- phenixbb - phenix-online.org

EMBO Workshop on Molecular Neurobiology, 13th to 17th May 2024, Crete
by Jonathan Elegheert 11 Mar '24

11 Mar '24

Dear all, I would like to bring to your attention the EMBO Workshop on Molecular Neurobiology (https://meetings.embo.org/event/24-mol-neurobiology), which will be held from 13th to 17th May 2024 on the beautiful Greek island of Crete, at the Fodele Beach resort (https://www.fodelebeach.gr/). This is a workshop covering the latest breakthroughs in structural biology, biophysics, imaging, and biological models in neurobiology. Given its cross-disciplinary nature, this EMBO workshop presents a broad overview of the field and an insight into the latest technologies and results. It provides a space for learning, for forging new collaborations, and for presenting ideas that will contribute to the future of molecular neurobiology. The workshop also presents an excellent opportunity for early-career scientists to present their work, with a large number of talks that will be selected from submitted abstracts. The workshop poster is attached to this mail, and more information, as well as the registration links, can be found on the following web page; https://meetings.embo.org/event/24-mol-neurobiology The abstract submission deadline is 6th of March. Please do not hesitate to contact me directly for any questions, and we hope to see many of you there! Best wishes, on behalf of the organising committee, Jonathan ----------------------------------------------------------------- Jonathan Elegheert, PhD Team Leader CNRS Scientist Interdisciplinary Institute for NeuroScience (IINS) <https://www.iins.u-bordeaux.fr/> UMR5297 CNRS / UB Centre Broca Nouvelle-Aquitaine 146 rue Léo Saignat BP 61292 33076 Bordeaux Cedex <https://goo.gl/maps/CFNm4dUvzrmmHUM1A> France T: +33 (0)5 33 51 48 57 E: jonathan.elegheert(a)u-bordeaux.fr W: https://www.iins.u-bordeaux.fr/ELEGHEERT Twitter: @ElegheertLab <https://twitter.com/ElegheertLab> -----------------------------------------------------------------

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Issue phenix.table1 macOS
by Xavier Brazzolotto 09 Mar '24

09 Mar '24

I am facing a strange issue with phenix.table1 Previously, I had generated a Table1 with the GUI that was ok. Recently, I have updated to Sonoma 14.4 and when I try to rerun phenix.table1 (or use similar model and with same reflections) do not get consistent results, especially in number of reflections, uniques, CC1/2, CC*... Besides, at the end of a refinement, I do also get an error when the program tries to auto-load the data (model and maps) in Coot… Any thoughts about this Xavier

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Macromolecular Crystallography - CSHL Course October 2024
by Paul Adams 06 Mar '24

06 Mar '24

Dear Colleagues, The Cold Spring Harbor Macromolecular Crystallography course will take place October 13-29th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow the link below to the course web site. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> Macromolecular Crystallography <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> October 13 - 29, 2024 Applications Due: July 15 Instructors Paul Adams, Lawrence Berkeley National Laboratory Dorothee Liebschner, Lawrence Berkeley National Laboratory Janet Newman, UNSW, Australia James Pflugrath, Rigaku Americas Corporation (ret.), Texas Co-Instructor Tom Peat, UNSW, Australia Topics Covered Basic Diffraction Theory Structure Presentation Coordinate Deposition Structure Validation Model Building and Refinement Electron Density Maps Improvement Using Predicted Models in Structure Solution and Completion Protein Structure Prediction Structure Solution by Experimental Phasing Methods (SAD, MAD, MIR, and others) and Molecular Replacement Data Collection and Processing Synchrotron X-ray Sources and Optics Crystallization (Proteins, Nucleic Acids, Complexes and Membrane Proteins) For further information and to apply please visit the Macromolecular Crystallography course website. <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road, Cold Spring Harbor, NY 11724 -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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map display after resolve_cryoem
by Valerie Biou 01 Mar '24

