industry Session - 9:00 AM – 12:00 PM *Industry Roundtable* – conference of developers and industry to discuss the future directions of Phenix. This session will be devoted to a discussion of AlphaFold/RosettaFold and future directions. *Industry consortium members are encouraged to attend.* The Zoom information is below. We look forward to having you join the meeting and discussion. Thank you, Ashley > >> Join Zoom Meeting >> https://lbnl.zoom.us/j/91935895632?pwd=apavpMaMGbJ0FLXw9Q8rCECI8iAyng.1 >> <https://www.google.com/url?q=https://lbnl.zoom.us/j/91935895632?pwd%3Dapavp…> >> >> Meeting ID: 919 3589 5632 >> Passcode: 730330 >> >> --- >> >> One tap mobile >> +12133388477,,91935895632# US (Los Angeles) >> +16692192599,,91935895632# US (San Jose) >> >> --- >> >> Dial by your location >> • +1 213 338 8477 US (Los Angeles) >> • +1 669 219 2599 US (San Jose) >> • +1 669 900 6833 US (San Jose) >> • +1 206 337 9723 US (Seattle) >> • +1 253 215 8782 US (Tacoma) >> • +1 346 248 7799 US (Houston) >> • +1 602 753 0140 US (Phoenix) >> • +1 720 928 9299 US (Denver) >> • +1 971 247 1195 US (Portland) >> • +1 470 250 9358 US (Atlanta) >> • +1 470 381 2552 US (Atlanta) >> • +1 646 518 9805 US (New York) >> • +1 646 558 8656 US (New York) >> • +1 651 372 8299 US (Minnesota) >> • +1 786 635 1003 US (Miami) >> • +1 267 831 0333 US (Philadelphia) >> • +1 301 715 8592 US (Washington DC) >> • +1 312 626 6799 US (Chicago) >> >> Meeting ID: 919 3589 5632 >> >> Find your local number: https://lbnl.zoom.us/u/adUP3eF75H >> <https://www.google.com/url?q=https://lbnl.zoom.us/u/adUP3eF75H&sa=D&source=…> >> >> --- >> >> Join by SIP >> • 91935895632(a)zoomcrc.com >> >> --- >> >> Join by H.323 >> • 144.195.19.161 (US West) >> • 206.247.11.121 (US East) >> • 115.114.131.7 (India Mumbai) >> • 115.114.115.7 (India Hyderabad) >> • 159.124.15.191 (Amsterdam Netherlands) >> • 159.124.47.249 (Germany) >> • 159.124.104.213 (Australia Sydney) >> • 159.124.74.212 (Australia Melbourne) >> • 64.211.144.160 (Brazil) >> • 159.124.168.213 (Canada Toronto) >> • 159.124.196.25 (Canada Vancouver) >> • 170.114.194.163 (Japan Tokyo) >> • 147.124.100.25 (Japan Osaka) >> >> Meeting ID: 919 3589 5632 >> Passcode: 730330 >> >> >> *If you would like to add company members to subscribe to our industry >> partners listserv, please email industry-join(a)phenix-online.org >> <industry-join(a)phenix-online.org> with “subscribe” (no quotes) as the >> subject line and nothing in the body. By subscribing, you will receive >> information about developer meetings, workshops, and industry-focused >> sessions that happen a few times a year. If you no longer want to receive >> these emails, you may choose to use "unsubscribe" in the subject line. This >> is not a discussion listserv. If you have software questions, >> please email help(a)phenix-online.org <help(a)phenix-online.org>.* >> >> >> Ashley Dawn (she/her/hers) Program Manager, Phenix Industrial Consortium <https://phenix-online.org/> Molecular Biophysics & Integrated Bioimaging (MBIB <https://biosciences.lbl.gov/mbib/>) Lawrence Berkeley Laboratory 510-486-5455

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Starts Monday - 2025 Spring Phenix Developers Meeting - March 17-19
by Ashley Dawn 12 Mar '25

