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ccp4 thread: "what happened to Molprobity"
by Pavel Afonine 01 May '24

01 May '24

Hi All, I hope someone from Molprobity end reads CCP4 mailing list where people report issues with Molprobity (server and from within Phenix). Just in case this needs someone's attention. Pavel

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on the criteria for outliers, phenix.molprobity and wwPDB validation
by Jorge Iulek 29 Apr '24

29 Apr '24

Hi all, I had already noticed that outliers spotted by phenix with its validation tool, with the nice feature to carry one straight to the "suspicious" residue in a coot session for visual inspection, differs a bit from what comes spotted from wwPDB validation, generally the latter spotting some few more residues. To one current structure, which at low resolution, I notice there is a bit larger difference between the number of spotted residues. I see from wwPDB validation, molprobity is also used to spot outliers for many of the analyses. I see the current molprobity version used is 4.02b-467, but I could not yet devise the molprobity version used by phenix. Of course, there would also be the "library" used in each case to spot the outliers. Maybe someone ever listed what is considered in each case, and their differences, or a link to that is welcome for me. What would be the best criteria for spotting is of course a good discussion. But a superficial question I would make is if there is a way to make phenix.molprobity output to resemble the one from wwPDB validation, at least the ones accounted by molprobity? Jorge

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Phenix resolve_cryo_em with local resolution
by Reza Khayat 29 Apr '24

29 Apr '24

Hi, Is it possible to run resolve_cryo_em and have it consider the local resolution of the two half maps in the final map? I have a 3.7Angstrom map were certain domains, too small for local refinement with single particle analysis, are smeared out in the resolve_cryo_em map. Their densities are stronger when I low pass filter the original maps. The adjust_local_resolution_coloring = True option seems to be what I need; however, including this option in the command line results in: Please run this program with the --show-defaults option to see what parameters are available. PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite") The command line I use is: phenix.resolve_cryo_em map_file_name=Class001_full_box_40.ccp4 half_map_file_name_1=Class001_half1_box_40.ccp4 half_map_file_name_2=Class001_half2_box_40.ccp4 resolution=4.0 dm_resolution=3.5 cycles=1 box_before_analysis=False density_modify_unsharpened_maps=True nproc=16 force_nproc=True model_1=Class001.pdb seq_file=Class001.fasta ncs_copies=1 output_directory="Class001_local" adjust_local_resolution_coloring=True > Class001_local.log Any help would be appreciated. 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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chain name lentgh
by Roberto Marabini 19 Apr '24

19 Apr '24

Hi, We are using phenix version 1.20.1-4487. The protein complex we are processing has more than 100 chains. For this complex we would like to use chain names longer than 2 characters but I see that phenix output truncates the names to the last two characters. Is there any way to avoid this constraint, that is, can we get output files with longer chain names? thanks for the help Roberto

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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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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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