01 Mar '24

Hello, I ran resolve_cryoem for solvent flattening and obtained a ccp4 map that behaves like a mask both in Coot and Chimera. the histogram is just a single line and the dimensions are different from my original map, even though in a second run I used restore_full_size = true in a second run. To be clear, my original map has 480^3 dimensions, and the output one is 125x140x224, which boxes my protein but I can't see the inside of the map. I guess there is something I didn't understand. Can you please help me? All the best, Valerie Valérie Biou, Ph.D. valerie.biou(a)ibpc.fr Laboratoire de Biologie Physico-Chimique des Protéines Membranaires umr7099.ibpc.fr <http://umr7099.ibpc.fr/> UMR 7099 CNRS/Univ. Paris-Cité Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie 75005 Paris - France Tel : +33 (0)1 5841 5099

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Re: [phenixbb] Joint X-ray / neutron refinement
by Kristoffer Lundgren 24 Feb '24

24 Feb '24

Hello phenixbb, When trying to do joint refinement in phenix.refine 1.21-5207 using the suggested joint_xn.eff file found at https://phenix-online.org/documentation/reference/refinement.html#neutron-a… as a template I get some error messages (running phenix.refine from the command line): Unrecognized PHIL parameters: ----------------------------- xray.refinement.refine.strategy (file "joint_xn.eff", line 33) xray.refinement.main.simulated_annealing (file "joint_xn.eff", line 36) xray.refinement.main.ordered_solvent (file "joint_xn.eff", line 37) xray.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 38) neutron.refinement.refine.strategy (file "joint_xn.eff", line 45) neutron.refinement.main.simulated_annealing (file "joint_xn.eff", line 48) neutron.refinement.main.ordered_solvent (file "joint_xn.eff", line 49) neutron.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 50) Can you please advice on how to proceed? It looks like the options supplied are not recognized at all by phenix.refine. Best regards Kristoffer From: <phenixbb-bounces(a)phenix-online.org> on behalf of Derek Logan <derek.logan(a)biochemistry.lu.se> Date: Monday, 22 January 2024 at 09:39 To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Ulf Ryde <ulf.ryde(a)compchem.lu.se>, "esko.oksanen_ess.eu" <esko.oksanen(a)ess.eu> Subject: ***SPAM*** [phenixbb] Joint X-ray / neutron refinement Hi phenixbb, I'm trying to understand the current status of joint X-ray/neutron refinement in phenix.refine. The announcement of the latest release mentions a change in the algorithm as described in the recent publication. In the documentation: Structure refinement in PHENIX<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> phenix-online.org<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> [AURqZhI53yp3gAAAABJRU5ErkJggg==]<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> it's described how you can run joint refinement using a parameter file. Does this mean that it is *only* possible in this way and not through the GUI? The GUI was very useful in the past as it automatically opened Coot with the maps for both X-rays and neutrons, and the refinement statistics for both were displayed in the GUI. As far as I can see joint refinement via the GUI last worked in version 1.19.2-4148 from 2021. Best regards Derek

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Rotamer error in real space refinement
by Nikos Pinotsis 23 Feb '24

23 Feb '24

Hi, I am using real space refine with the latest phenix 1.21-5207 for fitting a model into a cryoEM map. During refiment one Trp goes clearly out of density (vertical to the density) although the map is very well defined at this part of the protein. I tried local_grid_search either for every cycle or last, however it didn't fix the problem. I know that this is reported a couple of years ago as fixed (dev-4218), I am wondering if something changed during the last version. Another solution I can think it to keep the side chain of this Trp fixed. How can I do that? thanks Nikos -- ________________________________________ Nikos Pinotsis Associate Professor Biochemistry, Department of Chemistry National and Kapodistrian University of Athens

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Define bond between O3' of a nucleotide to P of 3DR HETATM ligand (abasic nucleotide)
by Mark Saper 23 Feb '24

23 Feb '24

I need to create a phosphodiester bond between O3’ of a DNA nucleotide and P of a 3DR HETATM ligand (a modified nucleotide). I also need to delete O3P of the 3DR nucleotide. How can I create this restraint? Also, how can I get COOT to display this bond? Thanks, Mark _____________________ Mark A. Saper, Ph.D. Dept of Microbiology and Molecular Genetics Hebrew University Faculty of Medicine saper(a)umich.edu <mailto:[email protected]> | +972 52 815-0480

