- phenixbb - phenix-online.org

refinement of an ensemble of structures -> cryoEM variability
by vincent Chaptal 12 Jan '22

12 Jan '22

Hi Phenix-ers, I thought to ask for something that I believe you have already implemented, but I'm not sure of the best tool to use. I have a cryoEM map where I refine my "high resolution" structure. I also have the 3D variability of this map that shows several maps varying around the consensus high-res map. I want to refine an ensemble (20) of structures, one for every 20 maps around the consensus map. Is there a tool in phenix to do this? I could refine individually the high-res structure into each map incrementally; since every map differs a little from the original one, Real-space-refinement could move the structure a little at a time. Then I could combine all the PDBs in an ensemble? A tool to refine variability would be very useful. Input could be a PDB and an ensemble of maps, and output would be all the PDBs combined? Thank you. All the best Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Excellent Opportunity for Postdoc in Ion-Channel Structural Biology
by Pramod Kumar 08 Jan '22

08 Jan '22

Dear Structural Biology Scholars, I would like to bring your attention to an excellent opportunity to unravel the structure-function details of ion-channels as a postdoc. The Grosman lab at the University of Illinois at Urbana-Champaign is actively looking to fill a recent opening of NIH-funded postdoctoral position. The laboratory has an excellent record in combining high-resolution electrophysiology, molecular simulations, and structural biology to address fundamental questions about ion-channel mechanisms. Previous experience with the purification of eukaryotic membrane proteins is a plus and structure determination using single-particle cryo-EM is highly preferred. Salary commensurate with the experience level. The University of Illinois Urbana Champaign is an excellent place for research and life with an easy commute, lower-cost housing, easy access to all needs, and a vibrant community with easily accessible cities like Chicago, Indianapolis, St. Louis. Interested individuals should contact Prof. Claudio Grosman ( grosman(a)illinois.edu) with a CV, a 1–2 page description of previous research, and names and contact information of 2–3 references. Students in their final year of Ph.D. training are also welcome to apply. Recent select publications from the Grosman lab are listed below. A complete list of publications from the Grosman lab can be found on Prof. Claudio Grosman’s NCBI bibliography page ( https://www.ncbi.nlm.nih.gov/myncbi/claudio.grosman.1/bibliography/public <https://urldefense.com/v3/__https:/www.ncbi.nlm.nih.gov/myncbi/claudio.gros…> ). *Recent Select Publications * *· Kumar P, Cymes GD, Grosman C. Structure and function at the lipid-protein interface of a pentameric ligand-gated ion channel. Proc. Natl. Acad. Sci. USA. 2021;118(23). * *doi: 10.1073/pnas.2100164118 * *· Cymes GD, Grosman C. Signal transduction through Cys-loop receptors is mediated by the nonspecific bumping of closely apposed domains. Proc. Natl. Acad. Sci. USA. 2021;118(14). doi: 10.1073/pnas.2021016118 * *doi: 10.1038/s41467-021-21680-9 * *· Kumar P, Wang Y, Zhang Z, Zhao Z, Cymes GD, Tajkhorshid E, Grosman C. Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer. Proc. Natl. Acad. Sci. USA. 2020;117(3):1788-1798. * *doi: 10.1073/pnas.1906823117 * -- Pramod Kumar, Ph.D.

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use mr_rosetta to prerefine structure
by Wei Wang 07 Jan '22

07 Jan '22

Dear all, I have a question regarding phenix.mr_rosetta. I manually build a model in Coot, and want to use phenix.mr_rosetta to prerefine the model. I followed the instruction on https://phenix-online.org/documentation/reference/mr_rosetta.html#rebuildin…. Basically, my scenario is like what’s written in NOTE 2: “have a model and just want to run pre-refinement and not anything else”. I noticed that if I put nproc=xx, then the job would eventually output no structures. I checked each subjob and found that they all failed. I suspect this behavior was caused by files overwritten by parallel jobs. When I don’t specify nproc, then there’s no problem. However, in this case, for number_of_prerefine_models=1000, it would take a very long time. I hope I described the behavior clearly. Is there a way of running the prerefine jobs in parallel? Thanks, Wei

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Phenix version 1.20 released
by Paul Adams 06 Jan '22

