- phenixbb - phenix-online.org

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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Re: [phenixbb] Phenix installation on macOS 14 Sonoma
by Klureza, Maggie 31 Dec '23

31 Dec '23

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

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geometrical restraints between symmetry related chains
by Jorge Iulek 29 Dec '23

29 Dec '23

Dear all, I am working currently on a structure that should be "peptide bond" between chains, but the "second" part of the chain is in a symmetry related peer. Numbering is continuous and there are justifications to why the chains are separately named with different chain ID's. By the way, this "connection" is "full of glycines" so a kind of flexible, but a continuous stretch can be seen at "reasonable" density (and despite low resolution). To better explain, say I have chain C residue x to be bound to chain K, at symm operation -x-1,y-1/2,-z-1/2, residue x + 1. I would prefer to really refine the presence of these "connecting" glycines, of course with due geometrical restraints imposed (precious at this low resolution). phenix.refine offers: refinement.geometry_restraints.edits at bond with the possibility to indicate the symmetry_operation for the "second atom" within the bond. But this "symmetry_operation" indication is not available (?) for the other geometry_restraints edits, like angle, dihedral, etc. (eventually, planarity might also make easier). Do I miss anything here? Currently, I see 3 possibilities: a) somehow (how?) I can add angle, dihedral restraints in involving chains in symmetry related operations b) I bring the symmetry related chain to its non "symmetry related" position and change chains names/residues ID, etc., so I go into this go/return of naming at each step of the refinement work/analysis c) I add "extra" ( + - like alternate conformation residues) residues to each end of the connection, such that these extra residues will receive due conventional geometrical restraints (as phenix.refine does for contiguous residues in a chain) but I force them to be on the same position (and probably declare 0.5 occupancy for these overlying residues). "a" should be the easiest, if available somehow; "b" would be cumbersome during the refinement/analysis process; "c" seems to be the most complex but maybe the best if it works. Nevertheless, someone might have an easier suggestion. Thanks, Jorge

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Phenix windows distortion windows
by Dmitry Semchonok 28 Dec '23

28 Dec '23

Dear colleagues, I am not sure of the reason, but when I run Phenix, I get the following distortion of the Phenix window. Then, the distortion disappears if I move the cursor somewhere else and click somewhere out of the Phenix window. (please see attachment) Do you know the reasons and how to fix that? Phenix version - 1.21-5187 WSL Windows 11 I will try to 1. roll-back windows drivers 2. update Phenix Kind regards, Dmitry

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Re: [phenixbb] phenixbb Digest, Vol 216, Issue 7 (out of office)
by Elisabeth Laurent 27 Dec '23

27 Dec '23

Thank you for your e-mail. I am out of office until January 2nd, 2024. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: bmca(a)boku.ac.at Thank you for your understanding. With kind regards, Elisabeth Laurent >>> <phenixbb-request(a)phenix-online.org> 27.12.23 17:32 >>> Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Re: phenix.model_vs_sequence not working as expected (Oleg Sobolev) 2. real space refinement of the model in cryo-EM map (Dmitry Semchonok) 3. Re: real space refinement of the model in cryo-EM map (Pavel Afonine) ---------------------------------------------------------------------- Message: 1 Date: Fri, 22 Dec 2023 11:21:13 -0800 From: Oleg Sobolev <osobolev(a)lbl.gov> To: "Tanner, John J." <TannerJJ(a)missouri.edu> Cc: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] phenix.model_vs_sequence not working as expected Message-ID: <CADd3otGkgta4heL2mHYB1sfkm_AxEw77Psd7RdS+pGQhjED7dA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi John, Thank you for reporting the issue. I have fixed it. This tool should work again in Phenix builds starting from 5188. Best regards, Oleg Sobolev. On Wed, Dec 20, 2023 at 9:35?AM Tanner, John J. <TannerJJ(a)missouri.edu> wrote: > I?ve noticed that command line phenix.model_vs_sequence does not work in > phenix-1.21rc1-5156. > > > > Here?s the data: > > > > [tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence > > /linux/src/phenix-1.21rc1-5156/build/bin/phenix.model_vs_sequence > > [tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb > ../depo/8DKP.fasta > > Traceback (most recent call last): > > File > "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", > line 75, in <module> > > run(sys.argv[1:]) > > File > "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", > line 48, in run > > pdb_in = iotbx.pdb.inpu(params.input.pdb_file) > > AttributeError: 'module' object has no attribute 'inpu' > > > > > > It worked fine in phenix-1.20.1-4487: > > > > [tannerjj@dizzy pdbs]$ source /linux/src/phenix-1.20.1-4487/phenix_env.csh > > [tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence > > /linux/src/phenix-1.20.1-4487/build/bin/phenix.model_vs_sequence > > [tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb > ../depo/8DKP.fasta > > Skipping non-polymer chain 'A' > > Skipping non-polymer chain 'B' > > Skipping non-polymer chain 'A' > > Skipping non-polymer chain 'B' > > Chain 'A': > > best matching sequence: 8DKP_1|Chains > > sequence identity: 100.00% > > 10 residue(s) missing from PDB chain (3 at start, 1 at end) > > 1 gap(s) in chain > > > > > > PDB file ---QSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX > > > |||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS > > > > > PDB file XGSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > > > || > > > sequence SGS--------------------------------------------------------- > > > > > PDB file XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA > > > ||||||||||||||| > > > sequence ---------------------------------------------MMGEQFVTGETIREA > > > > > PDB file LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > > > PDB file KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > > > PDB file LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > > > PDB file GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > > > PDB file EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > > > PDB file DPKVSIDELIADPVEVV- > > ||||||||||||||||| > > sequence DPKVSIDELIADPVEVVR > > > > Chain 'B': > > best matching sequence: 8DKP_1|Chains > > sequence identity: 100.00% > > 8 residue(s) missing from PDB chain (0 at start, 1 at end) > > 1 gap(s) in chain > > > > > > PDB file SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX > > > ||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS > > > > > PDB file XXSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > > > | > > > sequence SGS--------------------------------------------------------- > > > > > PDB file XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA > > > ||||||||||||||| > > > sequence ---------------------------------------------MMGEQFVTGETIREA > > > > > PDB file LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > > > PDB file KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > > > PDB file LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > > > PDB file GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > > > PDB file EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > > > PDB file DPKVSIDELIADPVEVV- > > ||||||||||||||||| > > sequence DPKVSIDELIADPVEVVR > > > > [tannerjj@dizzy pdbs]$ > > > > > > > _______________________________________________ > 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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real space refinement of the model in cryo-EM map
by Dmitry Semchonok 27 Dec '23