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Tenure track position in Protein Science for Pathogen Defense
by Cygler, Miroslaw 20 Feb '24

20 Feb '24

Dear Colleagues, I am excited to let you know that the Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, is searching for an exceptional candidate in the area of Protein Science for Pathogen Defense, to fill a tenure-track Canada Research Chair (CRC) Tier 2 position. The CRC program is the flagship of a national strategy to make Canada one of the world's top countries in research and development. We are looking for an outstanding early career scientist to establish and lead a groundbreaking research program in protein science to understand the mechanisms of bacterial and viral infection in humans or animals, to investigate host-pathogen interactions, or to discover novel mechanisms of defense against known and potential future pathogens. Within this broad scope, specific areas of interest include synthetic antigen design, the molecular basis of immune response to pathogens, mechanisms of antimicrobial resistance, and the prediction-guided design of artificial antibodies. We are interested in hiring a world-class expert in one or more of the following areas: (i) protein structure prediction and structural bioinformatics, (ii) protein design, and (iii) cryo-electron microscopy. A detailed advertisement with instruction how to apply is enclosed and can also be viewed here: <https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> Canada Research Chair (CRC) Tier 2 in Protein Science for Pathogen Defense<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> protection.outlook.com<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> [X]<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> . Regards, Mirek ======================================================= Dr. Miroslaw Cygler, FCAHS Professor, Dept. Biochem, Microbiol & Immune, U. of Saskatchewan Canada Research Chair in Molecular Medicine Using Synchrotron Light Health Sciences Building 3D30.6 (Box 9) 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada Email: miroslaw.cygler(a)usask.ca<mailto:[email protected]> Website: http://research-groups.usask.ca/cyglerlab/ Phone: 306-966-4361, cell: 306-203-2317 =======================================================

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Structural Biology Workshop, June 10-12, 2024, Arlington, VA
by Meilleur, Flora 15 Feb '24

15 Feb '24

Dear All, We would like to bring to your attention the 2024 Neutrons in Structural Biology workshop. This workshop will highlight the need for next-generation instruments and toolsets for structural biology, with a focus on neutrons and other complementary techniques, and the development of integrated experimental and computational frameworks that connect them. Neutrons in Structural Biology - Challenges & Opportunities June 10-12th 2024 Sheraton Pentagon City Hotel, Arlington, VA. For details and registration see: Neutrons in Structural Biology - Challenges & Opportunities<https://conference.sns.gov/event/402/> The workshop will include a 1-day satellite training workshop (June 10, 2024) to educate graduate students and postdoctoral researchers in the application of neutron techniques in structural biology. A limited numbers of travel awards are available to support graduate students and post-doctoral fellows attendance at the workshop. The travel award application deadline is April 12, 2024. Details here<https://conference.sns.gov/event/402/page/2891-travel-awards-deadline-april…>. Flora Meilleur on behalf of the organizing committee: Andrey Kovalevsky Flora Meilleur Dean Myles Hugh O'Neill Flora Meilleur, Ph.D. Neutron Scattering Scientist Neutron Sciences Directorate Oak Ridge National Laboratory Professor Molecular & Structural Biochemistry N C State University Editor, Journal of Applied Crystallography Office: 865-576-2779

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to leave atoms out of ADP restraints
by Jorge Iulek 13 Feb '24

13 Feb '24

Hi, all, The ADP restraints I refer to in this discussion are the ones that would make B-factors of nearby atoms to influence (or more or less resemble) each other. For some very disordered side chains, I would like to test "taking out" the "more disordered" atoms (maybe for high chi angle variability) of these restraints, for them to be more free to skyrocket, but also that they do not influence so much the main chain, in some cases where the flexibility difference between main and side chain seems to be significant. Is there a way to do so? Thanks, Jorge

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helical structure - Real space refinement
by Dmitry Semchonok 01 Feb '24

01 Feb '24

Dear colleagues, Is there any specific procedure for Real space refinement in Phenix, having a map and model when working with helical structure? Many thanks Kind regard, Dmitry

