- phenixbb - phenix-online.org

change sigma for an already restrained bond
by Jorge Iulek 19 Apr '24

19 Apr '24

Dear all, I would like to change the sigma value for an already restrained bond. I enter for phenix.refine: " bond { action = add delete *change atom_selection_1 = chain D and resid 493 and name CA atom_selection_2 = chain D and resid 493 and name CB symmetry_operation = None distance_ideal = 1.532 sigma = 1.02e-2 slack = None limit = -1.0 top_out = False } " In the log I get: " ... Custom bonds: bond: atom 1: "ATOM 14355 CA ALA D 493 .*. C " atom 2: "ATOM 14358 CB ALA D 493 .*. C " symmetry operation: x,y,z distance_model: 1.511 distance_ideal: 1.532 ideal - model: 0.021 slack: 0.000 delta_slack: 0.021 sigma: 0.0102 Total number of added/changed bonds: 1 ... " But in the .geo file I read: " User supplied restraints: 1 Sorted by residual: bond pdb=" CA ALA D 493 " pdb=" CB ALA D 493 " ideal model delta sigma weight residual 1.532 1.511 0.022 1.28e-02 6.10e+03 2.85e+00 " 1.28e-02 is the default value. On the other hand, sigma changes for angles and dihedrals seem to work as expected (the intended values are echoed to the .geo file). To add up, if a bond is *added*, the value is in the .geo file. I observe this for both 1.20.1-4487 1.21-5207 versions. So, in short, should I be allowed to *change the sigma* for a specific *bond*? How should I do it? Thanks Jorge

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iNEXT/3D-Bioinfo AI in structural biology workshop announcement
by Jon Agirre 15 Apr '24

15 Apr '24

Dear all, It is our pleasure to announce the joint iNEXT-Discovery and 3D-Bioinfo workshop on "AI advances in structural biology and drug discovery", to be held in Grenoble on 13-14 May 2024. The rapid advancements in Artificial Intelligence (AI) and Machine Learning (ML) have opened up new horizons in the field of Structural Biology and Drug Discovery. This workshop is addressed to scientists in industry and academia, and aims to bridge the gap between the recent developments in AI technologies and experimental approaches in translational research. From understanding biological structures to accelerating the drug discovery processes, participants will gain insights into the latest AI models, as well as high throughput experimental techniques. Through a series of invited and selected talks (abstract submission will remain open until 25 April 2024), attendees will explore the power of combining AI and experimental approaches in translational research. Abstracts will be considered for oral and poster presentations. Please register and send your abstract before 25 April 2024. Website: https://instruct-eric.org/events/ai-approaches-in-structural-biology-and-dr… Registration fee: £50 (includes catering) Venue: EPN campus, Grenoble, France. Dates: 13-14 May 2024 Best regards, Jon Agirre, on behalf of the organising committee: Jose A. Marquez (Instruct-ERIC), Magalie Matthieu (Sanofi-Aventis), Rebecca Thompson (ThermoFisher), Max Nanao (ESRF), Carlos Oscar Sorzano (Instruct-ERIC), Jon Agirre (Instruct-ERIC/3D-Bioinfo liaison), Sameer Velankar (EMBL-EBI, 3D-Bioinfo), Evangelia Chrysina (ICB-NHRF, Greece). -- Dr Jon Agirre Royal Society University Research Fellow (assistant professor) Main editor at Acta Crystallographica Section F: Structural Biology Communications CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir) York Structural Biology Laboratory, Department of Chemistry University of York, Heslington, YO10 5DD, York, UK

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Phenix version 1.21.1 released
by Paul Adams 09 Apr '24

09 Apr '24

The Phenix developers are pleased to announce that version 1.21.1 of Phenix is now available (build 1.21.1-5286). 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 this bug fix 1.21.1 version of Phenix include: - Added support for joint X-ray/neutron refinement to phenix.refine GUI - Fixed DMSO restraint - Fixed excessive printing when processing PAE matrix file - Added tutorial for low resolution restraints - Bugfix for LigandPipeline - Bugfix for PredictAndBuild - New program - phenix.renumber_fab: renumber FAB chains using Kabat, Chothia or Martin conventions 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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Re: [phenixbb] red blobs (Andrea Smith)
by Kay Diederichs 28 Mar '24

28 Mar '24

Hi Andrea, in your case, phenix.refine seems to fill bulk solvent into volumes that are not actually filled by solvent. It might help to optimize the mask, see https://phenix-online.org/documentation/reference/refinement.html#bulk-solv… "6. Mask parameters". Best, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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Partial occupancy refinement of overlapping inhibitor+water sites
by Matt Jordan McLeod 18 Mar '24

18 Mar '24

Hi all, I am trying to navigate phenix.refine to occupancy refine a partially occupied inhibitor vs. the waters that it displaces. For instance I have molecule resseq 802 in chain A, and waters 1-6 in chain W that are overlapping. When just refining occupancy of the molecule there are clear sites for the waters. How can I refine both of them together so that I can get an occupancy of the molecule vs the group of waters (which should have nearly identical occupancies)? Maybe, a bit more information on the differences in refinement strategy for the occupancy vs fix occupancy vs group occupancy would be more broadly helpful. I tried to make them all a group, but that didn't work as the refinement pushed the waters out and reduced their occupancies to ~0 while leaving the small molecule occupancy about the same as without water. [cid:2b35e3b8-08e5-44ae-9b70-8fdcff613f1a] *Waters are only placed, they are not refined), small molecule is refined to 0.71 occupancy.* -- Matthew Jordan McLeod, PhD Post-Doctoral Fellow | Thorne Lab Cornell University G11 Physical Sciences Building 142 Sciences Drive Ithaca, NY 14853-3501 (607) 279 9382