06 Jan '22

The Phenix developers are pleased to announce that version 1.20 of Phenix is now available (build 1.20-4459). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for the 1.20 version of Phenix include a number of tools to leverage new structure prediction methods: - New tools and methods - Phenix AlphaFold2 notebook: Run AlphaFold on Google Colab from Phenix GUI - phenix.process_predicted_model: Identify useful domains in AlphaFold model - phenix.dock_predicted_model: Dock domains of AlphaFold model into cryo-EM - phenix.rebuild_predicted_model: Rebuild AlphaFold model in cryo-EM map using docked domains - phenix.dock_and_rebuild : Process, dock and rebuild AlphaFold model with cryo-EM map - phenix.model_completion: Connect fragments and fill in gaps based on a map - phenix.rebuild_model: Rebuild a model using a map and keeping connectivity - phenix.replace_with_fragments_from_pdb: Rebuild a model using fragments from PDB - phenix.search_and_morph: SSM search PDB; morph to match target - phenix.fragment_search: Search for a fragment in PDB matching target - phenix.reverse_fragment: Reverse chain direction of a fragment - phenix.superpose_and_morph: SSM or least-squares superpose one model on another; optionally trim and morph to match - phenix.voyager.casp_rel_ellg: Calculate relative eLLG score for predicted model quality - phenix.match_maps: - Bug fix (superposed map was not matching target map) - phenix.real_space_refine: - Symmatry multiprocessing aware individual ADP and occupancy refinement - Multiple changes to improce runtime (for certain refinement strategies) - Make NQH flips symmetry aware - phenix.superpose_pdbs: - Add feature to transform additional models with matrix found with moving model - phenix.dock_in_map: - Allow splitting model into domains based on chain ID from phenix.process_predicted_model - Restraints - GeoStd updated with 12k plus entity restraints files - cis-PRO default updated to EH99 - phenix.fetch_pdb, iotbx.cif_as_mtz: - Bug fix: Multiple datasets with different unit cells in a cif file now preserved as multiple crystals in mtz file. 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 principally 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/leadership/) Principal Investigator, Computational Crystallography Initiative, LBL (https://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (https://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.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 33, Room 250 Building 978, Room 4126 Building 977, Room 268 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 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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Postdoc Position at Caltech
by Hoelz, Andre 21 Dec '21

21 Dec '21

The Hoelz laboratory at the California Institute of Technology seeks to recruit an outstanding postdoctoral scientist in structural cell biology. Our laboratory focuses on the structure-function relationships of the nuclear pore complex and associated nucleocytoplasmic transport machinery. This position requires a recent Ph.D. degree in biochemistry/biophysics with a strong background in biochemistry, x-ray crystallography, or cryo-electron microscopy/tomography. The successful applicant should be a highly motivated individual with good organizational, communication, and interpersonal skills. The laboratory is well-funded and equipped with modern biophysical instrumentation. Importantly, Caltech has an exceptional infrastructure for structural biology, including access to a high intensity, completely automated, state-of-the-art crystallography beamline at the Stanford Synchrotron Radiation Lightsource (SSRL), as well as an excellent cryo-electron microscopy facility with access to FEI Arctica and Titan Krios microscopes equipped with Gatan K3 cameras. The position is available immediately and funded for 3+ years. Depending on performance, the position can be extended for additional years. To apply, please send your CV, a statement of research interests, and the names and contact information of at least two references to André Hoelz (hoelz(a)caltech.edu). Selected Recent Publications Bley, C.J., Nie, S., Mobbs, G.W., Petrovic, S., Gres, A.T., Liu, X., Mukherjee, S., Harvey, S., Huber, F.M., Lin, D.H., Brown, B., Tang, A.W., Rundlet, E.J., Correia, A.R., Chen, S., Regmi, S.G., Dasso, M., Patke, A., Palazzo, A.F., Kossiakoff, A.A., Hoelz, A. (2021). BioRxiv (https://doi.org/10.1101/2021.10.26.465790). Petrovic, S., Samanta, D., Perriches, T., Bley, C.J., Thierbach, K., Brown, B., Nie, S., Mobbs, G.W., Liu, X., Hoelz, A. (2021). Architecture of the linker-scaffold in the nuclear pore. BioRxiv (https://doi.org/10.1101/2021.10.26.465796). Lin, D. H., Hoelz, A. (2019). The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725-783. Lin, D. H., Correia, A.C., Cai, S.W., Huber, F.M. Jette, C.A., Hoelz, A.* (2018). Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat. Commun., 2319. Huber, F., Hoelz, A., (2017). Molecular basis for protection of ribosomal protein L4 from cellular degradation, Nat. Commun. 8, 14354. Lin, D., Stuwe, T., Schilbach, S., Rundlet, E.J., Perriches, T., Mobbs, G., Fan, Y., Thierbach, K., Huber, F.M., Collins, L.N., Davenport, A.M., Jeon, Y.E., Hoelz, A. (2016). Architecture of the symmetric core of the nuclear pore, Science 352, aaf1015. [Cover] Stuwe, T., Bley, C.J., Thierbach, K., Petrovic, S., Schilbach, S., Mayo, D.J., Perriches, T., Rundlet, E.J., Jeon, Y.J., Collins, L.N., Huber, F.M., Lin, D.H., Paduch, M., Koide, A., Lu, V., Fischer, J., Hurt, E., Koide, S., Kossiakoff, A., Hoelz, A.* (2015). Architecture of the fungal nuclear pore inner ring complex, Science 350, 56-64. Stuwe, T., Correia, A., Lin, D. H., Paduch, M., Lu, V. T., Kossiakoff, A. A., Hoelz, A.* (2015). Architecture of the nuclear pore complex coat. Science 347, 1148-1152. Hoelz, A., Debler, E.W., Blobel, G. (2011). Structure of the Nuclear Pore Complex, Annu. Rev. Biochem. 80, 613-643.