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RealSpaceRefine Nucleic acid SS restraints ?
by CUNIASSE Philippe 31 Jan '24

31 Jan '24

Dear all, I am currently refining a protein-nucleic acid structure obtained by MDFF (NAMD) with a 2.9 Å cryo-EM map. Dues to the poor density of the map at the end of the DNA duplex (likely due to breathing at the ends of the duplex), the structure of the DNA tends to be distorted. I tried to set up a set of nucleic acid restraints (Base pairing and base stacking for the full sequence), however, despite the fact that the syntax was checked and no error message is present in the log file, it seems that the restraints are not taken into account as if the constant restraints were two weak. And indeed when examining the refined structure, the pairing and stacking restraints for the base pairs at the extremities of the DNA duplex are not fulfilled. Have you a suggestion to solve this problem ? Thanks in advance for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institute for Integrative Biology of the Cell (I2BC) UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex, France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ Web: https://www.i2bc.paris-saclay.fr [signature_2602492259]

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leave residue inside its electron density when neighbor is too close
by Murpholino Peligro 29 Jan '24

29 Jan '24

What is the recommended approach to tell phenix.refine to leave the residue inside its electron density? (crystal neighbors) The green model is the input to phenix.refine, the maps and the yellow model are the output of phenix.refine. As you can see, phenix.refine will move the residue outside the density (to avoid clashes I guess?) I have tried setting the occupancy of OXT to 0.5, but it is not good. (you can see there is a water in a special position, just above the bad residue) Any more ideas?

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phenix.mtriage output model-map
by joe.wilson2023 22 Jan '24

22 Jan '24

Dear Phenix team, I am new to Phenix and using the phenix.mtriage to get the map-model FSC results. It gives the correct results at the same time I also want to produce the mode-map used for the FSC calculation. Is there an option for this? If not how can I reproduce the same model-map with another phenix command? Many thanks, Joe

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ResolveCryoEM problem
by Luca Pellegrini 22 Jan '24

22 Jan '24

Hi, I am trying to run Resolve with two half maps and a sequence file with ncs copies of the sequence. Resolve stops with the message: “Need a symmetry file if ncs_copies > 1 and using models”. But I am not using models. Please advise. Regards, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Joint X-ray / neutron refinement
by Derek Logan 22 Jan '24

22 Jan '24

Hi phenixbb, I'm trying to understand the current status of joint X-ray/neutron refinement in phenix.refine. The announcement of the latest release mentions a change in the algorithm as described in the recent publication. In the documentation: <https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> Structure refinement in PHENIX<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> phenix-online.org<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> [X] <https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> it's described how you can run joint refinement using a parameter file. Does this mean that it is *only* possible in this way and not through the GUI? The GUI was very useful in the past as it automatically opened Coot with the maps for both X-rays and neutrons, and the refinement statistics for both were displayed in the GUI. As far as I can see joint refinement via the GUI last worked in version 1.19.2-4148 from 2021. Best regards Derek

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treating the water molecules in the model
by Dmitry Semchonok 20 Jan '24

20 Jan '24

Dear colleagues, Please share your experience with how you handle the water molecules. So, we have a refined model and added the water molecules using the Douse protocol. So, should we refine the model again afterwards? Or is the model considered ready? We tried to refine our model with water, but then the water molecules flew away from the places. Please let me know what is the correct way to proceed. Many thanks for considering my request. Sincerely, Dmitry

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General interest: Interoperability of crystallographic data and databases
by John R Helliwell 19 Jan '24

19 Jan '24

Dear Colleagues, I imagine you will be interested in this Feature Article on the "Interoperability of crystallographic data and databases" in the current issue of IUCrJ:- https://journals.iucr.org/m/issues/2024/01/00/lt5064/index.html Best wishes, John Emeritus Professor John R Helliwell DSc

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Post to the email list
by Supeshala Nawarathnage 18 Jan '24

18 Jan '24

Hello, I would like to request to add my email address to your mailing list. My email address is nawa.science(a)gmail.com Thank you. Sincerely, Supeshala Nawarathnage