12 Mar '25

Dear Consortium Members, The* 2025 Spring Phenix Developers Meeting <https://phenix-online.org/workshops/mar-2025-lanl/index.html>* is next week *March 17-19, 2025 *in Santa Fe, NM and online. The Phenix Developers will host a series of talks on Monday and Tuesday, March 17 & 18. And, we will host an *Industry Roundtable discussion on Wednesday, March 19* in the morning (USA Mountain Time). This is a chance to ask questions and discuss any issues directly with the Developers. The agenda posted on the workshop website <https://phenix-online.org/workshops/mar-2025-lanl/index.html> (login:workshop, pswd:phenix3py) shows the complete schedule for those attending in person. Here's the updated schedule of talks: Monday, March 17 – Talks - 09:00 – 09:05 AM Paul D. Adams, Introduction - 09:05 – 09:30 AM Dorothee Liebschner, Current status of DiSCaMB integration/Overview of MicroED models. - 09:30 – 09:55 AM Paulina Dominiak, Aspherical scattering factors in refinement of biomacromolecules - 09:55 – 10:20 AM Malgorzata Biczysko, Quantum refinement with machine learning: AQuaRef - 10:20 – 10:35 AM Break - 10:35 – 11:00 AM Tom Terwilliger, Is there a best assignment of side-chain alternative conformations to conformers? - 11:00 – 11:25 AM David Case, Creating and evaluating ensemble atomic models - 11:25 – 11:45 AM Billy Poon, Phenix updates - 11:45 - 12:10 PM Jane Richardson, Opportunities and concerns in RNA modeling - 12:10 – 12:30 PM Christopher Schlicksup, Exploration of per-atom real space refinement weight Tuesday, March 18 – Talks - 09:00 – 09:05 AM Paul D. Adams, Welcome - 09:05 – 09:30 AM Laura Pacoste, Developing electron diffraction methods to probe oxidation states in metalloenzymes (virtual) - 09:30 – 09:55 AM Airlie McCoy, phasertng updates (virtual) - 09:55 – 10:20 AM Pavel Afonine, I. Nuances, New Tools, and Methods for Visualizing and Validating Subtle Structural Details.II. Atomic Model Refinement Gets More Accurate: Combining Aspherical Density Models with Quantum-Based Restraints - 10:20 – 10:35 AM Alisia Fadini, AlphaFold as a Prior: Guiding Protein Structure Prediction Using Experimental Data with ROCKET - 10:35 – 11:00 AM Break - 11:00 – 11:25 AM Oleg Sobolev, Automatically Finding the Best Reference Model - 11:25 – 11:50 AM Nigel W. Moriarty, Paradigm Shift for Ligands in Phenix - Part Deux - 11:50 – 12:15 PM Christopher Williams, Further details of low-pLDDT AlphaFold2 predictions Wednesday, March 19 – Phenix Industry Session - 9:00 AM – 12:00 PM Industry Roundtable – conference of developers and industry to discuss the future directions of Phenix. This session will be devoted to a discussion of AlphaFold/RosettaFold and future directions. Industry consortium members are encouraged to attend. The Zoom information is below. We look forward to having you join the meeting and discussion. Thank you, Ashley > > > *If you would like to add company members to subscribe to our industry > partners listserv, please email industry-join(a)phenix-online.org > <industry-join(a)phenix-online.org> with “subscribe” (no quotes) as the > subject line and nothing in the body. By subscribing, you will receive > information about developer meetings, workshops, and industry-focused > sessions that happen a few times a year. If you no longer want to receive > these emails, you may choose to use "unsubscribe" in the subject line. This > is not a discussion listserv. If you have software questions, > please email help(a)phenix-online.org <help(a)phenix-online.org>.* > > Join Zoom Meeting > https://lbnl.zoom.us/j/91935895632?pwd=apavpMaMGbJ0FLXw9Q8rCECI8iAyng.1 > <https://www.google.com/url?q=https://lbnl.zoom.us/j/91935895632?pwd%3Dapavp…> > > Meeting ID: 919 3589 5632 > Passcode: 730330 > > --- > > One tap mobile > +12133388477,,91935895632# US (Los Angeles) > +16692192599,,91935895632# US (San Jose) > > --- > > Dial by your location > • +1 213 338 8477 US (Los Angeles) > • +1 669 219 2599 US (San Jose) > • +1 669 900 6833 US (San Jose) > • +1 206 337 9723 US (Seattle) > • +1 253 215 8782 US (Tacoma) > • +1 346 248 7799 US (Houston) > • +1 602 753 0140 US (Phoenix) > • +1 720 928 9299 US (Denver) > • +1 971 247 1195 US (Portland) > • +1 470 250 9358 US (Atlanta) > • +1 470 381 2552 US (Atlanta) > • +1 646 518 9805 US (New York) > • +1 646 558 8656 US (New York) > • +1 651 372 8299 US (Minnesota) > • +1 786 635 1003 US (Miami) > • +1 267 831 0333 US (Philadelphia) > • +1 301 715 8592 US (Washington DC) > • +1 312 626 6799 US (Chicago) > > Meeting ID: 919 3589 5632 > > Find your local number: https://lbnl.zoom.us/u/adUP3eF75H > <https://www.google.com/url?q=https://lbnl.zoom.us/u/adUP3eF75H&sa=D&source=…> > > --- > > Join by SIP > • 91935895632(a)zoomcrc.com > > --- > > Join by H.323 > • 144.195.19.161 (US West) > • 206.247.11.121 (US East) > • 115.114.131.7 (India Mumbai) > • 115.114.115.7 (India Hyderabad) > • 159.124.15.191 (Amsterdam Netherlands) > • 159.124.47.249 (Germany) > • 159.124.104.213 (Australia Sydney) > • 159.124.74.212 (Australia Melbourne) > • 64.211.144.160 (Brazil) > • 159.124.168.213 (Canada Toronto) > • 159.124.196.25 (Canada Vancouver) > • 170.114.194.163 (Japan Tokyo) > • 147.124.100.25 (Japan Osaka) > > Meeting ID: 919 3589 5632 > Passcode: 730330 > > > > ────── > >

