- phenixbb - phenix-online.org

RealSpaceRefine Nucleic acid SS restraints ?
by CUNIASSE Philippe 01 Feb '24

01 Feb '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 23 Jan '24

23 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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