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Updated links - Phenix version 1.21 released
by Paul Adams 18 Jan '24

18 Jan '24

The Phenix developers are pleased to announce that version 1.21 of Phenix is now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site: http://phenix-online.org/download Highlights for the 1.21 version of Phenix include: - Likelihood-based docking of models into cryo-EM maps. • Full support for structure determination with AlphaFold models. • New joint X-ray and neutron refinement algorithm. • Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ. Detailed changes are: - Full support for structure determination with AlphaFold models in Phenix GUI - PredictAndBuild X-ray and Cryo-EM structure solution from data and sequences - Phenix AlphaFold server - Video tutorials for prediction, X-ray structure solution and Cryo-EM map interpretation - Cryo-EM tools support ChimeraX visualization - Cryo-EM density modification and anisotropic scaling display local resolution - Tutorials available for automated structure determination with PredictAndBuild - New em_placement and emplace_local tools - likelihood-based docking of models into cryo-EM maps - MOPAC v22 is now distributed with Phenix - Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ - Available in phenix.refine and separate command-line tool, mmtbx.quantum_interface - Defaults to MOPAC's PM6-D3H4 - Higher level QM available via 3rd-party Orca package - Restraints - Approximately 27k of 37k restraints (QM calculated and validated) deployed in the GeoStd - Automated tests for programs in the Phenix GUI - ERRASER no longer supported and removed from installation - Remove rebuild_predicted_model (duplicated by predict_and_build) - JSON output added to MolProbity structure validation scripts Please note that this publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Phenix version 1.21 released
by Paul Adams 17 Jan '24

17 Jan '24

The Phenix developers are pleased to announce that version 1.21 of Phenix is now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for the 1.21 version of Phenix include: - Likelihood-based docking of models into cryo-EM maps. • Full support for structure determination with AlphaFold models. • New joint X-ray and neutron refinement algorithm. • Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ. Detailed changes are: - Full support for structure determination with AlphaFold models in Phenix GUI - PredictAndBuild X-ray and Cryo-EM structure solution from data and sequences - Phenix AlphaFold server - Video tutorials for prediction, X-ray structure solution and Cryo-EM map interpretation - Cryo-EM tools support ChimeraX visualization - Cryo-EM density modification and anisotropic scaling display local resolution - Tutorials available for automated structure determination with PredictAndBuild - New em_placement and emplace_local tools - likelihood-based docking of models into cryo-EM maps - MOPAC v22 is now distributed with Phenix - Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ - Available in phenix.refine and separate command-line tool, mmtbx.quantum_interface - Defaults to MOPAC's PM6-D3H4 - Higher level QM available via 3rd-party Orca package - Restraints - Approximately 27k of 37k restraints (QM calculated and validated) deployed in the GeoStd - Automated tests for programs in the Phenix GUI - ERRASER no longer supported and removed from installation - Remove rebuild_predicted_model (duplicated by predict_and_build) - JSON output added to MolProbity structure validation scripts Please note that this publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Phenix does not start
by Cygler, Miroslaw 11 Jan '24

11 Jan '24

Hi, I have recently upgraded my MacBook running M1 processor to the Sonoma 14.2.1 operating system. Now, when I tried to start Phenix GUI, a message pops up: “python quit unexpectedly” and guy does not open. Any advice would be helpful. Regards, Mirek

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Secondary structure weights for realspace refinement
by Reza Khayat 10 Jan '24

10 Jan '24

Hi, I hope all is well. Is there a way to alter the weights for secondary structure restraints? Thanks. Best wishes Reza Reza Khayat, PhD City College of New York Associate Professor Department of Chemistry and Biochemistry Co-Director NIH G-RISE program

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Input from the community for panel session: Crystallography is Dead! Long Live Crystallography!
by Nicholas Pearce 02 Jan '24