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2025 Spring Phenix Developers Meeting - March 17-19
by Ashley Dawn 28 Feb '25

28 Feb '25

Dear Consortium Members, The* 2025 Spring Phenix Developers Meeting <https://phenix-online.org/workshops/mar-2025-lanl/index.html>* <http:///>will be held *March 17-19, 2025 *in Santa Fe, NM and online. The Phenix Developers will host a series of talks on Monday and Tuesday, March 17 & 18. And, we will host an *Industry Roundtable discussion on Wednesday, March 19* in the morning (USA Mountain Time). This is a chance to ask questions and discuss any issues directly with the Developers. The agenda posted on the workshop website <https://phenix-online.org/workshops/mar-2025-lanl/index.html> (login:workshop, pswd:phenix3py) shows the complete schedule for those attending in person. Monday, March 17 – Talks - 09:00 – 09:05 AM Paul D. Adams, Introduction - 09:05 – 09:30 AM Paulina Dominiak, Aspherical scattering factors in refinement of biomacromolecules - 09:30 – 09:55 AM Dorothee Liebschner, Current status of DiSCaMB integration/Overview of MicroED models. - 09:55 – 10:20 AM Billy Poon, Phenix updates. - 10:20 – 10:35 AM Break - 10:35 – 11:00 AM Oleg Sobolev, Reference Model Restraints - 11:00 – 11:25 AM Tom Terwilliger, Is there a best assignment of side-chain alternative conformations to conformers? - 11:25 – 11:50 AM Malgorzata Biczysko, Quantum refinement with machine learning: AQuaRef - 11:50 – 12:15 PM Jane Richardson, Opportunities and concerns in RNA modeling Tuesday, March 18 – Talks - 09:00 – 09:05 AM Paul D. Adams, Welcome - 09:05 – 09:30 AM Laura Pacoste, title TBD (virtual) - 09:30 – 09:55 AM Airlie McCoy, phasertng updates - 09:55 – 10:20 AM Pavel Afonine, I. Nuances, New Tools, and Methods for Visualizing and Validating Subtle Structural Details.II. Atomic Model Refinement Gets More Accurate: Combining Aspherical Density Models with Quantum-Based Restraints. - 10:20 – 10:35 AM Alicia Fadini, AlphaFold as a Prior: Guiding Protein Structure Prediction Using Experimental Data with ROCKET - 10:35 – 11:00 AM Break - 11:00 – 11:25 AM David Case, Creating and evaluating atomic models using Xray and cryoEM data - 11:25 – 11:50 AM Nigel W. Moriarty, Paradigm Shift for Ligands in Phenix - Part Deux - 11:50 – 12:15 PM Christopher Williams, Further details of low-pLDDT AlphaFold2 predictions Wednesday, March 19 – Phenix Industry Session - 9:00 AM – 12:00 PM Industry Roundtable – conference of developers and industry to discuss the future directions of Phenix. This session will be devoted to a discussion of AlphaFold/RosettaFold and future directions. Industry consortium members are encouraged to attend. The Zoom information is below my signature. We look forward to having you join the meeting and discussion. Thank you, Ashley Ashley Dawn (she/her/hers) Program Manager, Phenix Industrial Consortium <https://phenix-online.org/> Molecular Biophysics & Integrated Bioimaging (MBIB <https://biosciences.lbl.gov/mbib/>) Lawrence Berkeley Laboratory 510-486-5455 *If you would like to add company members to subscribe to our industry partners listserv, please email industry-join(a)phenix-online.org <industry-join(a)phenix-online.org> with “subscribe” (no quotes) as the subject line and nothing in the body. By subscribing, you will receive information about developer meetings, workshops, and industry-focused sessions that happen a few times a year. If you no longer want to receive these emails, you may choose to use "unsubscribe" in the subject line. This is not a discussion listserv. If you have software questions, please email help(a)phenix-online.org <help(a)phenix-online.org>.* Join Zoom Meeting https://lbnl.zoom.us/j/91935895632?pwd=apavpMaMGbJ0FLXw9Q8rCECI8iAyng.1 <https://www.google.com/url?q=https://lbnl.zoom.us/j/91935895632?pwd%3Dapavp…> Meeting ID: 919 3589 5632 Passcode: 730330 --- One tap mobile +12133388477,,91935895632# US (Los Angeles) +16692192599,,91935895632# US (San Jose) --- Dial by your location • +1 213 338 8477 US (Los Angeles) • +1 669 219 2599 US (San Jose) • +1 669 900 6833 US (San Jose) • +1 206 337 9723 US (Seattle) • +1 253 215 8782 US (Tacoma) • +1 346 248 7799 US (Houston) • +1 602 753 0140 US (Phoenix) • +1 720 928 9299 US (Denver) • +1 971 247 1195 US (Portland) • +1 470 250 9358 US (Atlanta) • +1 470 381 2552 US (Atlanta) • +1 646 518 9805 US (New York) • +1 646 558 8656 US (New York) • +1 651 372 8299 US (Minnesota) • +1 786 635 1003 US (Miami) • +1 267 831 0333 US (Philadelphia) • +1 301 715 8592 US (Washington DC) • +1 312 626 6799 US (Chicago) Meeting ID: 919 3589 5632 Find your local number: https://lbnl.zoom.us/u/adUP3eF75H <https://www.google.com/url?q=https://lbnl.zoom.us/u/adUP3eF75H&sa=D&source=…> --- Join by SIP • 91935895632(a)zoomcrc.com --- Join by H.323 • 144.195.19.161 (US West) • 206.247.11.121 (US East) • 115.114.131.7 (India Mumbai) • 115.114.115.7 (India Hyderabad) • 159.124.15.191 (Amsterdam Netherlands) • 159.124.47.249 (Germany) • 159.124.104.213 (Australia Sydney) • 159.124.74.212 (Australia Melbourne) • 64.211.144.160 (Brazil) • 159.124.168.213 (Canada Toronto) • 159.124.196.25 (Canada Vancouver) • 170.114.194.163 (Japan Tokyo) • 147.124.100.25 (Japan Osaka) Meeting ID: 919 3589 5632 Passcode: 730330 ──────