27 Dec '23

Dear colleagues, Does anyone know how to improve the Ramachandran plot Z score (Rama-Z)? Ours seems to be too good (low) 🙂 Is there any cure in Phenix for that? Maybe changing certain parameters/restraints can aid? Thank you. Kind regards, Dmitry

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phenix.model_vs_sequence not working as expected
by Tanner, John J. 22 Dec '23

22 Dec '23

I’ve noticed that command line phenix.model_vs_sequence does not work in phenix-1.21rc1-5156. Here’s the data: [tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence /linux/src/phenix-1.21rc1-5156/build/bin/phenix.model_vs_sequence [tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb ../depo/8DKP.fasta Traceback (most recent call last): File "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", line 75, in <module> run(sys.argv[1:]) File "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", line 48, in run pdb_in = iotbx.pdb.inpu(params.input.pdb_file) AttributeError: 'module' object has no attribute 'inpu' It worked fine in phenix-1.20.1-4487: [tannerjj@dizzy pdbs]$ source /linux/src/phenix-1.20.1-4487/phenix_env.csh [tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence /linux/src/phenix-1.20.1-4487/build/bin/phenix.model_vs_sequence [tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb ../depo/8DKP.fasta Skipping non-polymer chain 'A' Skipping non-polymer chain 'B' Skipping non-polymer chain 'A' Skipping non-polymer chain 'B' Chain 'A': best matching sequence: 8DKP_1|Chains sequence identity: 100.00% 10 residue(s) missing from PDB chain (3 at start, 1 at end) 1 gap(s) in chain PDB file ---QSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX |||||||||||||||||||||||||||||||||||||||||||||||||||| sequence SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS PDB file XGSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX || sequence SGS--------------------------------------------------------- PDB file XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA ||||||||||||||| sequence ---------------------------------------------MMGEQFVTGETIREA PDB file LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI PDB file KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC PDB file LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD PDB file GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY PDB file EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN PDB file DPKVSIDELIADPVEVV- ||||||||||||||||| sequence DPKVSIDELIADPVEVVR Chain 'B': best matching sequence: 8DKP_1|Chains sequence identity: 100.00% 8 residue(s) missing from PDB chain (0 at start, 1 at end) 1 gap(s) in chain PDB file SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX ||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS PDB file XXSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | sequence SGS--------------------------------------------------------- PDB file XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA ||||||||||||||| sequence ---------------------------------------------MMGEQFVTGETIREA PDB file LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI PDB file KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC PDB file LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD PDB file GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY PDB file EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN PDB file DPKVSIDELIADPVEVV- ||||||||||||||||| sequence DPKVSIDELIADPVEVVR [tannerjj@dizzy pdbs]$

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