02 Jan '24

Hello, and happy new year! [and absolutely no apologies for cross-posting 😉] Tomorrow evening, we will have a panel discussion at the CCP4 study weekend about the future of crystallography, called “Crystallography is Dead. Long Live Crystallography!” [https://en.wikipedia.org/wiki/The_king_is_dead,_long_live_the_king]. Whether you’re attending the CCP4SW or not, we want to hear from the community about your thoughts on the subject (see the blurb below), so that we can discuss things the community is most interested in! if you have a few minutes, please do fill in the form (all questions are optional): https://forms.office.com/e/3K5qSMNpYh. Thanks, and looking forward to seeing some of you very soon! Your friendly neighbourhood scientific organisation team, Nicholas Pearce, Helen Ginn, and Clemens Vonrhein Blurb: In this session, we will discuss the current state and the future of crystallographic experiments in the context of structural biology: * what are the unconfronted problems that the field still faces? * what problems are now essentially solved? * where should future method development be focussed? * what challenges are emerging from new experimental developments? * do new experiments provide new perspectives on old problems? Inevitably, this will include discussion of whether these challenges are likely to be addressed by the application of recent advances in AI, and, with the continued developments in cryoEM, what is crystallography's role as a part of the structural biologist's toolbox? Panel Chair: Elspeth Garman Panel Members: Dave Brown, Arwen Pearson, Ashwin Chari Please submit questions for consideration during the panel discussion using the form below! and we look forward to seeing you on 3rd Jan! Some of the questions are asked mischievously - you are welcome to have some fun with your answers! All questions are optional! https://forms.office.com/e/3K5qSMNpYh

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Fwd: Phenix installation on macOS 14 Sonoma
by Billy Poon 31 Dec '23

31 Dec '23

Sorry if this is a duplicate, but I'm not sure if my response got sent to the bulletin board correctly. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org ---------- Forwarded message --------- From: Billy Poon <BKPoon(a)lbl.gov> Date: Sun, Dec 31, 2023 at 6:29 PM Subject: Re: [phenixbb] Phenix installation on macOS 14 Sonoma To: Klureza, Maggie <mklureza(a)g.harvard.edu> Cc: <phenixbb(a)phenix-online.org> Hi Maggie, Can you run the script from inside the sonoma_fix directory? That is, 1) Extract sonoma_fix.tar.gz 2) cd sonoma_fix 3) sudo ./fix_wxpython.sh /Applications/phenix-1.19.2-4158 Inside the sonoma_fix directory, there should be a "bin" directory with conda.exe. The installed versions of Phenix do not come with conda. The fix comes with a standalone version of conda that can modify the Phenix environment with the dependencies. Let us know if it's still not working. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Sun, Dec 31, 2023 at 5:49 PM Klureza, Maggie <mklureza(a)g.harvard.edu> wrote: > Hi all, > > Reviving this thread (or trying to, anyway - TBD if I can successfully > reply to a thread begun before I'd joined the phenixbb list!), I recently > updated my Mac OS to 14/Sonoma, and am now also having issues getting > Phenix to work. > > As directed on the installers page > <https://phenix-online.org/download/phenix/release/>, I downloaded the > supplied fix <https://phenix-online.org/download/sonoma_fix.tar.gz>, > extracted the tarball, and ran that code as `sudo > Downloads/sonoma_fix/fix_wxpython.sh /Applications/phenix-1.19.2-4158`. > This was the resulting output/error I got: > > Password: > Removing old version of wxPython > ================================ > Downloads/sonoma_fix/fix_wxpython.sh: line 36: ./bin/conda.exe: No such > file or directory > > Installing new version of wxPython > ================================== > Downloads/sonoma_fix/fix_wxpython.sh: line 42: ./bin/conda.exe: No such > file or directory > > The wxPython package has been updated in /Applications/phenix-1.20.1-4487. > > > Sure enough, when I went to my phenix installation and looked in > conda_base/bin, there was no file named `conda.exe` present. This was true > for both my prior installation (phenix-1.19.2-4158) and when I tried a > newly downloaded version (phenix-1.20.1-4487). > > Can anyone tell me how I get that conda.exe file included with the Phenix > download/how else I might be able to run Phenix with this OS? > > (I sent an email about this to help(a)phenix-online.org before thinking to > hunt through the phenixbb archive, so apologies to whoever checks that > email and is getting this message twice!) > > Many thanks, > Maggie > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

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