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Query re individual sites (real space)
by Oliver Clarke 21 Dec '21

21 Dec '21

Hi, While refining an X-ray structure using phenix.refine (v1.20-4444), I get the attached table during real-space refinement of coordinates. What are the criteria for selecting the correct weighting factor? I assumed it would be the delta between R/Rfree and/or the clash score, but it doesn't seem to exactly match either in this table (and the same for other iterations of refinement). Is it just incorrectly writing the clash score in the "Accepted refinement result" line? Shouldn't this match the line from the selected weight (here 0.125 so should be 6.1, not 7.1)? Cheers Oli

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Phenix.metal_coordination not working in 1.20-4444
by Oliver Clarke 20 Dec '21

20 Dec '21

Hi, When I try to run phenix.metal_coordination in v1.20-4444 (as phenix.metal_coordination whatever.pdb), I get the attached error. Traceback (most recent call last): File "/Applications/phenix-1.20-4444/build/../modules/elbow/elbow/command_line/metal_coordination.py", line 50, in <module> from metal_coordination_params import master_phil_string ImportError: No module named metal_coordination_params Cheers Oli

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Re: [phenixbb] sequence file error in phenix map-to-model
by Raja Dey 20 Dec '21

20 Dec '21

Hi Sharan, I am getting the same error saying , 'is not a known sequence type'. Also, please see the image enclosed below that tells how the template sequence file should look like. I tried with/without space after '>' sign and getting the same error message. [image: image.png] Any suggestion from anyone would be appreciated. Thanks, Raja On Mon, Dec 20, 2021 at 3:29 PM Sharan Karade <sharankarade(a)gmail.com> wrote: > Hi Raja, > > Try to use the file attached here. I hope it works. > > On Mon, Dec 20, 2021 at 3:27 PM Raja Dey <rddey80(a)gmail.com> wrote: > >> Sorry, the error message is >> D41-st-Trx-sequence.txt is not a known sequence type. >> >> Can someone help solving this problem? >> >> Best regards, >> Raja >> >> On Mon, Dec 20, 2021 at 12:02 PM Raja Dey <rddey80(a)gmail.com> wrote: >> >>> Hi, >>> I am getting an error with the sequence file attached. Could you please >>> tell me what's wrong with this file? The error is enclosed below: >>> Starting phenix >>> on Mon Dec 20 11:45:46 2021 by rdey >>> >>> =============================================================================== >>> >>> Processing files: >>> >>> ------------------------------------------------------------------------------- >>> >>> Found phil, >>> /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff >>> >>> Processing PHIL parameters: >>> >>> ------------------------------------------------------------------------------- >>> >>> Adding PHIL files: >>> ------------------ >>> >>> /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff >>> >>> Processing files from PHIL: >>> >>> ------------------------------------------------------------------------------- >>> >>> Found real_map, >>> /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc >>> >>> Files not used by program: >>> -------------------------- >>> /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt >>> /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec >>> >>> Final processed PHIL parameters: >>> >>> ------------------------------------------------------------------------------- >>> data_manager { >>> real_map_files = >>> "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" >>> default_real_map = >>> "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" >>> phil_files = >>> "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" >>> default_phil = >>> "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" >>> } >>> input_files { >>> map_file = >>> /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc >>> seq_file = /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt >>> ncs_file = >>> /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec >>> } >>> reconstruction_symmetry { >>> symmetry = """D2""" >>> } >>> control { >>> nproc = 2 >>> } >>> job_title = """D41-st-Trx-19Dec21""" >>> >>> >>> Starting job >>> >>> =============================================================================== >>> Validating inputs >>> >>> >>> Thanks a lot for your time. >>> Regards, >>> Raja >>> >>> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > > > > -- > Sharan Karade > Postdoc-fellow > IBBR-UMD, 9600 Gudelsky Dr, > Rockville > Maryland 20850 > > >

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sequence file error in phenix map-to-model
by Raja Dey 20 Dec '21

20 Dec '21

Hi, I am getting an error with the sequence file attached. Could you please tell me what's wrong with this file? The error is enclosed below: Starting phenix on Mon Dec 20 11:45:46 2021 by rdey =============================================================================== Processing files: ------------------------------------------------------------------------------- Found phil, /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found real_map, /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc Files not used by program: -------------------------- /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" default_real_map = "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" phil_files = "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" default_phil = "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" } input_files { map_file = /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc seq_file = /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt ncs_file = /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec } reconstruction_symmetry { symmetry = """D2""" } control { nproc = 2 } job_title = """D41-st-Trx-19Dec21""" Starting job =============================================================================== Validating inputs Thanks a lot for your time. Regards, Raja

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model shifts after real space refinement
by Ashok Nayak 15 Dec '21

15 Dec '21

Hi, Is there a way to say keep_origin=False in phenix real space refinement. I used it in the command line version of v3958. It didn't take that. There is a model shift after the refinement which I think is because the program brings the map to the origin and hence the refined model as well. Thanks, Ashok -- Post-Doctoral Fellow Department of Biochemistry and Molecular Biology, Sidney Kimmel cancer Center Thomas Jefferson University 1020 Locust Street, JAH Philadelphia, PA, 19107 Phone: 804-661-4620

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