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Save the Date - Phenix Developers Meeting - Industry Roundtable - 3/19
by Ashley Dawn 23 Jan '25

23 Jan '25

Dear Consortium Members, Please save the dates - we are planning the *Spring Phenix Developers Meeting* in Santa Fe, NM, on *March 17-19, 2025. * An agenda and Zoom links are forthcoming. You are invited to Developer's talks on Monday and Tuesday, March 17 & 18. And, we will host an Industry Roundtable discussion on *Wednesday, March 19* in the morning (USA Mountain Time). This is a chance to ask questions and discuss any issues directly with the Developers. If you would like to add company members to subscribe to our industry partners listserv, please email industry-join(a)phenix-online.org with “subscribe” (no quotes) as the subject line and nothing in the body. By subscribing, you will receive information about developer meetings, workshops, and industry-focused sessions that happen a few times a year. If you no longer want to receive these emails, you may choose to use "unsubscribe" in the subject line. This is not a discussion listserv. If you have software questions, please email help(a)phenix-online.org. Please let me know if you have questions or if you would like to reserve a spot to attend the meeting in person. Thank you, Ashley Ashley Dawn (she/her/hers) Program Manager, Phenix Industrial Consortium <https://phenix-online.org/> Molecular Biophysics & Integrated Bioimaging (MBIB <https://biosciences.lbl.gov/mbib/>) Lawrence Berkeley Laboratory 510-486-5455

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