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uniq segid problem
by jp d 14 Mar '24

14 Mar '24

hi, phenix is crashing with "segid is not unique" problems i have an old job that ran fine in 1.20, in 1.21-5207 i get this (same job script) Sorry: residue.id_str(suppress_segid=false): segid is not unique: pdbres="ALA 65 " segid="PPP " i think the appropriate place in the log is this: Chain: " " Number of atoms: 41993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Duplicate atoms: {' A,C1*': 112, ' A,C2': 112, ' A,C2*': 112, ' A,C3*': 112, ' A,C4': 112, ' A,C4*': 112, ' A, C5': 112, ' A,C5*': 112, ' A,C6': 112, ' A,C8': 112, ' A,N1': 112, ' A,N3': 112, ' A,N6': 112, ' A,N7': 112, ' A,N9': 1 12, ' A,O1P': 112, ' A,O2*': 112, ' A,O2P': 112, ' A,O3*': 112, ' A,O4*': 112, ' A,O5*': 112, ' A,P': 112, ' C,C1*': 71 , ' C,C2': 71, ' C,C2*': 71, ' C,C3*': 71, ' C,C4': 71, ' C,C4*': 71, ' C,C5': 71, ' C,C5*': 71, ' C,C6': 71, ' C,N1': 71, ' C,N3': 71, ' C,N4': 71, ' C,O1P': 71, ' C,O2': 71, ' C,O2*': 71, ' C,O2P': 71, ' C,O3*': 71, ' C,O4*': 71, ' C, O5*': 71, ' C,P': 71, ' G,C1*': 179, ' G,C2': 179, ' G,C2*': 179, ' G,C3*': 179, ' G,C4': 179, ' G,C4*': 179, ' G,C5': 179, ' G,C5*': 179, ' G,C6': 179, ' G,C8': 179, ' G,N1': 179, ' G,N2': 179, ' G,N3': 179, ' G,N7': 179, ' G,N9': 179, ' G,O1P': 179, ' G,O2*': 179, ' G,O2P': 179, ' G,O3*': 179, ' G,O4*': 179, ' G,O5*': 179, ' G,O6': 179, ' G,P': 179, ' U,C1*': 69, ' U,C2': 69, ' U,C2*': 69, ' U,C3*': 69, ' U,C4': 69, ' U,C4*': 69, ' U,C5': 69, ' U,C5*': 69, ' U,C6': 69, ' U,N1': 69, ' U,N3': 69, ' U,O1P': 69, ' U,O2': 69, ' U,O2*': 69, ' U,O2P': 69, ' U,O3*': 69, ' U,O4': 69, ' U,O4*': 69, ' U,O5*': 69, ' U,P': 69} Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 82, 'rna2p_pyr': 63, 'rna3p': 10, 'rna3p_pur': 497, 'rna3p_pyr': 444} Link IDs: {'rna2p': 146, 'rna3p': 1372} the 1.20 log does not have these messages and finished normally. maybe a wildcard problem with those stars ? we are not using the '*' in our files has anyone seen that ? should i go back to 1.20 ? or force it to use the 1.20 chem data lib ? thanks jpd

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red blobs
by Andrea Smith 14 Mar '24

14 Mar '24

Hi, i am working on a structure where I have a few relatively big red blobs (please see attached print screens with maps at 1.2 and 3.5 rmsd). The data were processed at BESSY, mtz was used in Phaser and refined in phenix.refine. Can someone explain why this happens (and whether it is an issue)? Thank you, Andrea

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Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble
by Elke De Zitter 13 Mar '24

13 Mar '24

Dear all, We have an immediate opening for a two-year postdoctoral researcher in SNaX team of the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The project focuses on the development and optimization of bio-scavengers targeting toxic organophosphorus compounds. The successful candidate will employ time-resolved crystallography and in silico protein design methodologies. The 2-year postdoctoral position is funded by the French National Research Agency via the University Grenoble Alpes, and is open for a young researcher. Applicants must have obtained a Ph.D. in structural biology, biochemistry, biophysics, physics, chemistry, or a related field, no more than three years before the start of the project. The candidate must show a track-record of publications in peer-reviewed journals, and is expected to be proficient in English and highly motivated to learn new skills. The candidate needs to be a good team player as well as being capable of working independently. Experience with one or more of the following skills would be highly evaluated: protein design or the usage of artificial intelligence for structural biology, protein expression and purification, protein crystallization and macromolecular crystallography, serial crystallography, programming or scripting. Interested candidates should apply through the University Grenoble Alpes job portal at https://emploi.univ-grenoble-alpes.fr/job-offers/postdoctoral-researcher-in… (application deadline: 02/04/2024 ). For inquiries regarding the position and application process, please contact Elke De Zitter at elke.de-zitter(a)ibs.fr . All the best, Elke Elke De Zitter Institut de Biologie Structurale - IBS group DYNAMOP 71 avenue des Martyrs 38044 Grenoble Cedex 9, France +33 4 57 42 86 56 elke.de-zitter(a)ibs.fr

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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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